Sender: LSF System <lsf@node1648>
Subject: Job 4398589: <iteration_215935> Done

Job <iteration_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1648>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935> was used as the working directory.
Started at Wed Oct 24 20:03:44 2012
Results reported at Wed Oct 24 20:03:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
echo starting
ls iteration*/exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo some scatter or gather jobs failed;
echo ${return_code} > exited;
exit 1;
fi
ls exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo previous iteration failed;
echo ${return_code} > exited;
exit 1;
fi
/xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 215935 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
return_code=$?
if [ ${return_code} -ne 0 ]; then
echo iterator failed ${return_code};
echo ${return_code} > exited;
exit ${return_code};
fi
cat iteration1/jobSubmissions.txt >> jobSubmissions.txt
rm -f iteration1/jobSubmissions.txt
echo '*** Scatter Gather stdandard out:' 2>&1
cat iteration1/scatter-gather.out.txt 2>&1
rm -f iteration1/scatter-gather.out.txt 2>&1
echo '*** Scatter Gather stdandard err:' 2>&1
cat iteration1/scatter-gather.err.txt 2>&1
rm -f iteration1/scatter-gather.err.txt 2>&1
ls iteration1/sg-next-iteration.txt 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
rm -f iteration1/sg-next-iteration.txt
else
rm -f scatterGatherParameters.txt
rm -f programParameters.txt
mv iteration1/* /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935
rmdir iteration*
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :      0.21 sec.
    Max Memory :        11 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

starting
ls: iteration*/exited: No such file or directory
ls: exited: No such file or directory
Running scatter-gather-iterator with the following args: /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 215935 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
Finished in 1 iterations
*** Scatter Gather stdandard out:
Sender: LSF System <lsf@node1650>
Subject: Job 4398584: <gather_215935> Done

Job <gather_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1650>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1> was used as the working directory.
Started at Wed Oct 24 19:41:55 2012
Results reported at Wed Oct 24 20:03:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
ls scatter.*/exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo some scatter jobs failed;
echo ${return_code} > exited;
exit 1;
fi
if [ `ls -1 scatter.*/success | wc -l` -ne 200 ]; then
echo expected result files missing, try rerunning;
echo 1 > exited;
exit 1;
fi
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 0  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
echo gather failed;
echo ${return_code} > exited;
exit ${return_code};
fi
rm -f prepareResults.out
echo '*** Prepare stdandard out:' 2>&1
cat prepare.out 2>&1
rm -f prepare.out 2>&1
echo '*** Prepare stdandard err:' 2>&1
cat prepare.err 2>&1
rm -f prepare.err 2>&1
echo '*** Scatter stdandard out:' 2>&1
cat scatter.*/scatter.out 2>&1
rm -f scatter.*/scatter.out 2>&1
echo '*** Scatter stdandard err:' 2>&1
cat scatter.*/scatter.err 2>&1
rm -f scatter.*/scatter.err 2>&1
echo '*** Scatter retry log:'
head scatter.*.tries
echo
rm -f scatter.*.tries
rm -f scatter.*/success
rm -f scatter.*/java.opts
rmdir scatter.*
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :   1201.33 sec.
    Max Memory :      2500 MB
    Max Swap   :      3527 MB

    Max Processes  :         9
    Max Threads    :        60

The output (if any) follows:

ls: scatter.*/exited: No such file or directory
fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
0
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 0
                            is_scatter: 0
                             is_gather: 1

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Saved ./CESC.mutation_filtering_report.txt
Writing coverage to ./CESC.per_exon.coverage.txt
  [save_struct] 15/46 16/46 17/46 18/46 19/46 20/46 21/46 22/46 23/46 24/46 25/46 26/46 27/46 28/46 29/46 30/46 31/46 32/46 33/46 34/46 35/46 36/46 37/46 38/46 39/46 40/46 41/46 42/46 43/46 44/46 45/46 46/46  [collapse] [write]
Outputting gene_sample_coverage_table: ./CESC.per_gene.coverage.txt
Outputting gene_sample_mutation_counts_table: ./CESC.per_gene.mutation_counts.txt
Mutation breakdown by type

      Frame_Shift_Del: [19]
      Frame_Shift_Ins: [17]
         In_Frame_Del: [9]
         In_Frame_Ins: [1]
    Missense_Mutation: [4748]
    Nonsense_Mutation: [449]
     Nonstop_Mutation: [11]
               Silent: [1883]
          Splice_Site: [84]
            ----TOTAL: [7221]
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Gather job: collecting partial results

Running MutSig 2:
Gather job: collecting partial results
Outputting significance table: ./CESC.sig_genes.txt
Done
Mapping 640 genesets from /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt to list of project genes.
100/640 200/640 300/640 400/640 500/640 600/640 
Total of 616 genesets contain at least one project gene.
Finding number of unique sites, unique patients: 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients
Analyzing silent/nonsilent ratios
Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Calculating significance of each gene.
Using projection method.
In gene APOPTOSIS the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 85453   n = 1	mu =   4.43e-07
In gene APOPTOSIS_GENMAPP the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 55368   n = 1	mu =   4.43e-07
In gene APOPTOSIS_KEGG the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 64790   n = 1	mu =   4.43e-07
In gene CASPASEPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 28854   n = 1	mu =   4.43e-07
In gene CELL_CYCLE_KEGG the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 165306  n = 1	mu =   4.43e-07
In gene CERAMIDEPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 30121   n = 1	mu =   4.43e-07
In gene D4GDIPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 19275   n = 1	mu =   4.43e-07
In gene DEATHPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 49879   n = 1	mu =   4.43e-07
In gene DNA_REPLICATION_REACTOME the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 76443   n = 1	mu =   4.43e-07
In gene FASPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 61574   n = 1	mu =   4.43e-07
In gene G1_TO_S_CELL_CYCLE_REACTOME the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 114564  n = 1	mu =   4.43e-07
In gene HIVNEFPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 103303  n = 1	mu =   4.43e-07
In gene HSA01430_CELL_COMMUNICATION the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 372855  n = 1	mu =   4.43e-07
In gene HSA04110_CELL_CYCLE the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 204133  n = 1	mu =   4.43e-07
In gene HSA04115_P53_SIGNALING_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 97331   n = 1	mu =   4.43e-07
In gene HSA04210_APOPTOSIS the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 124164  n = 1	mu =   4.43e-07
In gene HSA04620_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 133795  n = 1	mu =   4.43e-07
In gene HSA05050_DENTATORUBROPALLIDOLUYSIAN_ATROPHY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 35814   n = 1	mu =   4.43e-07
In gene MITOCHONDRIAPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 20084   n = 1	mu =   4.43e-07
In gene RHOPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 69089   n = 1	mu =   4.43e-07
In gene SA_CASPASE_CASCADE the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 26686   n = 1	mu =   4.43e-07
In gene SA_FAS_SIGNALING the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 5670    n = 1	mu =   4.43e-07
In gene SIG_CHEMOTAXIS the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 105712  n = 1	mu =   4.43e-07
In gene SODDPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 12142   n = 1	mu =   4.43e-07
In gene ST_FAS_SIGNALING_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 109138  n = 1	mu =   4.43e-07
In gene ST_GA13_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 73380   n = 1	mu =   4.43e-07
In gene ST_TUMOR_NECROSIS_FACTOR_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 40373   n = 1	mu =   4.43e-07
In gene TNFR1PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 58010   n = 1	mu =   4.43e-07
Done
Outputting significance table: ./CESC.sig_genesets.txt
Done
Mapping 640 genesets from /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt to list of project genes.
100/640 200/640 300/640 400/640 500/640 600/640 
Total of 616 genesets contain at least one project gene.
Finding number of unique sites, unique patients: 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients
Analyzing silent/nonsilent ratios
Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Calculating significance of each gene.
Using projection method.
In gene APOPTOSIS the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 85453   n = 1	mu =   4.43e-07
In gene APOPTOSIS_GENMAPP the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 55368   n = 1	mu =   4.43e-07
In gene APOPTOSIS_KEGG the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 64790   n = 1	mu =   4.43e-07
In gene CASPASEPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 28854   n = 1	mu =   4.43e-07
In gene CELL_CYCLE_KEGG the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 165306  n = 1	mu =   4.43e-07
In gene CERAMIDEPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 29129   n = 1	mu =   4.43e-07
In gene D4GDIPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 19275   n = 1	mu =   4.43e-07
In gene DEATHPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 49879   n = 1	mu =   4.43e-07
In gene DNA_REPLICATION_REACTOME the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 76443   n = 1	mu =   4.43e-07
In gene FASPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 61574   n = 1	mu =   4.43e-07
In gene G1_TO_S_CELL_CYCLE_REACTOME the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 114564  n = 1	mu =   4.43e-07
In gene HIVNEFPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 103303  n = 1	mu =   4.43e-07
In gene HSA01430_CELL_COMMUNICATION the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 372855  n = 1	mu =   4.43e-07
In gene HSA04110_CELL_CYCLE the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 204133  n = 1	mu =   4.43e-07
In gene HSA04115_P53_SIGNALING_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 97331   n = 1	mu =   4.43e-07
In gene HSA04210_APOPTOSIS the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 120877  n = 1	mu =   4.43e-07
In gene HSA04620_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 129516  n = 1	mu =   4.43e-07
In gene HSA05050_DENTATORUBROPALLIDOLUYSIAN_ATROPHY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 35814   n = 1	mu =   4.43e-07
In gene MITOCHONDRIAPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 20084   n = 1	mu =   4.43e-07
In gene RHOPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 69089   n = 1	mu =   4.43e-07
In gene SA_CASPASE_CASCADE the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 26686   n = 1	mu =   4.43e-07
In gene SA_FAS_SIGNALING the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 5670    n = 1	mu =   4.43e-07
In gene SIG_CHEMOTAXIS the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 102425  n = 1	mu =   4.43e-07
In gene SODDPATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 12142   n = 1	mu =   4.43e-07
In gene ST_FAS_SIGNALING_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 108146  n = 1	mu =   4.43e-07
In gene ST_GA13_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 73380   n = 1	mu =   4.43e-07
In gene ST_TUMOR_NECROSIS_FACTOR_PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 40373   n = 1	mu =   4.43e-07
In gene TNFR1PATHWAY the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 58010   n = 1	mu =   4.43e-07
Done
Outputting significance table: ./CESC.sig_genesets_2.txt
Done
Loaded COSMIC database from /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
WARNING: unknown chromosome(s):
    {''}

COSMIC analysis:  gene 1000/4519 2000/4519 3000/4519 4000/4519 
Loading refseq database...

Mutation coordinate error (line 663): Length of alternate bases must equal length of refence bases.
119249758	119249759	GA	GA	T
Mutation coordinate error (line 1548): Length of alternate bases must equal length of refence bases.
29091840	29091841	TG	TG	C
Mutation coordinate error (line 1613): Length of alternate bases must equal length of refence bases.
58018106	58018107	GG	GG	T
Mutation coordinate error (line 2411): Length of alternate bases must equal length of refence bases.
46060338	46060339	CC	CC	A
Mutation coordinate error (line 2686): Length of alternate bases must equal length of refence bases.
10401063	10401064	CC	CC	T
Mutation coordinate error (line 2777): Length of alternate bases must equal length of refence bases.
141446613	141446614	GG	GG	T
Mutation coordinate error (line 2783): Length of alternate bases must equal length of refence bases.
33371529	33371530	GG	GG	T
Mutation coordinate error (line 2921): Length of alternate bases must equal length of refence bases.
68266312	68266313	GC	GC	A
Mutation coordinate error (line 3493): Length of alternate bases must equal length of refence bases.
143604	143605	CC	CC	T
Mutation coordinate error (line 3887): Length of alternate bases must equal length of refence bases.
5020587	5020588	GC	GC	C
Mutation coordinate error (line 4257): Length of alternate bases must equal length of refence bases.
46198872	46198873	GG	GG	A
Mutation coordinate error (line 4406): Length of alternate bases must equal length of refence bases.
56603037	56603038	CC	CC	T
Mutation coordinate error (line 4783): Length of alternate bases must equal length of refence bases.
40714664	40714665	CC	CC	T
Mutation coordinate error (line 5082): Length of alternate bases must equal length of refence bases.
91182267	91182268	GG	GG	A
Mutation coordinate error (line 5160): Length of alternate bases must equal length of refence bases.
4702154	4702155	GA	GA	C

Error in maflite format!  The faulty lines displayed above will not be included in output.
Ignoring the mutations listed above.
Analyzing clustered mutations
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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100/3999 200/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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300/3999 convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
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400/3999 500/3999 600/3999 700/3999 convert_chr: assuming human for chrX/chrY
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800/3999 900/3999 convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
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1000/3999 convert_chr: assuming human for chrX/chrY
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1100/3999 convert_chr: assuming human for chrX/chrY
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1200/3999 1300/3999 convert_chr: assuming human for chrX/chrY
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1400/3999 convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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1500/3999 convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
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1600/3999 convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
1700/3999 WARNING: unknown chromosome(s):
    'chr17_ctg5_hap1'

WARNING: unknown chromosome(s):
    'chr17_ctg5_hap1'

convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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1800/3999 1900/3999 convert_chr: assuming human for chrX/chrY
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2000/3999 convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
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2100/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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2200/3999 convert_chr: assuming human for chrX/chrY
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2300/3999 convert_chr: assuming human for chrX/chrY
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2400/3999 convert_chr: assuming human for chrX/chrY
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2500/3999 convert_chr: assuming human for chrX/chrY
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2600/3999 convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
2700/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
WARNING: unknown chromosome(s):
    'chr6_ssto_hap7'

WARNING: unknown chromosome(s):
    'chr6_ssto_hap7'

2800/3999 2900/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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3000/3999 3100/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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3200/3999 convert_chr: assuming human for chrX/chrY
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3300/3999 convert_chr: assuming human for chrX/chrY
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3400/3999 3500/3999 3600/3999 3700/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
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convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
3800/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
3900/3999 convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY

Analyzing gene-gene correlations and anti-correlations
Performing permutations:
0.01	2/1000000	0.00	0.005	210.0	1/1 pairs	2/2 genes done

Top gene-gene pairs:
MAPK1	PIK3CA	0.147899	0.147899	none
Analyzing power per gene...
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Generating gene coverage plots...
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/1.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/2.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/3.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/4.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/5.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/6.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/7.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/8.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/9.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/10.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/11.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/12.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/13.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/14.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/15.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/16.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/17.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/18.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/19.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/20.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/21.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/22.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/23.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/24.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/25.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/26.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/27.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/28.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/29.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/30.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/31.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/32.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/33.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/34.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/35.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/36.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/37.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/38.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/39.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/40.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/41.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/42.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/43.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/44.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/45.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/46.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/47.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/48.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/49.png
Superimposing mutations
Outputting figure to ./CESC.gene_coverage_plots/50.png
generate_gene_coverage_plots finished
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 0 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200
*** Prepare stdandard out:
cat: prepare.out: No such file or directory
*** Prepare stdandard err:
cat: prepare.err: No such file or directory
*** Scatter stdandard out:
Sender: LSF System <lsf@node1430>
Subject: Job 4397751: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1430>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000001> was used as the working directory.
Started at Wed Oct 24 16:07:43 2012
Results reported at Wed Oct 24 16:11:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000001.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000001.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 1  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000001.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    299.91 sec.
    Max Memory :      1654 MB
    Max Swap   :      3991 MB

    Max Processes  :         7
    Max Threads    :        60

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
1
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 1
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 1: processing genes 1 - 90
Calculating significance of each gene.
Using projection method.
1	A1BG	6.878099e-02
2	A1CF	1
3	A2BP1	1
4	A2M	3.056538e-02
5	A2ML1	4.098059e-01
6	A4GALT	1
7	A4GNT	7.351835e-02
8	AAAS	1
9	AACS	1
10	AADAC	1
11	AADACL2	1.461925e-01
12	AADACL3	1
13	AADACL4	1
14	AADAT	1
15	AAGAB	1
16	AAK1	1
17	AAMP	1
18	AANAT	1
19	AARS	2.123604e-02
20	AARS2	3.893937e-01
21	AARSD1	1
22	AASDH	2.958037e-01
23	AASDHPPT	1
24	AASS	1
25	AATF	1.832614e-01
26	AATK	1
27	ABAT	1
28	ABCA1	4.820852e-01
29	ABCA10	1.724545e-01
30	ABCA12	1.213675e-02
31	ABCA13	1
32	ABCA2	1
33	ABCA3	3.489757e-01
34	ABCA4	1
35	ABCA5	1.894261e-01
36	ABCA6	4.270655e-01
37	ABCA7	2.767379e-01
38	ABCA8	6.654945e-02
39	ABCA9	1
40	ABCB1	1
41	ABCB10	1
42	ABCB11	1
43	ABCB4	1
44	ABCB5	1
45	ABCB6	1.696389e-02
46	ABCB7	1
47	ABCB8	1
48	ABCB9	1
49	ABCC1	1
50	ABCC10	1
51	ABCC11	1
52	ABCC12	1
53	ABCC2	1
54	ABCC3	2.154576e-02
55	ABCC4	1
56	ABCC5	4.346341e-01
57	ABCC6	1
58	ABCC8	5.687960e-01
59	ABCC9	1
60	ABCD1	1.034191e-01
61	ABCD2	1.692598e-01
62	ABCD3	1
63	ABCD4	2.112927e-02
64	ABCE1	1
65	ABCF1	1
66	ABCF2	1
67	ABCF3	3.370905e-01
68	ABCG1	1
69	ABCG2	1
70	ABCG4	1
71	ABCG5	1
72	ABCG8	1.296878e-01
73	ABHD1	1
74	ABHD10	1
75	ABHD11	1
76	ABHD12	1
77	ABHD12B	1
78	ABHD13	1
79	ABHD14A	1
80	ABHD14B	1
81	ABHD15	1
82	ABHD2	1
83	ABHD3	1
84	ABHD4	1
85	ABHD5	1
86	ABHD6	1
87	ABHD8	1
88	ABI1	1
89	ABI2	1
90	ABI3	1
Done

Running MutSig 2:
Scatter job 1: processing genes 1 - 90
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ABCA12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.162458e-02	ci left: 5.960420e-01	ci right 6.152964e-01	k: 6057	n:10000
Cons ci ratio: 2.064286e-02	ci left: 7.746878e-01	ci right 7.909471e-01	k: 7829	n:10000
KS ci ratio: 4.299881e-02	ci left: 4.440068e-01	ci right 4.636202e-01	k: 4538	n:10000
ABCA12   10000 perm   3 sec   (2860 perm/sec)   p_kst 4.538000e-01   p_cons 7.829000e-01   p_joint 6.057000e-01

Outputting figure to mutsig2_images.part000000000001/ABCA12.4_8031_10000_0.4538_0.7829_0.6057.png
                gene_name: ABCA12
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 11 percent done.
ABCC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.752814e-02	ci left: 8.259500e-01	ci right 8.406553e-01	k: 8334	n:10000
KS ci ratio: 9.988650e-03	ci left: 9.342335e-01	ci right 9.437088e-01	k: 9391	n:10000
ABCC3   10000 perm   2 sec   (4397 perm/sec)   p_kst 9.391000e-01   p_cons 8.334000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000001/ABCC3.3_4792_10000_0.9391_0.8334_1.png
                gene_name: ABCC3
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 22 percent done.
A2M
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.742366e-02	ci left: 5.132551e-01	ci right 5.329314e-01	k: 5231	n:10000
Cons ci ratio: 7.936930e-03	ci left: 9.567051e-01	ci right 9.644236e-01	k: 9607	n:10000
KS ci ratio: 1.086341e-01	ci left: 1.089077e-01	ci right 1.215175e-01	k: 1151	n:10000
A2M   10000 perm   2 sec   (4756 perm/sec)   p_kst 1.151000e-01   p_cons 9.607000e-01   p_joint 5.231000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 5.874813e-03	ci left: 9.541480e-01	ci right 9.598182e-01	k: 19141	n:20000
KS ci ratio: 7.830386e-02	ci left: 1.069730e-01	ci right 1.157403e-01	k: 2226	n:20000
A2M   20000 perm   5 sec   (4261 perm/sec)   p_kst 1.113000e-01   p_cons 9.570500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000001/A2M.2_4569_20000_0.1113_0.95705_1.png
                gene_name: A2M
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
AARS
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.331963e-02	ci left: 5.707557e-01	ci right 5.901974e-01	k: 5805	n:10000
Cons ci ratio: 6.058452e-02	ci left: 2.860725e-01	ci right 3.040471e-01	k: 2950	n:10000
KS ci ratio: 8.676772e-02	ci left: 1.620951e-01	ci right 1.768979e-01	k: 1694	n:10000
AARS   10000 perm   2 sec   (4839 perm/sec)   p_kst 1.694000e-01   p_cons 2.950000e-01   p_joint 5.805000e-01

Outputting figure to mutsig2_images.part000000000001/AARS.2_2987_10000_0.1694_0.295_0.5805.png
                gene_name: AARS
               theta_stop: 0.087 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.29 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 44 percent done.
AATF
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.956251e-01	ci left: 3.481398e-02	ci right 4.245779e-02	k: 385	n:10000
Cons ci ratio: 2.427486e-02	ci left: 7.139129e-01	ci right 7.315572e-01	k: 7228	n:10000
KS ci ratio: 3.981388e-01	ci left: 7.692674e-03	ci right 1.160097e-02	k: 95	n:10000
AATF   10000 perm   2 sec   (5743 perm/sec)   p_kst 9.500000e-03   p_cons 7.228000e-01   p_joint 3.850000e-02

Joint ci ratio: 1.654508e-01	ci left: 2.503753e-02	ci right 2.960129e-02	k: 545	n:20000
Cons ci ratio: 1.694269e-02	ci left: 7.217750e-01	ci right 7.341586e-01	k: 14560	n:20000
KS ci ratio: 2.646529e-01	ci left: 9.413987e-03	ci right 1.233084e-02	k: 216	n:20000
AATF   20000 perm   4 sec   (4937 perm/sec)   p_kst 1.080000e-02   p_cons 7.280000e-01   p_joint 2.725000e-02

Joint ci ratio: 1.475034e-01	ci left: 2.130123e-02	ci right 2.472534e-02	k: 689	n:30000
Cons ci ratio: 1.380113e-02	ci left: 7.238646e-01	ci right 7.339577e-01	k: 21868	n:30000
KS ci ratio: 2.152558e-01	ci left: 9.755930e-03	ci right 1.214020e-02	k: 327	n:30000
AATF   30000 perm   6 sec   (4659 perm/sec)   p_kst 1.090000e-02   p_cons 7.289333e-01   p_joint 2.296667e-02

Joint ci ratio: 1.268976e-01	ci left: 2.181961e-02	ci right 2.480015e-02	k: 931	n:40000
Cons ci ratio: 1.198871e-02	ci left: 7.233339e-01	ci right 7.320830e-01	k: 29109	n:40000
KS ci ratio: 1.873585e-01	ci left: 9.810223e-03	ci right 1.186172e-02	k: 432	n:40000
AATF   40000 perm   9 sec   (4527 perm/sec)   p_kst 1.080000e-02   p_cons 7.277250e-01   p_joint 2.327500e-02

Joint ci ratio: 1.095235e-01	ci left: 2.361023e-02	ci right 2.636530e-02	k: 1248	n:50000
Cons ci ratio: 1.075728e-02	ci left: 7.225296e-01	ci right 7.303641e-01	k: 36323	n:50000
KS ci ratio: 1.692061e-01	ci left: 9.720862e-03	ci right 1.153663e-02	k: 530	n:50000
AATF   50000 perm   11 sec   (4435 perm/sec)   p_kst 1.060000e-02   p_cons 7.264600e-01   p_joint 2.496000e-02

Joint ci ratio: 9.929686e-02	ci left: 2.405815e-02	ci right 2.658805e-02	k: 1518	n:60000
Cons ci ratio: 9.855688e-03	ci left: 7.214248e-01	ci right 7.285868e-01	k: 43501	n:60000
KS ci ratio: 1.530378e-01	ci left: 9.988355e-03	ci right 1.165947e-02	k: 648	n:60000
AATF   60000 perm   14 sec   (4360 perm/sec)   p_kst 1.080000e-02   p_cons 7.250167e-01   p_joint 2.530000e-02

Joint ci ratio: 9.182929e-02	ci left: 2.420512e-02	ci right 2.654873e-02	k: 1775	n:70000
Cons ci ratio: 9.123022e-03	ci left: 7.217618e-01	ci right 7.283909e-01	k: 50756	n:70000
KS ci ratio: 1.415125e-01	ci left: 1.007507e-02	ci right 1.162302e-02	k: 758	n:70000
AATF   70000 perm   16 sec   (4267 perm/sec)   p_kst 1.082857e-02   p_cons 7.250857e-01   p_joint 2.535714e-02

Joint ci ratio: 8.611017e-02	ci left: 2.416163e-02	ci right 2.634799e-02	k: 2019	n:80000
Cons ci ratio: 8.535914e-03	ci left: 7.218790e-01	ci right 7.280797e-01	k: 57999	n:80000
KS ci ratio: 1.317166e-01	ci left: 1.022830e-02	ci right 1.168250e-02	k: 875	n:80000
AATF   80000 perm   19 sec   (4165 perm/sec)   p_kst 1.093750e-02   p_cons 7.249875e-01   p_joint 2.523750e-02

Joint ci ratio: 8.068604e-02	ci left: 2.452345e-02	ci right 2.659618e-02	k: 2299	n:90000
Cons ci ratio: 8.050852e-03	ci left: 7.219028e-01	ci right 7.277493e-01	k: 65235	n:90000
KS ci ratio: 1.230835e-01	ci left: 1.045807e-02	ci right 1.184038e-02	k: 1002	n:90000
AATF   90000 perm   22 sec   (4112 perm/sec)   p_kst 1.113333e-02   p_cons 7.248333e-01   p_joint 2.554444e-02

Joint ci ratio: 7.661565e-02	ci left: 2.453175e-02	ci right 2.649590e-02	k: 2550	n:100000
Cons ci ratio: 7.635670e-03	ci left: 7.221608e-01	ci right 7.277061e-01	k: 72494	n:100000
KS ci ratio: 1.157446e-01	ci left: 1.068323e-02	ci right 1.200535e-02	k: 1133	n:100000
AATF   100000 perm   25 sec   (4059 perm/sec)   p_kst 1.133000e-02   p_cons 7.249400e-01   p_joint 2.550000e-02

Joint ci ratio: 7.310501e-02	ci left: 2.454070e-02	ci right 2.641170e-02	k: 2801	n:110000
Cons ci ratio: 7.284875e-03	ci left: 7.220409e-01	ci right 7.273291e-01	k: 79716	n:110000
KS ci ratio: 1.101530e-01	ci left: 1.075448e-02	ci right 1.201694e-02	k: 1251	n:110000
AATF   110000 perm   27 sec   (4002 perm/sec)   p_kst 1.137273e-02   p_cons 7.246909e-01   p_joint 2.546364e-02

Joint ci ratio: 7.013091e-02	ci left: 2.448435e-02	ci right 2.627202e-02	k: 3044	n:120000
Cons ci ratio: 6.968900e-03	ci left: 7.224891e-01	ci right 7.275500e-01	k: 87003	n:120000
KS ci ratio: 1.049909e-01	ci left: 1.088006e-02	ci right 1.209372e-02	k: 1377	n:120000
AATF   120000 perm   30 sec   (3942 perm/sec)   p_kst 1.147500e-02   p_cons 7.250250e-01   p_joint 2.536667e-02

Joint ci ratio: 5.878933e-02	ci left: 3.209618e-02	ci right 3.404779e-02	k: 4298	n:130000
Cons ci ratio: 6.710005e-03	ci left: 7.217232e-01	ci right 7.265899e-01	k: 94141	n:130000
KS ci ratio: 1.011064e-01	ci left: 1.085249e-02	ci right 1.201561e-02	k: 1485	n:130000
AATF   130000 perm   33 sec   (3884 perm/sec)   p_kst 1.142308e-02   p_cons 7.241615e-01   p_joint 3.306154e-02

Joint ci ratio: 5.657941e-02	ci left: 3.221127e-02	ci right 3.409384e-02	k: 4640	n:140000
Cons ci ratio: 6.468422e-03	ci left: 7.216574e-01	ci right 7.263476e-01	k: 101361	n:140000
KS ci ratio: 9.731507e-02	ci left: 1.089927e-02	ci right 1.202110e-02	k: 1603	n:140000
AATF   140000 perm   37 sec   (3825 perm/sec)   p_kst 1.145000e-02   p_cons 7.240071e-01   p_joint 3.314286e-02

Outputting figure to mutsig2_images.part000000000001/AATF.2_1731_140000_0.01145_0.72401_0.033143.png
                gene_name: AATF
               theta_stop: 0.097 
                    nperm: 140000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.011 
       ci_ks_bounds_right: 0.012 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.033 
     ci_joint_bounds_left: 0.032 
    ci_joint_bounds_right: 0.034 

Current progress: 56 percent done.
ABCA10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.463565e-03	ci left: 9.613148e-01	ci right 9.686110e-01	k: 9651	n:10000
Cons ci ratio: 6.066330e-03	ci left: 9.735507e-01	ci right 9.795672e-01	k: 9767	n:10000
KS ci ratio: 2.471742e-02	ci left: 7.065452e-01	ci right 7.243291e-01	k: 7155	n:10000
ABCA10   10000 perm   2 sec   (4558 perm/sec)   p_kst 7.155000e-01   p_cons 9.767000e-01   p_joint 9.651000e-01

Outputting figure to mutsig2_images.part000000000001/ABCA10.2_4780_10000_0.7155_0.9767_0.9651.png
                gene_name: ABCA10
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 67 percent done.
ABCA8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.561466e-02	ci left: 1.658291e-01	ci right 1.807618e-01	k: 1732	n:10000
Cons ci ratio: 1.089014e-01	ci left: 1.084196e-01	ci right 1.210058e-01	k: 1146	n:10000
KS ci ratio: 1.719499e-01	ci left: 4.513859e-02	ci right 5.372632e-02	k: 493	n:10000
ABCA8   10000 perm   2 sec   (4463 perm/sec)   p_kst 4.930000e-02   p_cons 1.146000e-01   p_joint 1.732000e-01

Joint ci ratio: 1.310813e-01	ci left: 3.998807e-02	ci right 4.564582e-02	k: 855	n:20000
Cons ci ratio: 7.676089e-02	ci left: 1.109048e-01	ci right 1.198074e-01	k: 2306	n:20000
KS ci ratio: 1.206295e-01	ci left: 4.711722e-02	ci right 5.321441e-02	k: 1002	n:20000
ABCA8   20000 perm   5 sec   (4002 perm/sec)   p_kst 5.010000e-02   p_cons 1.153000e-01   p_joint 4.275000e-02

Joint ci ratio: 1.140274e-01	ci left: 3.573495e-02	ci right 4.008846e-02	k: 1136	n:30000
Cons ci ratio: 6.063836e-02	ci left: 1.185468e-01	ci right 1.259932e-01	k: 3667	n:30000
KS ci ratio: 9.755917e-02	ci left: 4.857001e-02	ci right 5.358405e-02	k: 1531	n:30000
ABCA8   30000 perm   8 sec   (3863 perm/sec)   p_kst 5.103333e-02   p_cons 1.222333e-01   p_joint 3.786667e-02

Joint ci ratio: 7.720245e-02	ci left: 5.820763e-02	ci right 6.290642e-02	k: 2421	n:40000
Cons ci ratio: 5.306401e-02	ci left: 1.168553e-01	ci right 1.232500e-01	k: 4801	n:40000
KS ci ratio: 8.424304e-02	ci left: 4.918271e-02	ci right 5.353272e-02	k: 2053	n:40000
ABCA8   40000 perm   11 sec   (3747 perm/sec)   p_kst 5.132500e-02   p_cons 1.200250e-01   p_joint 6.052500e-02

Outputting figure to mutsig2_images.part000000000001/ABCA8.2_4894_40000_0.051325_0.12003_0.060525.png
                gene_name: ABCA8
               theta_stop: 0.084 
                    nperm: 40000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.049 
       ci_ks_bounds_right: 0.054 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.061 
     ci_joint_bounds_left: 0.058 
    ci_joint_bounds_right: 0.063 

Current progress: 78 percent done.
ABCB6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.096042e-01	ci left: 1.071510e-01	ci right 1.196752e-01	k: 1133	n:10000
Cons ci ratio: 2.348632e-01	ci left: 2.391158e-02	ci right 3.036784e-02	k: 270	n:10000
KS ci ratio: 1.247955e-01	ci left: 8.416945e-02	ci right 9.547082e-02	k: 897	n:10000
ABCB6   10000 perm   2 sec   (5925 perm/sec)   p_kst 8.970000e-02   p_cons 2.700000e-02   p_joint 1.133000e-01

Joint ci ratio: 1.011086e-01	ci left: 6.635513e-02	ci right 7.347052e-02	k: 1397	n:20000
Cons ci ratio: 1.675123e-01	ci left: 2.441395e-02	ci right 2.892508e-02	k: 532	n:20000
KS ci ratio: 8.752461e-02	ci left: 8.714669e-02	ci right 9.517263e-02	k: 1822	n:20000
ABCB6   20000 perm   4 sec   (5119 perm/sec)   p_kst 9.110000e-02   p_cons 2.660000e-02   p_joint 6.985000e-02

Joint ci ratio: 4.546763e-02	ci left: 1.940322e-01	ci right 2.030929e-01	k: 5956	n:30000
Cons ci ratio: 1.355170e-01	ci left: 2.529183e-02	ci right 2.900051e-02	k: 813	n:30000
KS ci ratio: 7.214093e-02	ci left: 8.635850e-02	ci right 9.285457e-02	k: 2687	n:30000
ABCB6   30000 perm   6 sec   (4860 perm/sec)   p_kst 8.956667e-02   p_cons 2.710000e-02   p_joint 1.985333e-01

Joint ci ratio: 4.167120e-02	ci left: 1.773616e-01	ci right 1.849347e-01	k: 7245	n:40000
Cons ci ratio: 1.166091e-01	ci left: 2.587068e-02	ci right 2.909841e-02	k: 1098	n:40000
KS ci ratio: 6.207738e-02	ci left: 8.782900e-02	ci right 9.348059e-02	k: 3625	n:40000
ABCB6   40000 perm   9 sec   (4698 perm/sec)   p_kst 9.062500e-02   p_cons 2.745000e-02   p_joint 1.811250e-01

Joint ci ratio: 3.731090e-02	ci left: 1.774551e-01	ci right 1.842220e-01	k: 9041	n:50000
Cons ci ratio: 1.040943e-01	ci left: 2.614254e-02	ci right 2.903266e-02	k: 1378	n:50000
KS ci ratio: 5.550024e-02	ci left: 8.819660e-02	ci right 9.325104e-02	k: 4535	n:50000
ABCB6   50000 perm   11 sec   (4566 perm/sec)   p_kst 9.070000e-02   p_cons 2.756000e-02   p_joint 1.808200e-01

Joint ci ratio: 3.191017e-02	ci left: 1.977499e-01	ci right 2.041791e-01	k: 12057	n:60000
Cons ci ratio: 9.504840e-02	ci left: 2.625487e-02	ci right 2.889109e-02	k: 1653	n:60000
KS ci ratio: 5.060433e-02	ci left: 8.861132e-02	ci right 9.322834e-02	k: 5454	n:60000
ABCB6   60000 perm   13 sec   (4456 perm/sec)   p_kst 9.090000e-02   p_cons 2.755000e-02   p_joint 2.009500e-01

Outputting figure to mutsig2_images.part000000000001/ABCB6.2_2605_60000_0.0909_0.02755_0.20095.png
                gene_name: ABCB6
               theta_stop: 0.095 
                    nperm: 60000 
                     p_ks: 0.091 
        ci_ks_bounds_left: 0.089 
       ci_ks_bounds_right: 0.093 
                   p_cons: 0.028 
      ci_cons_bounds_left: 0.026 
     ci_cons_bounds_right: 0.029 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.20 

Current progress: 89 percent done.
ABCD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.036773e-02	ci left: 6.153256e-01	ci right 6.344016e-01	k: 6249	n:10000
Cons ci ratio: 5.383424e-02	ci left: 3.370699e-01	ci right 3.558196e-01	k: 3464	n:10000
KS ci ratio: 2.200419e-02	ci left: 7.519090e-01	ci right 7.687391e-01	k: 7604	n:10000
ABCD4   10000 perm   2 sec   (5376 perm/sec)   p_kst 7.604000e-01   p_cons 3.464000e-01   p_joint 6.249000e-01

Outputting figure to mutsig2_images.part000000000001/ABCD4.2_1897_10000_0.7604_0.3464_0.6249.png
                gene_name: ABCD4
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.63 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000001
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 1 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4397753: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000002> was used as the working directory.
Started at Wed Oct 24 16:07:43 2012
Results reported at Wed Oct 24 16:10:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000002.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000002.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 2  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000002.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    171.28 sec.
    Max Memory :      1486 MB
    Max Swap   :      4006 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
2
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 2
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 2: processing genes 91 - 179
Calculating significance of each gene.
Using projection method.
91	ABI3BP	1
92	ABL1	1.153528e-01
93	ABL2	1
94	ABLIM1	1.275426e-01
95	ABLIM2	1
96	ABLIM3	1
97	ABO	1
98	ABP1	1
99	ABR	8.810373e-03
100	ABRA	1
101	ABT1	1
102	ABTB1	1
103	ABTB2	1
104	ACAA1	1
105	ACAA2	1
106	ACACA	5.789359e-01
107	ACACB	1.999984e-01
108	ACAD10	1
109	ACAD11	1
110	ACAD8	1
111	ACAD9	1
112	ACADL	1
113	ACADM	1
114	ACADS	9.559381e-02
115	ACADSB	1
116	ACADVL	2.059298e-01
117	ACAN	1
118	ACAP1	2.659106e-02
119	ACAP2	6.348731e-02
120	ACAP3	1
121	ACAT1	1
122	ACAT2	1
123	ACBD3	1
124	ACBD4	1.032896e-01
125	ACBD5	1
126	ACBD6	1
127	ACBD7	1
128	ACCN1	1
129	ACCN2	1
130	ACCN3	1
131	ACCN4	1
132	ACCN5	1
133	ACCS	1
134	ACCSL	1
135	ACD	1
136	ACE	1
137	ACE2	1
138	ACER1	1
139	ACER2	1
140	ACER3	1
141	ACHE	1
142	ACIN1	1
143	ACLY	1.247975e-01
144	ACMSD	1
145	ACN9	1
146	ACO1	2.645487e-01
147	ACO2	1
148	ACOT1	1
149	ACOT11	1
150	ACOT12	2.447879e-01
151	ACOT13	1
152	ACOT2	1
153	ACOT4	1
154	ACOT6	1
155	ACOT7	1
156	ACOT8	1
157	ACOT9	1
158	ACOX1	1
159	ACOX2	1
160	ACOX3	1
161	ACOXL	1
162	ACP1	1
163	ACP2	1
164	ACP5	3.664285e-02
165	ACP6	8.678411e-02
166	ACPL2	1
167	ACPP	1
168	ACPT	1
169	ACR	1
170	ACRBP	1
171	ACRC	1
172	ACRV1	1
173	ACSBG1	1
174	ACSBG2	1
175	ACSF2	1
176	ACSF3	1
177	ACSL1	1.465373e-01
178	ACSL3	5.202740e-02
179	ACSL4	1
Done

Running MutSig 2:
Scatter job 2: processing genes 91 - 179
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ACAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.031915e-01	ci left: 1.195555e-01	ci right 1.326632e-01	k: 1260	n:10000
Cons ci ratio: 9.901168e-03	ci left: 9.352693e-01	ci right 9.446723e-01	k: 9401	n:10000
KS ci ratio: 1.645486e-01	ci left: 4.926618e-02	ci right 5.819605e-02	k: 536	n:10000
ACAP1   10000 perm   2 sec   (6040 perm/sec)   p_kst 5.360000e-02   p_cons 9.401000e-01   p_joint 1.260000e-01

Joint ci ratio: 8.605233e-02	ci left: 8.994073e-02	ci right 9.807774e-02	k: 1879	n:20000
Cons ci ratio: 6.949165e-03	ci left: 9.375423e-01	ci right 9.441288e-01	k: 18818	n:20000
KS ci ratio: 1.167586e-01	ci left: 5.022695e-02	ci right 5.650370e-02	k: 1066	n:20000
ACAP1   20000 perm   6 sec   (3575 perm/sec)   p_kst 5.330000e-02   p_cons 9.409000e-01   p_joint 9.395000e-02

Joint ci ratio: 6.072327e-02	ci left: 1.182508e-01	ci right 1.256893e-01	k: 3658	n:30000
Cons ci ratio: 5.642707e-03	ci left: 9.387846e-01	ci right 9.441295e-01	k: 28245	n:30000
KS ci ratio: 9.579296e-02	ci left: 5.032870e-02	ci right 5.542499e-02	k: 1585	n:30000
ACAP1   30000 perm   8 sec   (3875 perm/sec)   p_kst 5.283333e-02   p_cons 9.415000e-01   p_joint 1.219333e-01

Outputting figure to mutsig2_images.part000000000002/ACAP1.3_2311_30000_0.052833_0.9415_0.12193.png
                gene_name: ACAP1
               theta_stop: 0.096 
                    nperm: 30000 
                     p_ks: 0.053 
        ci_ks_bounds_left: 0.050 
       ci_ks_bounds_right: 0.055 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 20 percent done.
ABR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.277544e-02	ci left: 5.787803e-01	ci right 5.981681e-01	k: 5885	n:10000
KS ci ratio: 2.802675e-02	ci left: 6.523307e-01	ci right 6.709750e-01	k: 6617	n:10000
ABR   10000 perm   2 sec   (5805 perm/sec)   p_kst 6.617000e-01   p_cons 5.885000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000002/ABR.2_2811_10000_0.6617_0.5885_1.png
                gene_name: ABR
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 40 percent done.
ACACB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.981480e-02	ci left: 7.884733e-01	ci right 8.043536e-01	k: 7965	n:10000
KS ci ratio: 4.899491e-02	ci left: 3.806225e-01	ci right 3.998415e-01	k: 3902	n:10000
ACACB   10000 perm   2 sec   (4404 perm/sec)   p_kst 3.902000e-01   p_cons 7.965000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000002/ACACB.2_7585_10000_0.3902_0.7965_1.png
                gene_name: ACACB
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
ACAP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.930388e-01	ci left: 3.576701e-02	ci right 4.350411e-02	k: 395	n:10000
Cons ci ratio: 3.073991e-01	ci left: 1.354008e-02	ci right 1.854760e-02	k: 159	n:10000
KS ci ratio: 8.443842e-02	ci left: 1.697609e-01	ci right 1.848276e-01	k: 1772	n:10000
ACAP2   10000 perm   2 sec   (6237 perm/sec)   p_kst 1.772000e-01   p_cons 1.590000e-02   p_joint 3.950000e-02

Joint ci ratio: 1.613936e-01	ci left: 2.633371e-02	ci right 3.100466e-02	k: 572	n:20000
Cons ci ratio: 2.212663e-01	ci left: 1.373916e-02	ci right 1.720379e-02	k: 308	n:20000
KS ci ratio: 6.003736e-02	ci left: 1.703988e-01	ci right 1.809957e-01	k: 3513	n:20000
ACAP2   20000 perm   4 sec   (5557 perm/sec)   p_kst 1.756500e-01   p_cons 1.540000e-02   p_joint 2.860000e-02

Joint ci ratio: 1.004241e-01	ci left: 4.590106e-02	ci right 5.078689e-02	k: 1449	n:30000
Cons ci ratio: 1.774827e-01	ci left: 1.457862e-02	ci right 1.744955e-02	k: 479	n:30000
KS ci ratio: 4.857396e-02	ci left: 1.740163e-01	ci right 1.827127e-01	k: 5350	n:30000
ACAP2   30000 perm   6 sec   (5238 perm/sec)   p_kst 1.783333e-01   p_cons 1.596667e-02   p_joint 4.830000e-02

Joint ci ratio: 8.740651e-02	ci left: 4.577863e-02	ci right 4.998732e-02	k: 1914	n:40000
Cons ci ratio: 1.537051e-01	ci left: 1.476904e-02	ci right 1.725194e-02	k: 639	n:40000
KS ci ratio: 4.210829e-02	ci left: 1.743120e-01	ci right 1.818348e-01	k: 7122	n:40000
ACAP2   40000 perm   8 sec   (5052 perm/sec)   p_kst 1.780500e-01   p_cons 1.597500e-02   p_joint 4.785000e-02

Joint ci ratio: 7.850238e-02	ci left: 4.563227e-02	ci right 4.938048e-02	k: 2374	n:50000
Cons ci ratio: 1.381822e-01	ci left: 1.474446e-02	ci right 1.695227e-02	k: 791	n:50000
KS ci ratio: 3.761339e-02	ci left: 1.750927e-01	ci right 1.818247e-01	k: 8922	n:50000
ACAP2   50000 perm   10 sec   (4907 perm/sec)   p_kst 1.784400e-01   p_cons 1.582000e-02   p_joint 4.748000e-02

Joint ci ratio: 5.876855e-02	ci left: 6.700097e-02	ci right 7.107417e-02	k: 4141	n:60000
Cons ci ratio: 1.263049e-01	ci left: 1.480119e-02	ci right 1.681270e-02	k: 947	n:60000
KS ci ratio: 3.431397e-02	ci left: 1.755757e-01	ci right 1.817221e-01	k: 10718	n:60000
ACAP2   60000 perm   13 sec   (4792 perm/sec)   p_kst 1.786333e-01   p_cons 1.578333e-02   p_joint 6.901667e-02

Joint ci ratio: 5.493195e-02	ci left: 6.594842e-02	ci right 6.968750e-02	k: 4746	n:70000
Cons ci ratio: 1.186365e-01	ci left: 1.444531e-02	ci right 1.628089e-02	k: 1074	n:70000
KS ci ratio: 3.188584e-02	ci left: 1.747325e-01	ci right 1.804085e-01	k: 12429	n:70000
ACAP2   70000 perm   15 sec   (4692 perm/sec)   p_kst 1.775571e-01   p_cons 1.534286e-02   p_joint 6.780000e-02

Joint ci ratio: 5.193648e-02	ci left: 6.474593e-02	ci right 6.821059e-02	k: 5317	n:80000
Cons ci ratio: 1.109547e-01	ci left: 1.450944e-02	ci right 1.622597e-02	k: 1228	n:80000
KS ci ratio: 2.989395e-02	ci left: 1.742613e-01	ci right 1.795621e-01	k: 14152	n:80000
ACAP2   80000 perm   17 sec   (4584 perm/sec)   p_kst 1.769000e-01   p_cons 1.535000e-02   p_joint 6.646250e-02

Joint ci ratio: 4.855347e-02	ci left: 6.589128e-02	ci right 6.918110e-02	k: 6077	n:90000
Cons ci ratio: 1.047873e-01	ci left: 1.450819e-02	ci right 1.612327e-02	k: 1377	n:90000
KS ci ratio: 2.815865e-02	ci left: 1.746771e-01	ci right 1.796771e-01	k: 15945	n:90000
ACAP2   90000 perm   20 sec   (4491 perm/sec)   p_kst 1.771667e-01   p_cons 1.530000e-02   p_joint 6.752222e-02

Joint ci ratio: 4.928390e-02	ci left: 5.803173e-02	ci right 6.097388e-02	k: 5949	n:100000
Cons ci ratio: 1.000796e-01	ci left: 1.435324e-02	ci right 1.587507e-02	k: 1510	n:100000
KS ci ratio: 2.674464e-02	ci left: 1.744697e-01	ci right 1.792090e-01	k: 17683	n:100000
ACAP2   100000 perm   23 sec   (4405 perm/sec)   p_kst 1.768300e-01   p_cons 1.510000e-02   p_joint 5.949000e-02

Joint ci ratio: 4.667649e-02	ci left: 5.884640e-02	ci right 6.166775e-02	k: 6627	n:110000
Cons ci ratio: 9.574734e-02	ci left: 1.428995e-02	ci right 1.573579e-02	k: 1650	n:110000
KS ci ratio: 2.547568e-02	ci left: 1.748571e-01	ci right 1.793782e-01	k: 19482	n:110000
ACAP2   110000 perm   25 sec   (4325 perm/sec)   p_kst 1.771091e-01   p_cons 1.500000e-02   p_joint 6.024545e-02

Outputting figure to mutsig2_images.part000000000002/ACAP2.2_2429_110000_0.17711_0.015_0.060245.png
                gene_name: ACAP2
               theta_stop: 0.096 
                    nperm: 110000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.015 
      ci_cons_bounds_left: 0.014 
     ci_cons_bounds_right: 0.016 
                  p_joint: 0.060 
     ci_joint_bounds_left: 0.059 
    ci_joint_bounds_right: 0.062 

Current progress: 80 percent done.
ACLY
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.682802e-02	ci left: 5.212613e-01	ci right 5.409206e-01	k: 5311	n:10000
KS ci ratio: 2.953145e-02	ci left: 6.283912e-01	ci right 6.473284e-01	k: 6379	n:10000
ACLY   10000 perm   2 sec   (5715 perm/sec)   p_kst 6.379000e-01   p_cons 5.311000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000002/ACLY.2_3418_10000_0.6379_0.5311_1.png
                gene_name: ACLY
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000002
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 2 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4397757: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000003> was used as the working directory.
Started at Wed Oct 24 16:07:57 2012
Results reported at Wed Oct 24 16:10:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000003.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000003.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 3  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000003.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    159.04 sec.
    Max Memory :      1484 MB
    Max Swap   :      4014 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
3
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 3
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 3: processing genes 180 - 269
Calculating significance of each gene.
Using projection method.
180	ACSL5	1
181	ACSL6	1
182	ACSM1	1
183	ACSM2A	1
184	ACSM2B	1
185	ACSM3	1
186	ACSM4	1
187	ACSM5	1
188	ACSS1	1
189	ACSS2	3.015954e-01
190	ACSS3	1
191	ACTA1	1
192	ACTA2	1
193	ACTB	4.480011e-02
194	ACTBL2	1
195	ACTC1	1
196	ACTG1	1
197	ACTG2	1
198	ACTL6A	1
199	ACTL6B	1
200	ACTL7A	1
201	ACTL7B	1
202	ACTL8	1
203	ACTL9	1
204	ACTN1	1.123873e-01
205	ACTN2	1
206	ACTN3	1.562202e-02
207	ACTN4	1.359512e-01
208	ACTR10	1
209	ACTR1A	1
210	ACTR1B	1
211	ACTR2	1
212	ACTR3	1
213	ACTR3B	1
214	ACTR5	1
215	ACTR6	1
216	ACTR8	1
217	ACTRT1	5.627353e-03
218	ACTRT2	1
219	ACVR1	1
220	ACVR1B	1
221	ACVR1C	1
222	ACVR2A	1
223	ACVR2B	1
224	ACVRL1	1
225	ACY1	2.294432e-02
226	ACY3	1
227	ACYP1	1
228	ACYP2	1
229	ADA	1
230	ADAD1	1.390398e-01
231	ADAD2	1
232	ADAL	1
233	ADAM10	2.536829e-01
234	ADAM11	1
235	ADAM12	1
236	ADAM15	3.530636e-01
237	ADAM17	3.565828e-01
238	ADAM18	1
239	ADAM19	1
240	ADAM2	1
241	ADAM20	1
242	ADAM21	1
243	ADAM22	1
244	ADAM23	1
245	ADAM28	1
246	ADAM29	9.123099e-02
247	ADAM30	1.210614e-01
248	ADAM32	1
249	ADAM33	1
250	ADAM7	1
251	ADAM8	1
252	ADAM9	1
253	ADAMDEC1	1
254	ADAMTS1	6.614063e-03
255	ADAMTS10	2.339049e-01
256	ADAMTS12	1
257	ADAMTS13	1
258	ADAMTS14	3.675709e-01
259	ADAMTS15	1
260	ADAMTS16	2.120969e-02
261	ADAMTS17	1.623730e-01
262	ADAMTS18	1
263	ADAMTS19	2.982214e-01
264	ADAMTS2	1.146157e-01
265	ADAMTS20	9.888159e-03
266	ADAMTS3	9.974118e-02
267	ADAMTS4	1
268	ADAMTS5	1
269	ADAMTS6	4.446748e-01
Done

Running MutSig 2:
Scatter job 3: processing genes 180 - 269
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ADAMTS16
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.770450e-02	ci left: 8.231021e-01	ci right 8.379049e-01	k: 8306	n:10000
Cons ci ratio: 3.463711e-02	ci left: 5.517079e-01	ci right 5.712563e-01	k: 5615	n:10000
KS ci ratio: 2.439601e-02	ci left: 7.118940e-01	ci right 7.295772e-01	k: 7208	n:10000
ADAMTS16   10000 perm   2 sec   (5098 perm/sec)   p_kst 7.208000e-01   p_cons 5.615000e-01   p_joint 8.306000e-01

Outputting figure to mutsig2_images.part000000000003/ADAMTS16.4_3767_10000_0.7208_0.5615_0.8306.png
                gene_name: ADAMTS16
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.82 
    ci_joint_bounds_right: 0.84 

Current progress: 17 percent done.
ADAMTS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.204644e-02	ci left: 7.512008e-01	ci right 7.680477e-01	k: 7597	n:10000
KS ci ratio: 4.722967e-02	ci left: 3.981463e-01	ci right 4.175075e-01	k: 4078	n:10000
ADAMTS1   10000 perm   2 sec   (5349 perm/sec)   p_kst 4.078000e-01   p_cons 7.597000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000003/ADAMTS1.3_2940_10000_0.4078_0.7597_1.png
                gene_name: ADAMTS1
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
ADAMTS20
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.803054e-02	ci left: 8.178151e-01	ci right 8.327949e-01	k: 8254	n:10000
KS ci ratio: 3.443362e-02	ci left: 5.546142e-01	ci right 5.741482e-01	k: 5644	n:10000
ADAMTS20   10000 perm   2 sec   (4633 perm/sec)   p_kst 5.644000e-01   p_cons 8.254000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000003/ADAMTS20.3_5888_10000_0.5644_0.8254_1.png
                gene_name: ADAMTS20
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
ACTN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.279304e-02	ci left: 8.978526e-01	ci right 9.095111e-01	k: 9038	n:10000
KS ci ratio: 3.515339e-02	ci left: 5.443933e-01	ci right 5.639751e-01	k: 5542	n:10000
ACTN3   10000 perm   2 sec   (5731 perm/sec)   p_kst 5.542000e-01   p_cons 9.038000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000003/ACTN3.2_2790_10000_0.5542_0.9038_1.png
                gene_name: ACTN3
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
ACTRT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.723101e-01	ci left: 1.753307e-02	ci right 2.315124e-02	k: 202	n:10000
Cons ci ratio: 2.945635e-01	ci left: 1.483579e-02	ci right 2.005075e-02	k: 173	n:10000
KS ci ratio: 4.651369e-02	ci left: 4.055180e-01	ci right 4.249314e-01	k: 4152	n:10000
ACTRT1   10000 perm   1 sec   (6935 perm/sec)   p_kst 4.152000e-01   p_cons 1.730000e-02   p_joint 2.020000e-02

Joint ci ratio: 6.132228e-02	ci left: 1.644223e-01	ci right 1.748740e-01	k: 3392	n:20000
Cons ci ratio: 2.095217e-01	ci left: 1.539613e-02	ci right 1.904617e-02	k: 343	n:20000
KS ci ratio: 3.279855e-02	ci left: 4.097551e-01	ci right 4.234692e-01	k: 8332	n:20000
ACTRT1   20000 perm   3 sec   (6109 perm/sec)   p_kst 4.166000e-01   p_cons 1.715000e-02   p_joint 1.696000e-01

Joint ci ratio: 6.634589e-02	ci left: 1.007646e-01	ci right 1.077123e-01	k: 3126	n:30000
Cons ci ratio: 1.722679e-01	ci left: 1.550360e-02	ci right 1.845768e-02	k: 508	n:30000
KS ci ratio: 2.671839e-02	ci left: 4.121440e-01	ci right 4.233386e-01	k: 12532	n:30000
ACTRT1   30000 perm   5 sec   (5662 perm/sec)   p_kst 4.177333e-01   p_cons 1.693333e-02   p_joint 1.042000e-01

Joint ci ratio: 4.572816e-02	ci left: 1.516394e-01	ci right 1.587607e-01	k: 6207	n:40000
Cons ci ratio: 1.488176e-01	ci left: 1.577991e-02	ci right 1.834090e-02	k: 681	n:40000
KS ci ratio: 2.303050e-02	ci left: 4.151816e-01	ci right 4.248800e-01	k: 16801	n:40000
ACTRT1   40000 perm   7 sec   (5441 perm/sec)   p_kst 4.200250e-01   p_cons 1.702500e-02   p_joint 1.551750e-01

Joint ci ratio: 1.060069e-01	ci left: 2.520711e-02	ci right 2.804821e-02	k: 1330	n:50000
Cons ci ratio: 1.335458e-01	ci left: 1.580765e-02	ci right 1.808893e-02	k: 846	n:50000
KS ci ratio: 2.053200e-02	ci left: 4.172862e-01	ci right 4.259629e-01	k: 21081	n:50000
ACTRT1   50000 perm   9 sec   (5266 perm/sec)   p_kst 4.216200e-01   p_cons 1.692000e-02   p_joint 2.660000e-02

Joint ci ratio: 9.762817e-02	ci left: 2.488773e-02	ci right 2.745838e-02	k: 1569	n:60000
Cons ci ratio: 1.218737e-01	ci left: 1.591605e-02	ci right 1.799772e-02	k: 1016	n:60000
KS ci ratio: 1.871388e-02	ci left: 4.184266e-01	ci right 4.263476e-01	k: 25343	n:60000
ACTRT1   60000 perm   12 sec   (5148 perm/sec)   p_kst 4.223833e-01   p_cons 1.693333e-02   p_joint 2.615000e-02

Joint ci ratio: 7.589169e-02	ci left: 3.531921e-02	ci right 3.811936e-02	k: 2569	n:70000
Cons ci ratio: 1.114789e-01	ci left: 1.638868e-02	ci right 1.833733e-02	k: 1214	n:70000
KS ci ratio: 1.732314e-02	ci left: 4.187941e-01	ci right 4.261266e-01	k: 29572	n:70000
ACTRT1   70000 perm   14 sec   (5041 perm/sec)   p_kst 4.224571e-01   p_cons 1.734286e-02   p_joint 3.670000e-02

Joint ci ratio: 8.363681e-02	ci left: 2.560611e-02	ci right 2.785339e-02	k: 2137	n:80000
Cons ci ratio: 1.041864e-01	ci left: 1.648084e-02	ci right 1.830440e-02	k: 1390	n:80000
KS ci ratio: 1.617268e-02	ci left: 4.199852e-01	ci right 4.268453e-01	k: 33873	n:80000
ACTRT1   80000 perm   16 sec   (4949 perm/sec)   p_kst 4.234125e-01   p_cons 1.737500e-02   p_joint 2.671250e-02

Joint ci ratio: 6.691226e-02	ci left: 3.550286e-02	ci right 3.797156e-02	k: 3305	n:90000
Cons ci ratio: 9.851262e-02	ci left: 1.643650e-02	ci right 1.815037e-02	k: 1555	n:90000
KS ci ratio: 1.524506e-02	ci left: 4.202688e-01	ci right 4.267361e-01	k: 38115	n:90000
ACTRT1   90000 perm   18 sec   (4869 perm/sec)   p_kst 4.235000e-01   p_cons 1.727778e-02   p_joint 3.672222e-02

Outputting figure to mutsig2_images.part000000000003/ACTRT1.2_1135_90000_0.4235_0.017278_0.036722.png
                gene_name: ACTRT1
               theta_stop: 0.099 
                    nperm: 90000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.017 
      ci_cons_bounds_left: 0.016 
     ci_cons_bounds_right: 0.018 
                  p_joint: 0.037 
     ci_joint_bounds_left: 0.036 
    ci_joint_bounds_right: 0.038 

Current progress: 83 percent done.
ADAMTS3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.949659e-02	ci left: 7.937479e-01	ci right 8.094760e-01	k: 8017	n:10000
KS ci ratio: 1.952724e-02	ci left: 7.932406e-01	ci right 8.089836e-01	k: 8012	n:10000
ADAMTS3   10000 perm   2 sec   (5658 perm/sec)   p_kst 8.012000e-01   p_cons 8.017000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000003/ADAMTS3.2_3706_10000_0.8012_0.8017_1.png
                gene_name: ADAMTS3
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.81 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000003
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 3 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4397762: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000004> was used as the working directory.
Started at Wed Oct 24 16:07:57 2012
Results reported at Wed Oct 24 16:10:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000004.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000004.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 4  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000004.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    187.36 sec.
    Max Memory :      1388 MB
    Max Swap   :      4022 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
4
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 4
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 4: processing genes 270 - 359
Calculating significance of each gene.
Using projection method.
270	ADAMTS7	1
271	ADAMTS8	1
272	ADAMTS9	6.332033e-01
273	ADAMTSL1	2.819418e-01
274	ADAMTSL2	1
275	ADAMTSL3	2.648904e-01
276	ADAMTSL4	2.354431e-01
277	ADAMTSL5	1.542875e-02
278	ADAP1	1
279	ADAP2	1
280	ADAR	1.822873e-01
281	ADARB1	1
282	ADARB2	1
283	ADAT1	1.890565e-01
284	ADAT2	1
285	ADAT3	1
286	ADC	1
287	ADCK1	2.253254e-01
288	ADCK2	1
289	ADCK4	1
290	ADCK5	1
291	ADCY1	4.385354e-01
292	ADCY10	1.891016e-01
293	ADCY2	1
294	ADCY3	1
295	ADCY4	1.243062e-01
296	ADCY5	2.077567e-01
297	ADCY6	1
298	ADCY7	4.102648e-01
299	ADCY8	1
300	ADCY9	1.190376e-01
301	ADCYAP1	1
302	ADCYAP1R1	1
303	ADD1	1
304	ADD2	3.728301e-01
305	ADD3	1
306	ADH1A	1
307	ADH1B	6.174954e-02
308	ADH1C	1
309	ADH4	1.766653e-01
310	ADH5	1
311	ADH6	1
312	ADH7	1
313	ADHFE1	1
314	ADI1	1
315	ADIG	1
316	ADIPOQ	1
317	ADIPOR1	1
318	ADIPOR2	1
319	ADK	7.413161e-02
320	ADM	1
321	ADM2	1
322	ADNP	1
323	ADNP2	1
324	ADO	1
325	ADORA1	1
326	ADORA2A	1
327	ADORA2B	1
328	ADORA3	1
329	ADPGK	1
330	ADPRH	1
331	ADPRHL1	1
332	ADPRHL2	1.499600e-01
333	ADRA1A	7.573284e-02
334	ADRA1B	1
335	ADRA1D	1
336	ADRA2A	1
337	ADRA2B	1
338	ADRA2C	3.704948e-02
339	ADRB1	1
340	ADRB2	1
341	ADRBK1	2.180728e-01
342	ADRBK2	1
343	ADRM1	1.924126e-01
344	ADSL	1
345	ADSS	1
346	ADSSL1	1
347	AEBP1	5.713490e-02
348	AEBP2	1
349	AEN	1
350	AES	1
351	AFAP1	1
352	AFAP1L1	1
353	AFAP1L2	1
354	AFF1	4.929887e-01
355	AFF2	3.413098e-01
356	AFF3	3.757885e-02
357	AFF4	1
358	AFG3L2	1
359	AFM	1
Done

Running MutSig 2:
Scatter job 4: processing genes 270 - 359
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
AFF3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.043788e-01	ci left: 1.171118e-01	ci right 1.301083e-01	k: 1235	n:10000
Cons ci ratio: 2.043162e-01	ci left: 3.186407e-02	ci right 3.920972e-02	k: 354	n:10000
KS ci ratio: 3.797479e-02	ci left: 5.059517e-01	ci right 5.256391e-01	k: 5158	n:10000
AFF3   10000 perm   2 sec   (4753 perm/sec)   p_kst 5.158000e-01   p_cons 3.540000e-02   p_joint 1.235000e-01

Joint ci ratio: 6.020370e-02	ci left: 1.696083e-01	ci right 1.801863e-01	k: 3497	n:20000
Cons ci ratio: 1.472962e-01	ci left: 3.167591e-02	ci right 3.676068e-02	k: 683	n:20000
KS ci ratio: 2.725749e-02	ci left: 5.013957e-01	ci right 5.153019e-01	k: 10167	n:20000
AFF3   20000 perm   8 sec   (2469 perm/sec)   p_kst 5.083500e-01   p_cons 3.415000e-02   p_joint 1.748500e-01

Joint ci ratio: 5.739427e-02	ci left: 1.306909e-01	ci right 1.384466e-01	k: 4036	n:30000
Cons ci ratio: 1.257663e-01	ci left: 2.939074e-02	ci right 3.336736e-02	k: 940	n:30000
KS ci ratio: 2.223616e-02	ci left: 5.031257e-01	ci right 5.144726e-01	k: 15264	n:30000
AFF3   30000 perm   11 sec   (2799 perm/sec)   p_kst 5.088000e-01   p_cons 3.133333e-02   p_joint 1.345333e-01

Joint ci ratio: 5.209468e-02	ci left: 1.207603e-01	ci right 1.272444e-01	k: 4959	n:40000
Cons ci ratio: 1.091720e-01	ci left: 2.951782e-02	ci right 3.295067e-02	k: 1248	n:40000
KS ci ratio: 1.927177e-02	ci left: 5.035128e-01	ci right 5.133360e-01	k: 20337	n:40000
AFF3   40000 perm   13 sec   (3006 perm/sec)   p_kst 5.084250e-01   p_cons 3.120000e-02   p_joint 1.239750e-01

Joint ci ratio: 3.795033e-02	ci left: 1.725121e-01	ci right 1.792056e-01	k: 8792	n:50000
Cons ci ratio: 9.688852e-02	ci left: 3.016204e-02	ci right 3.325265e-02	k: 1584	n:50000
KS ci ratio: 1.723680e-02	ci left: 5.040476e-01	ci right 5.128314e-01	k: 25422	n:50000
AFF3   50000 perm   16 sec   (3116 perm/sec)   p_kst 5.084400e-01   p_cons 3.168000e-02   p_joint 1.758400e-01

Outputting figure to mutsig2_images.part000000000004/AFF3.3_3848_50000_0.50844_0.03168_0.17584.png
                gene_name: AFF3
               theta_stop: 0.097 
                    nperm: 50000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.032 
      ci_cons_bounds_left: 0.030 
     ci_cons_bounds_right: 0.033 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 25 percent done.
ADCY10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.885856e-02	ci left: 4.944505e-01	ci right 5.141470e-01	k: 5043	n:10000
Cons ci ratio: 5.584290e-02	ci left: 3.207846e-01	ci right 3.393145e-01	k: 3300	n:10000
KS ci ratio: 1.814923e-02	ci left: 8.158839e-01	ci right 8.309272e-01	k: 8235	n:10000
ADCY10   10000 perm   2 sec   (4557 perm/sec)   p_kst 8.235000e-01   p_cons 3.300000e-01   p_joint 5.043000e-01

Outputting figure to mutsig2_images.part000000000004/ADCY10.2_4961_10000_0.8235_0.33_0.5043.png
                gene_name: ADCY10
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 50 percent done.
ADCY9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.291978e-02	ci left: 3.448197e-01	ci right 3.636653e-01	k: 3542	n:10000
KS ci ratio: 7.529607e-03	ci left: 9.606854e-01	ci right 9.680409e-01	k: 9645	n:10000
ADCY9   10000 perm   2 sec   (4630 perm/sec)   p_kst 9.645000e-01   p_cons 3.542000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000004/ADCY9.2_4102_10000_0.9645_0.3542_1.png
                gene_name: ADCY9
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
AEBP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.931451e-02	ci left: 6.318096e-01	ci right 6.507081e-01	k: 6413	n:10000
Cons ci ratio: 4.601716e-03	ci left: 9.840410e-01	ci right 9.886693e-01	k: 9865	n:10000
KS ci ratio: 3.546746e-02	ci left: 5.399856e-01	ci right 5.595854e-01	k: 5498	n:10000
AEBP1   10000 perm   2 sec   (5395 perm/sec)   p_kst 5.498000e-01   p_cons 9.865000e-01   p_joint 6.413000e-01

Outputting figure to mutsig2_images.part000000000004/AEBP1.2_3561_10000_0.5498_0.9865_0.6413.png
                gene_name: AEBP1
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000004
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 4 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 4397764: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000005> was used as the working directory.
Started at Wed Oct 24 16:07:57 2012
Results reported at Wed Oct 24 16:10:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000005.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000005.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 5  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000005.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    169.60 sec.
    Max Memory :      1373 MB
    Max Swap   :      3917 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
5
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 5
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 5: processing genes 360 - 449
Calculating significance of each gene.
Using projection method.
360	AFMID	1
361	AFP	1
362	AFTPH	1
363	AGA	1
364	AGAP1	1
365	AGAP11	1
366	AGAP2	3.679738e-01
367	AGAP3	1
368	AGAP4	1
369	AGAP7	1
370	AGAP8	1
371	AGBL1	1
372	AGBL2	1
373	AGBL5	5.823342e-02
374	AGER	1
375	AGFG1	1
376	AGFG2	1
377	AGGF1	1
378	AGK	1
379	AGL	5.501474e-01
380	AGMAT	1
381	AGPAT1	1
382	AGPAT2	1
383	AGPAT3	1
384	AGPAT4	1
385	AGPAT5	1
386	AGPAT6	1.632202e-01
387	AGPAT9	1
388	AGPHD1	1
389	AGPS	1
390	AGR2	1
391	AGR3	1
392	AGRN	2.023104e-01
393	AGRP	1
394	AGT	1
395	AGTPBP1	1
396	AGTR1	1
397	AGTR2	1
398	AGTRAP	1
399	AGXT	1
400	AGXT2	1
401	AGXT2L1	1
402	AGXT2L2	1.422249e-01
403	AHCTF1	7.109146e-01
404	AHCY	1
405	AHCYL1	7.067477e-02
406	AHCYL2	1
407	AHDC1	1
408	AHI1	2.512599e-01
409	AHNAK	9.326244e-01
410	AHNAK2	4.481356e-01
411	AHR	3.986329e-02
412	AHRR	1
413	AHSA1	1
414	AHSA2	1
415	AHSG	1
416	AHSP	1
417	AICDA	1
418	AIDA	1
419	AIF1	1
420	AIF1L	1
421	AIFM1	1
422	AIFM2	1
423	AIFM3	2.521456e-01
424	AIG1	1
425	AIM1	3.592834e-01
426	AIM1L	1
427	AIM2	7.982319e-02
428	AIMP1	1
429	AIMP2	1.221957e-01
430	AIP	1
431	AIPL1	1
432	AIRE	1
433	AJAP1	1
434	AK1	1
435	AK2	1
436	AK3	1
437	AK3L1	1
438	AK5	1
439	AK7	1.659328e-02
440	AKAP1	3.227435e-01
441	AKAP10	1
442	AKAP11	4.904693e-01
443	AKAP12	1
444	AKAP13	1
445	AKAP14	1
446	AKAP2	1
447	AKAP3	6.251055e-02
448	AKAP4	1
449	AKAP5	1
Done

Running MutSig 2:
Scatter job 5: processing genes 360 - 449
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
AHNAK2
Processing conservation and coverage...
57% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.402527e-02	ci left: 2.108283e-01	ci right 2.271357e-01	k: 2189	n:10000
Cons ci ratio: 7.479096e-02	ci left: 2.073764e-01	ci right 2.235897e-01	k: 2154	n:10000
KS ci ratio: 8.377868e-02	ci left: 1.720224e-01	ci right 1.871647e-01	k: 1795	n:10000
AHNAK2   10000 perm   4 sec   (2682 perm/sec)   p_kst 1.795000e-01   p_cons 2.154000e-01   p_joint 2.189000e-01

Outputting figure to mutsig2_images.part000000000005/AHNAK2.6_17416_10000_0.1795_0.2154_0.2189.png
                gene_name: AHNAK2
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.23 

Current progress: 17 percent done.
AGBL5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.098776e-01	ci left: 1.066631e-01	ci right 1.191634e-01	k: 1128	n:10000
Cons ci ratio: 1.052552e-01	ci left: 1.153530e-01	ci right 1.282683e-01	k: 1217	n:10000
KS ci ratio: 8.818083e-02	ci left: 1.576751e-01	ci right 1.723206e-01	k: 1649	n:10000
AGBL5   10000 perm   2 sec   (5383 perm/sec)   p_kst 1.649000e-01   p_cons 1.217000e-01   p_joint 1.128000e-01

Joint ci ratio: 5.809124e-02	ci left: 1.800351e-01	ci right 1.908565e-01	k: 3708	n:20000
Cons ci ratio: 7.437585e-02	ci left: 1.173959e-01	ci right 1.265143e-01	k: 2438	n:20000
KS ci ratio: 6.242218e-02	ci left: 1.595342e-01	ci right 1.698635e-01	k: 3293	n:20000
AGBL5   20000 perm   4 sec   (4806 perm/sec)   p_kst 1.646500e-01   p_cons 1.219000e-01   p_joint 1.854000e-01

Outputting figure to mutsig2_images.part000000000005/AGBL5.5_2782_20000_0.16465_0.1219_0.1854.png
                gene_name: AGBL5
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 33 percent done.
AHCTF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.798239e-02	ci left: 5.058516e-01	ci right 5.255392e-01	k: 5157	n:10000
Cons ci ratio: 7.570976e-02	ci left: 2.033338e-01	ci right 2.194347e-01	k: 2113	n:10000
KS ci ratio: 2.839059e-02	ci left: 6.464944e-01	ci right 6.652148e-01	k: 6559	n:10000
AHCTF1   10000 perm   2 sec   (4558 perm/sec)   p_kst 6.559000e-01   p_cons 2.113000e-01   p_joint 5.157000e-01

Outputting figure to mutsig2_images.part000000000005/AHCTF1.3_6972_10000_0.6559_0.2113_0.5157.png
                gene_name: AHCTF1
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.52 
     ci_joint_bounds_left: 0.51 
    ci_joint_bounds_right: 0.53 

Current progress: 50 percent done.
AHR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.113034e-02	ci left: 6.035728e-01	ci right 6.227612e-01	k: 6132	n:10000
KS ci ratio: 3.054934e-02	ci left: 6.125124e-01	ci right 6.316164e-01	k: 6221	n:10000
AHR   10000 perm   2 sec   (5935 perm/sec)   p_kst 6.221000e-01   p_cons 6.132000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000005/AHR.2_2591_10000_0.6221_0.6132_1.png
                gene_name: AHR
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
AK7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.166397e-02	ci left: 1.474675e-01	ci right 1.617343e-01	k: 1545	n:10000
Cons ci ratio: 7.514666e-02	ci left: 2.057986e-01	ci right 2.219684e-01	k: 2138	n:10000
KS ci ratio: 1.835874e-01	ci left: 3.958555e-02	ci right 4.768301e-02	k: 435	n:10000
AK7   10000 perm   2 sec   (5659 perm/sec)   p_kst 4.350000e-02   p_cons 2.138000e-01   p_joint 1.545000e-01

Joint ci ratio: 1.129508e-01	ci left: 5.358313e-02	ci right 6.004647e-02	k: 1135	n:20000
Cons ci ratio: 5.300338e-02	ci left: 2.090261e-01	ci right 2.204570e-01	k: 4294	n:20000
KS ci ratio: 1.275416e-01	ci left: 4.221676e-02	ci right 4.801642e-02	k: 901	n:20000
AK7   20000 perm   4 sec   (5233 perm/sec)   p_kst 4.505000e-02   p_cons 2.147000e-01   p_joint 5.675000e-02

Joint ci ratio: 9.906753e-02	ci left: 4.713763e-02	ci right 5.208339e-02	k: 1487	n:30000
Cons ci ratio: 4.322384e-02	ci left: 2.104946e-01	ci right 2.198273e-01	k: 6454	n:30000
KS ci ratio: 1.045026e-01	ci left: 4.245416e-02	ci right 4.716783e-02	k: 1343	n:30000
AK7   30000 perm   6 sec   (5040 perm/sec)   p_kst 4.476667e-02   p_cons 2.151333e-01   p_joint 4.956667e-02

Joint ci ratio: 8.534367e-02	ci left: 4.795789e-02	ci right 5.225773e-02	k: 2003	n:40000
Cons ci ratio: 3.776212e-02	ci left: 2.082017e-01	ci right 2.162401e-01	k: 8488	n:40000
KS ci ratio: 9.039666e-02	ci left: 4.286675e-02	ci right 4.694965e-02	k: 1795	n:40000
AK7   40000 perm   8 sec   (4832 perm/sec)   p_kst 4.487500e-02   p_cons 2.122000e-01   p_joint 5.007500e-02

Outputting figure to mutsig2_images.part000000000005/AK7.2_2244_40000_0.044875_0.2122_0.050075.png
                gene_name: AK7
               theta_stop: 0.090 
                    nperm: 40000 
                     p_ks: 0.045 
        ci_ks_bounds_left: 0.043 
       ci_ks_bounds_right: 0.047 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.050 
     ci_joint_bounds_left: 0.048 
    ci_joint_bounds_right: 0.052 

Current progress: 83 percent done.
AKAP3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.905110e-03	ci left: 9.748256e-01	ci right 9.806915e-01	k: 9779	n:10000
Cons ci ratio: 2.520978e-02	ci left: 6.983735e-01	ci right 7.163055e-01	k: 7074	n:10000
KS ci ratio: 2.101274e-02	ci left: 7.685089e-01	ci right 7.849296e-01	k: 7768	n:10000
AKAP3   10000 perm   2 sec   (6013 perm/sec)   p_kst 7.768000e-01   p_cons 7.074000e-01   p_joint 9.779000e-01

Outputting figure to mutsig2_images.part000000000005/AKAP3.2_2574_10000_0.7768_0.7074_0.9779.png
                gene_name: AKAP3
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000005
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 5 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4397767: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000006> was used as the working directory.
Started at Wed Oct 24 16:08:02 2012
Results reported at Wed Oct 24 16:09:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000006.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000006.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 6  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000006.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    128.15 sec.
    Max Memory :      1195 MB
    Max Swap   :      3948 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
6
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 6
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 6: processing genes 450 - 538
Calculating significance of each gene.
Using projection method.
450	AKAP6	2.574027e-01
451	AKAP7	1
452	AKAP8	3.184424e-01
453	AKAP8L	1
454	AKAP9	8.829299e-01
455	AKD1	1
456	AKIRIN1	1
457	AKIRIN2	3.670351e-02
458	AKNA	3.895946e-01
459	AKNAD1	3.113692e-02
460	AKR1A1	1
461	AKR1B1	1
462	AKR1B10	1
463	AKR1B15	1
464	AKR1C1	1
465	AKR1C2	1
466	AKR1C3	1
467	AKR1C4	1
468	AKR1D1	1
469	AKR1E2	1
470	AKR7A2	1
471	AKR7A3	1
472	AKR7L	7.820312e-02
473	AKT1	1
474	AKT1S1	1
475	AKT2	1
476	AKT3	2.432356e-01
477	AKTIP	1
478	ALAD	1
479	ALAS1	1
480	ALAS2	5.001107e-02
481	ALB	1
482	ALCAM	5.510516e-03
483	ALDH16A1	1
484	ALDH18A1	1
485	ALDH1A1	1
486	ALDH1A2	1.578176e-01
487	ALDH1A3	1
488	ALDH1B1	1
489	ALDH1L1	1
490	ALDH1L2	1
491	ALDH2	1
492	ALDH3A1	1
493	ALDH3A2	1
494	ALDH3B1	1
495	ALDH3B2	1
496	ALDH4A1	2.115590e-01
497	ALDH5A1	1
498	ALDH6A1	1
499	ALDH7A1	1
500	ALDH8A1	2.384495e-01
501	ALDH9A1	1
502	ALDOA	1
503	ALDOB	1
504	ALDOC	1
505	ALG1	2.101970e-01
506	ALG10	1
507	ALG10B	1
508	ALG11	1
509	ALG12	1
510	ALG13	1.843940e-01
511	ALG14	1
512	ALG1L	1
513	ALG2	1
514	ALG3	1
515	ALG5	1
516	ALG6	1.130263e-01
517	ALG8	1
518	ALG9	1
519	ALK	5.073325e-01
520	ALKBH1	1
521	ALKBH2	1
522	ALKBH3	1
523	ALKBH4	1
524	ALKBH5	6.661914e-02
525	ALKBH6	1
526	ALKBH7	1
527	ALKBH8	1
528	ALLC	1
529	ALMS1	8.432961e-01
530	ALOX12	1
531	ALOX12B	1
532	ALOX15	1
533	ALOX15B	1.832553e-01
534	ALOX5	1
535	ALOX5AP	1
536	ALOXE3	1
537	ALPI	1.820893e-01
538	ALPK1	1.256332e-01
Done

Running MutSig 2:
Scatter job 6: processing genes 450 - 538
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
AKAP6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.947729e-02	ci left: 4.865527e-01	ci right 5.062494e-01	k: 4964	n:10000
Cons ci ratio: 1.966806e-02	ci left: 7.909075e-01	ci right 8.067181e-01	k: 7989	n:10000
KS ci ratio: 5.209730e-02	ci left: 3.519757e-01	ci right 3.709051e-01	k: 3614	n:10000
AKAP6   10000 perm   2 sec   (4449 perm/sec)   p_kst 3.614000e-01   p_cons 7.989000e-01   p_joint 4.964000e-01

Outputting figure to mutsig2_images.part000000000006/AKAP6.3_7008_10000_0.3614_0.7989_0.4964.png
                gene_name: AKAP6
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 33 percent done.
AKNAD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.068814e-02	ci left: 4.714637e-01	ci right 4.911472e-01	k: 4813	n:10000
Cons ci ratio: 7.653682e-02	ci left: 1.997852e-01	ci right 2.157854e-01	k: 2077	n:10000
KS ci ratio: 2.294549e-02	ci left: 7.361346e-01	ci right 7.533227e-01	k: 7448	n:10000
AKNAD1   10000 perm   2 sec   (5948 perm/sec)   p_kst 7.448000e-01   p_cons 2.077000e-01   p_joint 4.813000e-01

Outputting figure to mutsig2_images.part000000000006/AKNAD1.2_2571_10000_0.7448_0.2077_0.4813.png
                gene_name: AKNAD1
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 67 percent done.
ALCAM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.696950e-02	ci left: 6.694464e-01	ci right 6.878494e-01	k: 6787	n:10000
Cons ci ratio: 3.556068e-02	ci left: 5.386835e-01	ci right 5.582883e-01	k: 5485	n:10000
KS ci ratio: 3.857208e-02	ci left: 4.981503e-01	ci right 5.178450e-01	k: 5080	n:10000
ALCAM   10000 perm   2 sec   (5901 perm/sec)   p_kst 5.080000e-01   p_cons 5.485000e-01   p_joint 6.787000e-01

Outputting figure to mutsig2_images.part000000000006/ALCAM.2_1812_10000_0.508_0.5485_0.6787.png
                gene_name: ALCAM
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.69 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000006
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 6 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1428>
Subject: Job 4397770: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000007> was used as the working directory.
Started at Wed Oct 24 16:08:02 2012
Results reported at Wed Oct 24 19:36:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000007.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000007.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 7  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000007.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :  13370.89 sec.
    Max Memory :      1670 MB
    Max Swap   :      4040 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
7
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 7
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 7: processing genes 539 - 628
Calculating significance of each gene.
Using projection method.
539	ALPK2	2.404390e-01
540	ALPK3	1
541	ALPL	1
542	ALPP	1
543	ALPPL2	1
544	ALS2	2.229358e-01
545	ALS2CL	2.100020e-01
546	ALS2CR11	1
547	ALS2CR12	1
548	ALS2CR4	1
549	ALS2CR8	1.834735e-01
550	ALX1	1
551	ALX3	1
552	ALX4	6.222923e-02
553	AMAC1	1
554	AMAC1L2	1
555	AMAC1L3	1
556	AMACR	1
557	AMBN	1
558	AMBP	1
559	AMBRA1	1
560	AMD1	1.382268e-01
561	AMDHD1	1.900609e-01
562	AMDHD2	1
563	AMELX	1
564	AMFR	1
565	AMHR2	1
566	AMICA1	1
567	AMIGO1	2.492566e-02
568	AMIGO2	1
569	AMIGO3	1
570	AMMECR1	1
571	AMMECR1L	5.342072e-02
572	AMN	1
573	AMN1	1
574	AMOT	7.001115e-02
575	AMOTL1	2.517010e-01
576	AMOTL2	1
577	AMPD1	2.481360e-01
578	AMPD2	1
579	AMPD3	1
580	AMPH	1.595617e-01
581	AMT	1
582	AMTN	1
583	AMY2A	1.714429e-02
584	AMY2B	2.385133e-02
585	AMZ1	1
586	AMZ2	1
587	ANAPC1	4.919078e-02
588	ANAPC10	1
589	ANAPC11	1
590	ANAPC13	1
591	ANAPC16	1
592	ANAPC2	1
593	ANAPC4	1
594	ANAPC5	1
595	ANAPC7	1
596	ANG	1
597	ANGEL1	3.170144e-01
598	ANGEL2	1
599	ANGPT1	1
600	ANGPT2	1
601	ANGPT4	2.639756e-02
602	ANGPTL1	1.418235e-01
603	ANGPTL2	1
604	ANGPTL3	1
605	ANGPTL4	1
606	ANGPTL5	1
607	ANGPTL6	1
608	ANGPTL7	1
609	ANK1	6.638322e-02
610	ANK2	4.283847e-01
611	ANK3	3.064926e-01
612	ANKAR	3.389574e-01
613	ANKDD1A	1
614	ANKFN1	3.524633e-01
615	ANKFY1	1
616	ANKH	1
617	ANKHD1	1
618	ANKHD1-EIF4EBP3	1
619	ANKIB1	7.693340e-02
620	ANKK1	1
621	ANKLE1	1
622	ANKLE2	1.656023e-01
623	ANKMY1	1
624	ANKMY2	1
625	ANKRA2	1
626	ANKRD1	1
627	ANKRD10	1
628	ANKRD11	1
Done

Running MutSig 2:
Scatter job 7: processing genes 539 - 628
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ANAPC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.079994e-01	ci left: 1.100791e-01	ci right 1.227454e-01	k: 1163	n:10000
Cons ci ratio: 4.495000e-02	ci left: 4.221625e-01	ci right 4.416772e-01	k: 4319	n:10000
KS ci ratio: 1.372648e-01	ci left: 7.020239e-02	ci right 8.064655e-02	k: 753	n:10000
ANAPC1   10000 perm   3 sec   (3298 perm/sec)   p_kst 7.530000e-02   p_cons 4.319000e-01   p_joint 1.163000e-01

Joint ci ratio: 7.189615e-02	ci left: 1.247282e-01	ci right 1.340798e-01	k: 2587	n:20000
Cons ci ratio: 3.128075e-02	ci left: 4.329051e-01	ci right 4.467124e-01	k: 8796	n:20000
KS ci ratio: 9.678552e-02	ci left: 7.211979e-02	ci right 7.950409e-02	k: 1515	n:20000
ANAPC1   20000 perm   9 sec   (2190 perm/sec)   p_kst 7.575000e-02   p_cons 4.398000e-01   p_joint 1.293500e-01

Outputting figure to mutsig2_images.part000000000007/ANAPC1.3_6023_20000_0.07575_0.4398_0.12935.png
                gene_name: ANAPC1
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.076 
        ci_ks_bounds_left: 0.072 
       ci_ks_bounds_right: 0.080 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 17 percent done.
ANK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.846905e-02	ci left: 3.009417e-01	ci right 3.191691e-01	k: 3100	n:10000
Cons ci ratio: 3.814999e-02	ci left: 5.036510e-01	ci right 5.233411e-01	k: 5135	n:10000
KS ci ratio: 1.056010e-01	ci left: 1.146691e-01	ci right 1.275526e-01	k: 1210	n:10000
ANK1   10000 perm   3 sec   (3927 perm/sec)   p_kst 1.210000e-01   p_cons 5.135000e-01   p_joint 3.100000e-01

Joint ci ratio: 5.622832e-02	ci left: 1.899738e-01	ci right 2.010149e-01	k: 3909	n:20000
Cons ci ratio: 2.683804e-02	ci left: 5.091472e-01	ci right 5.230482e-01	k: 10322	n:20000
KS ci ratio: 7.368931e-02	ci left: 1.193638e-01	ci right 1.285458e-01	k: 2478	n:20000
ANK1   20000 perm   6 sec   (3621 perm/sec)   p_kst 1.239000e-01   p_cons 5.161000e-01   p_joint 1.954500e-01

Outputting figure to mutsig2_images.part000000000007/ANK1.3_6298_20000_0.1239_0.5161_0.19545.png
                gene_name: ANK1
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 33 percent done.
ANK2
Processing conservation and coverage...
82% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.758897e-02	ci left: 5.110539e-01	ci right 5.307340e-01	k: 5209	n:10000
Cons ci ratio: 8.423637e-02	ci left: 1.704491e-01	ci right 1.855389e-01	k: 1779	n:10000
KS ci ratio: 1.382680e-02	ci left: 8.830891e-01	ci right 8.954831e-01	k: 8894	n:10000
ANK2   10000 perm   4 sec   (2557 perm/sec)   p_kst 8.894000e-01   p_cons 1.779000e-01   p_joint 5.209000e-01

Outputting figure to mutsig2_images.part000000000007/ANK2.3_12123_10000_0.8894_0.1779_0.5209.png
                gene_name: ANK2
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.52 
     ci_joint_bounds_left: 0.51 
    ci_joint_bounds_right: 0.53 

Current progress: 50 percent done.
ALPK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.440314e-02	ci left: 8.745949e-01	ci right 8.873822e-01	k: 8811	n:10000
Cons ci ratio: 2.732877e-02	ci left: 6.636054e-01	ci right 6.820938e-01	k: 6729	n:10000
KS ci ratio: 6.227196e-02	ci left: 2.748786e-01	ci right 2.926475e-01	k: 2837	n:10000
ALPK2   10000 perm   3 sec   (3977 perm/sec)   p_kst 2.837000e-01   p_cons 6.729000e-01   p_joint 8.811000e-01

Outputting figure to mutsig2_images.part000000000007/ALPK2.2_6561_10000_0.2837_0.6729_0.8811.png
                gene_name: ALPK2
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.87 
    ci_joint_bounds_right: 0.89 

Current progress: 67 percent done.
ALS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919608e+00	ci left: 0	ci right 3.688199e-04	k: 0	n:10000
Cons ci ratio: 1.409374e-01	ci left: 6.671876e-02	ci right 7.693236e-02	k: 717	n:10000
KS ci ratio: 1.599773e+00	ci left: 1.623679e-04	ci right 1.166444e-03	k: 5	n:10000
ALS2   10000 perm   2 sec   (4522 perm/sec)   p_kst 5.000000e-04   p_cons 7.170000e-02   p_joint 0

Joint ci ratio: 3.919804e+00	ci left: 0	ci right 1.844270e-04	k: 0	n:20000
Cons ci ratio: 9.884653e-02	ci left: 6.928546e-02	ci right 7.653930e-02	k: 1457	n:20000
KS ci ratio: 1.239272e+00	ci left: 2.057886e-04	ci right 8.540675e-04	k: 9	n:20000
ALS2   20000 perm   5 sec   (4063 perm/sec)   p_kst 4.500000e-04   p_cons 7.285000e-02   p_joint 0

Joint ci ratio: 1.385721e+00	ci left: 9.381708e-05	ci right 4.806964e-04	k: 7	n:30000
Cons ci ratio: 8.121018e-02	ci left: 6.913257e-02	ci right 7.501729e-02	k: 2161	n:30000
KS ci ratio: 1.011870e+00	ci left: 2.551537e-04	ci right 7.828635e-04	k: 14	n:30000
ALS2   30000 perm   8 sec   (3900 perm/sec)   p_kst 4.666667e-04   p_cons 7.203333e-02   p_joint 2.333333e-04

Joint ci ratio: 1.306503e+00	ci left: 8.634963e-05	ci right 3.940415e-04	k: 8	n:40000
Cons ci ratio: 7.122184e-02	ci left: 6.788717e-02	ci right 7.292541e-02	k: 2815	n:40000
KS ci ratio: 9.505257e-01	ci left: 2.286513e-04	ci right 6.494939e-04	k: 16	n:40000
ALS2   40000 perm   11 sec   (3784 perm/sec)   p_kst 4.000000e-04   p_cons 7.037500e-02   p_joint 2.000000e-04

Joint ci ratio: 1.959902e+00	ci left: 1.237361e-05	ci right 1.753353e-04	k: 3	n:50000
Cons ci ratio: 6.360575e-02	ci left: 6.835001e-02	ci right 7.286000e-02	k: 3529	n:50000
KS ci ratio: 8.355546e-01	ci left: 2.600048e-04	ci right 6.419433e-04	k: 21	n:50000
ALS2   50000 perm   14 sec   (3659 perm/sec)   p_kst 4.200000e-04   p_cons 7.058000e-02   p_joint 6.000000e-05

Joint ci ratio: 9.238066e-01	ci left: 1.650605e-04	ci right 4.536055e-04	k: 17	n:60000
Cons ci ratio: 5.787305e-02	ci left: 6.897391e-02	ci right 7.310104e-02	k: 4261	n:60000
KS ci ratio: 7.406313e-01	ci left: 2.965731e-04	ci right 6.546594e-04	k: 27	n:60000
ALS2   60000 perm   17 sec   (3579 perm/sec)   p_kst 4.500000e-04   p_cons 7.101667e-02   p_joint 2.833333e-04

Joint ci ratio: 8.991812e-01	ci left: 1.524060e-04	ci right 4.063662e-04	k: 18	n:70000
Cons ci ratio: 5.374510e-02	ci left: 6.872720e-02	ci right 7.253706e-02	k: 4943	n:70000
KS ci ratio: 7.038918e-01	ci left: 2.891734e-04	ci right 6.117563e-04	k: 30	n:70000
ALS2   70000 perm   20 sec   (3510 perm/sec)   p_kst 4.285714e-04   p_cons 7.061429e-02   p_joint 2.571429e-04

Joint ci ratio: 8.991973e-01	ci left: 1.333545e-04	ci right 3.555738e-04	k: 18	n:80000
Cons ci ratio: 5.017032e-02	ci left: 6.911846e-02	ci right 7.268773e-02	k: 5671	n:80000
KS ci ratio: 5.976300e-01	ci left: 3.783992e-04	ci right 7.095820e-04	k: 42	n:80000
ALS2   80000 perm   23 sec   (3454 perm/sec)   p_kst 5.250000e-04   p_cons 7.088750e-02   p_joint 2.250000e-04

Joint ci ratio: 5.434461e-01	ci left: 4.219488e-04	ci right 7.449956e-04	k: 51	n:90000
Cons ci ratio: 4.727714e-02	ci left: 6.928644e-02	ci right 7.265239e-02	k: 6386	n:90000
KS ci ratio: 5.434461e-01	ci left: 4.219488e-04	ci right 7.449956e-04	k: 51	n:90000
ALS2   90000 perm   27 sec   (3394 perm/sec)   p_kst 5.666667e-04   p_cons 7.095556e-02   p_joint 5.666667e-04

Joint ci ratio: 1.239545e+00	ci left: 4.115453e-05	ci right 1.708411e-04	k: 9	n:100000
Cons ci ratio: 4.505871e-02	ci left: 6.877244e-02	ci right 7.195254e-02	k: 7035	n:100000
KS ci ratio: 5.101874e-01	ci left: 4.404469e-04	ci right 7.497208e-04	k: 58	n:100000
ALS2   100000 perm   30 sec   (3341 perm/sec)   p_kst 5.800000e-04   p_cons 7.035000e-02   p_joint 9.000000e-05

Joint ci ratio: 1.181860e+00	ci left: 4.359528e-05	ci right 1.671787e-04	k: 10	n:110000
Cons ci ratio: 4.303842e-02	ci left: 6.861601e-02	ci right 7.164306e-02	k: 7713	n:110000
KS ci ratio: 4.823717e-01	ci left: 4.560798e-04	ci right 7.531010e-04	k: 65	n:110000
ALS2   110000 perm   33 sec   (3292 perm/sec)   p_kst 5.909091e-04   p_cons 7.011818e-02   p_joint 9.090909e-05

Joint ci ratio: 1.181865e+00	ci left: 3.996227e-05	ci right 1.532476e-04	k: 10	n:120000
Cons ci ratio: 4.135771e-02	ci left: 6.820773e-02	ci right 7.109644e-02	k: 8357	n:120000
KS ci ratio: 4.787685e-01	ci left: 4.253947e-04	ci right 6.996825e-04	k: 66	n:120000
ALS2   120000 perm   37 sec   (3247 perm/sec)   p_kst 5.500000e-04   p_cons 6.964167e-02   p_joint 8.333333e-05

Joint ci ratio: 1.181870e+00	ci left: 3.688820e-05	ci right 1.414597e-04	k: 10	n:130000
Cons ci ratio: 3.979075e-02	ci left: 6.808528e-02	ci right 7.085704e-02	k: 9030	n:130000
KS ci ratio: 4.618467e-01	ci left: 4.265746e-04	ci right 6.888496e-04	k: 71	n:130000
ALS2   130000 perm   41 sec   (3201 perm/sec)   p_kst 5.461538e-04   p_cons 6.946154e-02   p_joint 7.692308e-05

Joint ci ratio: 1.181874e+00	ci left: 3.425329e-05	ci right 1.313557e-04	k: 10	n:140000
Cons ci ratio: 3.832363e-02	ci left: 6.820158e-02	ci right 7.087343e-02	k: 9734	n:140000
KS ci ratio: 4.555687e-01	ci left: 4.087383e-04	ci right 6.555742e-04	k: 73	n:140000
ALS2   140000 perm   44 sec   (3158 perm/sec)   p_kst 5.214286e-04   p_cons 6.952857e-02   p_joint 7.142857e-05

Joint ci ratio: 1.131557e+00	ci left: 3.660829e-05	ci right 1.312098e-04	k: 11	n:150000
Cons ci ratio: 3.706495e-02	ci left: 6.810571e-02	ci right 7.068430e-02	k: 10408	n:150000
KS ci ratio: 4.381510e-01	ci left: 4.169884e-04	ci right 6.563412e-04	k: 79	n:150000
ALS2   150000 perm   48 sec   (3111 perm/sec)   p_kst 5.266667e-04   p_cons 6.938667e-02   p_joint 7.333333e-05

Joint ci ratio: 1.131561e+00	ci left: 3.432024e-05	ci right 1.230094e-04	k: 11	n:160000
Cons ci ratio: 3.577031e-02	ci left: 6.856853e-02	ci right 7.107209e-02	k: 11170	n:160000
KS ci ratio: 4.154023e-01	ci left: 4.411387e-04	ci right 6.775721e-04	k: 88	n:160000
ALS2   160000 perm   52 sec   (3048 perm/sec)   p_kst 5.500000e-04   p_cons 6.981250e-02   p_joint 6.875000e-05

Joint ci ratio: 1.087168e+00	ci left: 3.647449e-05	ci right 1.233002e-04	k: 12	n:170000
Cons ci ratio: 3.472147e-02	ci left: 6.853479e-02	ci right 7.096226e-02	k: 11856	n:170000
KS ci ratio: 4.063727e-01	ci left: 4.362862e-04	ci right 6.636642e-04	k: 92	n:170000
ALS2   170000 perm   57 sec   (3002 perm/sec)   p_kst 5.411765e-04   p_cons 6.974118e-02   p_joint 7.058824e-05

Joint ci ratio: 1.012095e+00	ci left: 4.252247e-05	ci right 1.304945e-04	k: 14	n:180000
Cons ci ratio: 3.371070e-02	ci left: 6.869316e-02	ci right 7.105405e-02	k: 12576	n:180000
KS ci ratio: 3.958709e-01	ci left: 4.370236e-04	ci right 6.573598e-04	k: 97	n:180000
ALS2   180000 perm   61 sec   (2954 perm/sec)   p_kst 5.388889e-04   p_cons 6.986667e-02   p_joint 7.777778e-05

Joint ci ratio: 1.012097e+00	ci left: 4.028441e-05	ci right 1.236265e-04	k: 14	n:190000
Cons ci ratio: 3.281787e-02	ci left: 6.869998e-02	ci right 7.099738e-02	k: 13270	n:190000
KS ci ratio: 3.899499e-01	ci left: 4.282514e-04	ci right 6.401046e-04	k: 100	n:190000
ALS2   190000 perm   65 sec   (2920 perm/sec)   p_kst 5.263158e-04   p_cons 6.984211e-02   p_joint 7.368421e-05

Joint ci ratio: 9.506969e-01	ci left: 4.572758e-05	ci right 1.299117e-04	k: 16	n:200000
Cons ci ratio: 3.196535e-02	ci left: 6.881605e-02	ci right 7.105644e-02	k: 13986	n:200000
KS ci ratio: 3.736536e-01	ci left: 4.475224e-04	ci right 6.573952e-04	k: 109	n:200000
ALS2   200000 perm   69 sec   (2885 perm/sec)   p_kst 5.450000e-04   p_cons 6.993000e-02   p_joint 8.000000e-05

Joint ci ratio: 8.764948e-01	ci left: 5.447343e-05	ci right 1.412862e-04	k: 19	n:210000
Cons ci ratio: 3.120682e-02	ci left: 6.879411e-02	ci right 7.097969e-02	k: 14675	n:210000
KS ci ratio: 3.607630e-01	ci left: 4.607934e-04	ci right 6.676842e-04	k: 117	n:210000
ALS2   210000 perm   74 sec   (2851 perm/sec)   p_kst 5.571429e-04   p_cons 6.988095e-02   p_joint 9.047619e-05

Joint ci ratio: 8.764968e-01	ci left: 5.199733e-05	ci right 1.348642e-04	k: 19	n:220000
Cons ci ratio: 3.049984e-02	ci left: 6.877474e-02	ci right 7.090933e-02	k: 15364	n:220000
KS ci ratio: 3.562648e-01	ci left: 4.522561e-04	ci right 6.521951e-04	k: 120	n:220000
ALS2   220000 perm   79 sec   (2801 perm/sec)   p_kst 5.454545e-04   p_cons 6.983636e-02   p_joint 8.636364e-05

Joint ci ratio: 8.553732e-01	ci left: 5.311609e-05	ci right 1.342941e-04	k: 20	n:230000
Cons ci ratio: 2.984983e-02	ci left: 6.871008e-02	ci right 7.079643e-02	k: 16042	n:230000
KS ci ratio: 3.463851e-01	ci left: 4.603427e-04	ci right 6.569478e-04	k: 127	n:230000
ALS2   230000 perm   84 sec   (2751 perm/sec)   p_kst 5.521739e-04   p_cons 6.974783e-02   p_joint 8.695652e-05

Joint ci ratio: 8.173356e-01	ci left: 5.744788e-05	ci right 1.387812e-04	k: 22	n:240000
Cons ci ratio: 2.921620e-02	ci left: 6.875471e-02	ci right 7.079736e-02	k: 16745	n:240000
KS ci ratio: 3.372843e-01	ci left: 4.678254e-04	ci right 6.612351e-04	k: 134	n:240000
ALS2   240000 perm   89 sec   (2699 perm/sec)   p_kst 5.583333e-04   p_cons 6.977083e-02   p_joint 9.166667e-05

Joint ci ratio: 7.839592e-01	ci left: 6.150995e-05	ci right 1.428370e-04	k: 24	n:250000
Cons ci ratio: 2.862305e-02	ci left: 6.878826e-02	ci right 7.078973e-02	k: 17446	n:250000
KS ci ratio: 3.288650e-01	ci left: 4.747716e-04	ci right 6.651181e-04	k: 141	n:250000
ALS2   250000 perm   94 sec   (2670 perm/sec)   p_kst 5.640000e-04   p_cons 6.978400e-02   p_joint 9.600000e-05

Joint ci ratio: 7.839608e-01	ci left: 5.914415e-05	ci right 1.373434e-04	k: 24	n:260000
Cons ci ratio: 2.806878e-02	ci left: 6.880051e-02	ci right 7.076294e-02	k: 18142	n:260000
KS ci ratio: 3.243298e-01	ci left: 4.706344e-04	ci right 6.561785e-04	k: 145	n:260000
ALS2   260000 perm   98 sec   (2643 perm/sec)   p_kst 5.576923e-04   p_cons 6.977692e-02   p_joint 9.230769e-05

Joint ci ratio: 7.687368e-01	ci left: 5.992191e-05	ci right 1.366819e-04	k: 25	n:270000
Cons ci ratio: 2.753607e-02	ci left: 6.885636e-02	ci right 7.078252e-02	k: 18850	n:270000
KS ci ratio: 3.178639e-01	ci left: 4.736351e-04	ci right 6.558825e-04	k: 151	n:270000
ALS2   270000 perm   103 sec   (2617 perm/sec)   p_kst 5.592593e-04   p_cons 6.981481e-02   p_joint 9.259259e-05

Joint ci ratio: 7.687382e-01	ci left: 5.778181e-05	ci right 1.318005e-04	k: 25	n:280000
Cons ci ratio: 2.706161e-02	ci left: 6.877013e-02	ci right 7.066021e-02	k: 19519	n:280000
KS ci ratio: 3.147743e-01	ci left: 4.665830e-04	ci right 6.440207e-04	k: 154	n:280000
ALS2   280000 perm   108 sec   (2588 perm/sec)   p_kst 5.500000e-04   p_cons 6.971071e-02   p_joint 8.928571e-05

Joint ci ratio: 7.687395e-01	ci left: 5.578931e-05	ci right 1.272558e-04	k: 25	n:290000
Cons ci ratio: 2.660165e-02	ci left: 6.873467e-02	ci right 7.059118e-02	k: 20201	n:290000
KS ci ratio: 3.127648e-01	ci left: 4.568471e-04	ci right 6.292516e-04	k: 156	n:290000
ALS2   290000 perm   113 sec   (2562 perm/sec)   p_kst 5.379310e-04   p_cons 6.965862e-02   p_joint 8.620690e-05

Joint ci ratio: 7.687407e-01	ci left: 5.392964e-05	ci right 1.230140e-04	k: 25	n:300000
Cons ci ratio: 2.615159e-02	ci left: 6.876478e-02	ci right 7.059021e-02	k: 20902	n:300000
KS ci ratio: 3.023494e-01	ci left: 4.754576e-04	ci right 6.477623e-04	k: 167	n:300000
ALS2   300000 perm   118 sec   (2536 perm/sec)   p_kst 5.566667e-04   p_cons 6.967333e-02   p_joint 8.333333e-05

Joint ci ratio: 7.687418e-01	ci left: 5.218995e-05	ci right 1.190459e-04	k: 25	n:310000
Cons ci ratio: 2.570445e-02	ci left: 6.888940e-02	ci right 7.068640e-02	k: 21633	n:310000
KS ci ratio: 2.929095e-01	ci left: 4.929562e-04	ci right 6.649906e-04	k: 178	n:310000
ALS2   310000 perm   123 sec   (2510 perm/sec)   p_kst 5.741935e-04   p_cons 6.978387e-02   p_joint 8.064516e-05

Joint ci ratio: 7.543713e-01	ci left: 5.307586e-05	ci right 1.190478e-04	k: 26	n:320000
Cons ci ratio: 2.528616e-02	ci left: 6.897230e-02	ci right 7.074175e-02	k: 22353	n:320000
KS ci ratio: 2.881204e-01	ci left: 4.949353e-04	ci right 6.643220e-04	k: 184	n:320000
ALS2   320000 perm   129 sec   (2484 perm/sec)   p_kst 5.750000e-04   p_cons 6.985313e-02   p_joint 8.125000e-05

Joint ci ratio: 7.543723e-01	ci left: 5.146748e-05	ci right 1.154404e-04	k: 26	n:330000
Cons ci ratio: 2.487954e-02	ci left: 6.909257e-02	ci right 7.083620e-02	k: 23087	n:330000
KS ci ratio: 2.850559e-01	ci left: 4.911872e-04	ci right 6.571814e-04	k: 188	n:330000
ALS2   330000 perm   134 sec   (2459 perm/sec)   p_kst 5.696970e-04   p_cons 6.996061e-02   p_joint 7.878788e-05

Joint ci ratio: 7.278936e-01	ci left: 5.472361e-05	ci right 1.190207e-04	k: 28	n:340000
Cons ci ratio: 2.450962e-02	ci left: 6.911240e-02	ci right 7.083023e-02	k: 23789	n:340000
KS ci ratio: 2.799189e-01	ci left: 4.958706e-04	ci right 6.598951e-04	k: 195	n:340000
ALS2   340000 perm   140 sec   (2434 perm/sec)   p_kst 5.735294e-04   p_cons 6.996765e-02   p_joint 8.235294e-05

Joint ci ratio: 6.929320e-01	ci left: 6.018076e-05	ci right 1.257177e-04	k: 31	n:350000
Cons ci ratio: 2.414831e-02	ci left: 6.917105e-02	ci right 7.086465e-02	k: 24505	n:350000
KS ci ratio: 2.757302e-01	ci left: 4.976516e-04	ci right 6.593749e-04	k: 201	n:350000
ALS2   350000 perm   145 sec   (2410 perm/sec)   p_kst 5.742857e-04   p_cons 7.001429e-02   p_joint 8.857143e-05

Joint ci ratio: 6.929329e-01	ci left: 5.850905e-05	ci right 1.222256e-04	k: 31	n:360000
Cons ci ratio: 2.381878e-02	ci left: 6.913822e-02	ci right 7.080760e-02	k: 25189	n:360000
KS ci ratio: 2.723801e-01	ci left: 4.967625e-04	ci right 6.558999e-04	k: 206	n:360000
ALS2   360000 perm   151 sec   (2382 perm/sec)   p_kst 5.722222e-04   p_cons 6.996944e-02   p_joint 8.611111e-05

Joint ci ratio: 6.929337e-01	ci left: 5.692770e-05	ci right 1.189223e-04	k: 31	n:370000
Cons ci ratio: 2.349456e-02	ci left: 6.915033e-02	ci right 7.079696e-02	k: 25889	n:370000
KS ci ratio: 2.723822e-01	ci left: 4.833361e-04	ci right 6.381736e-04	k: 206	n:370000
ALS2   370000 perm   157 sec   (2354 perm/sec)   p_kst 5.567568e-04   p_cons 6.997027e-02   p_joint 8.378378e-05

Joint ci ratio: 6.929346e-01	ci left: 5.542959e-05	ci right 1.157928e-04	k: 31	n:380000
Cons ci ratio: 2.318136e-02	ci left: 6.917241e-02	ci right 7.079731e-02	k: 26593	n:380000
KS ci ratio: 2.704306e-01	ci left: 4.779741e-04	ci right 6.298105e-04	k: 209	n:380000
ALS2   380000 perm   163 sec   (2329 perm/sec)   p_kst 5.500000e-04   p_cons 6.998158e-02   p_joint 8.157895e-05

Joint ci ratio: 6.823547e-01	ci left: 5.612367e-05	ci right 1.158300e-04	k: 32	n:390000
Cons ci ratio: 2.287946e-02	ci left: 6.919860e-02	ci right 7.080267e-02	k: 27299	n:390000
KS ci ratio: 2.685203e-01	ci left: 4.728908e-04	ci right 6.218726e-04	k: 212	n:390000
ALS2   390000 perm   169 sec   (2306 perm/sec)   p_kst 5.435897e-04   p_cons 6.999744e-02   p_joint 8.205128e-05

Joint ci ratio: 6.722450e-01	ci left: 5.678986e-05	ci right 1.158587e-04	k: 33	n:400000
Cons ci ratio: 2.259469e-02	ci left: 6.919128e-02	ci right 7.077496e-02	k: 27992	n:400000
KS ci ratio: 2.654232e-01	ci left: 4.727320e-04	ci right 6.196604e-04	k: 217	n:400000
ALS2   400000 perm   175 sec   (2284 perm/sec)   p_kst 5.425000e-04   p_cons 6.998000e-02   p_joint 8.250000e-05

Joint ci ratio: 6.722458e-01	ci left: 5.540473e-05	ci right 1.130330e-04	k: 33	n:410000
Cons ci ratio: 2.232867e-02	ci left: 6.913590e-02	ci right 7.069945e-02	k: 28665	n:410000
KS ci ratio: 2.618441e-01	ci left: 4.748691e-04	ci right 6.201457e-04	k: 223	n:410000
ALS2   410000 perm   181 sec   (2263 perm/sec)   p_kst 5.439024e-04   p_cons 6.991463e-02   p_joint 8.048780e-05

Joint ci ratio: 6.444149e-01	ci left: 6.003393e-05	ci right 1.186627e-04	k: 36	n:420000
Cons ci ratio: 2.207588e-02	ci left: 6.905959e-02	ci right 7.060350e-02	k: 29328	n:420000
KS ci ratio: 2.584061e-01	ci left: 4.769171e-04	ci right 6.205953e-04	k: 229	n:420000
ALS2   420000 perm   187 sec   (2242 perm/sec)   p_kst 5.452381e-04   p_cons 6.982857e-02   p_joint 8.571429e-05

Joint ci ratio: 6.358791e-01	ci left: 6.058539e-05	ci right 1.186019e-04	k: 37	n:430000
Cons ci ratio: 2.181350e-02	ci left: 6.909335e-02	ci right 7.061943e-02	k: 30037	n:430000
KS ci ratio: 2.545609e-01	ci left: 4.810588e-04	ci right 6.234859e-04	k: 236	n:430000
ALS2   430000 perm   194 sec   (2219 perm/sec)   p_kst 5.488372e-04   p_cons 6.985349e-02   p_joint 8.604651e-05

Joint ci ratio: 6.358798e-01	ci left: 5.920843e-05	ci right 1.159064e-04	k: 37	n:440000
Cons ci ratio: 2.156704e-02	ci left: 6.908498e-02	ci right 7.059342e-02	k: 30728	n:440000
KS ci ratio: 2.513984e-01	ci left: 4.828975e-04	ci right 6.238148e-04	k: 242	n:440000
ALS2   440000 perm   200 sec   (2199 perm/sec)   p_kst 5.500000e-04   p_cons 6.983636e-02   p_joint 8.409091e-05

Joint ci ratio: 6.197782e-01	ci left: 6.162918e-05	ci right 1.184743e-04	k: 39	n:450000
Cons ci ratio: 2.131964e-02	ci left: 6.913235e-02	ci right 7.062430e-02	k: 31444	n:450000
KS ci ratio: 2.498615e-01	ci left: 4.784143e-04	ci right 6.170370e-04	k: 245	n:450000
ALS2   450000 perm   207 sec   (2179 perm/sec)   p_kst 5.444444e-04   p_cons 6.987556e-02   p_joint 8.666667e-05

Joint ci ratio: 6.121732e-01	ci left: 6.212372e-05	ci right 1.184082e-04	k: 40	n:460000
Cons ci ratio: 2.107950e-02	ci left: 6.918425e-02	ci right 7.066030e-02	k: 32163	n:460000
KS ci ratio: 2.454116e-01	ci left: 4.863654e-04	ci right 6.243997e-04	k: 254	n:460000
ALS2   460000 perm   213 sec   (2159 perm/sec)   p_kst 5.521739e-04   p_cons 6.991957e-02   p_joint 8.695652e-05

Joint ci ratio: 6.121738e-01	ci left: 6.080192e-05	ci right 1.158890e-04	k: 40	n:470000
Cons ci ratio: 2.085276e-02	ci left: 6.920016e-02	ci right 7.066047e-02	k: 32866	n:470000
KS ci ratio: 2.430406e-01	ci left: 4.860045e-04	ci right 6.224027e-04	k: 259	n:470000
ALS2   470000 perm   220 sec   (2140 perm/sec)   p_kst 5.510638e-04   p_cons 6.992766e-02   p_joint 8.510638e-05

Joint ci ratio: 5.909345e-01	ci left: 6.483264e-05	ci right 1.206663e-04	k: 43	n:480000
Cons ci ratio: 2.063218e-02	ci left: 6.922170e-02	ci right 7.066683e-02	k: 33572	n:480000
KS ci ratio: 2.402838e-01	ci left: 4.876226e-04	ci right 6.226914e-04	k: 265	n:480000
ALS2   480000 perm   227 sec   (2118 perm/sec)   p_kst 5.520833e-04   p_cons 6.994167e-02   p_joint 8.958333e-05

Joint ci ratio: 5.843317e-01	ci left: 6.524659e-05	ci right 1.205450e-04	k: 44	n:490000
Cons ci ratio: 2.043674e-02	ci left: 6.912666e-02	ci right 7.055598e-02	k: 34221	n:490000
KS ci ratio: 2.363183e-01	ci left: 4.949422e-04	ci right 6.294450e-04	k: 274	n:490000
ALS2   490000 perm   234 sec   (2095 perm/sec)   p_kst 5.591837e-04   p_cons 6.983878e-02   p_joint 8.979592e-05

Joint ci ratio: 5.779453e-01	ci left: 6.564735e-05	ci right 1.204252e-04	k: 45	n:500000
Cons ci ratio: 2.022462e-02	ci left: 6.917683e-02	ci right 7.059216e-02	k: 34941	n:500000
KS ci ratio: 2.341990e-01	ci left: 4.944539e-04	ci right 6.274444e-04	k: 279	n:500000
ALS2   500000 perm   241 sec   (2077 perm/sec)   p_kst 5.580000e-04   p_cons 6.988200e-02   p_joint 9.000000e-05

Joint ci ratio: 5.717639e-01	ci left: 6.603560e-05	ci right 1.203071e-04	k: 46	n:510000
Cons ci ratio: 2.002229e-02	ci left: 6.920363e-02	ci right 7.060518e-02	k: 35650	n:510000
KS ci ratio: 2.329549e-01	ci left: 4.902967e-04	ci right 6.213677e-04	k: 282	n:510000
ALS2   510000 perm   248 sec   (2058 perm/sec)   p_kst 5.529412e-04   p_cons 6.990196e-02   p_joint 9.019608e-05

Joint ci ratio: 5.599731e-01	ci left: 6.806117e-05	ci right 1.223848e-04	k: 48	n:520000
Cons ci ratio: 1.983354e-02	ci left: 6.917970e-02	ci right 7.056741e-02	k: 36333	n:520000
KS ci ratio: 2.293360e-01	ci left: 4.971737e-04	ci right 6.277262e-04	k: 291	n:520000
ALS2   520000 perm   255 sec   (2040 perm/sec)   p_kst 5.596154e-04   p_cons 6.987115e-02   p_joint 9.230769e-05

Joint ci ratio: 5.599736e-01	ci left: 6.677698e-05	ci right 1.200757e-04	k: 48	n:530000
Cons ci ratio: 1.964062e-02	ci left: 6.921871e-02	ci right 7.059355e-02	k: 37049	n:530000
KS ci ratio: 2.285554e-01	ci left: 4.913501e-04	ci right 6.198722e-04	k: 293	n:530000
ALS2   530000 perm   262 sec   (2021 perm/sec)   p_kst 5.528302e-04   p_cons 6.990377e-02   p_joint 9.056604e-05

Joint ci ratio: 5.543455e-01	ci left: 6.713123e-05	ci right 1.199623e-04	k: 49	n:540000
Cons ci ratio: 1.945737e-02	ci left: 6.922869e-02	ci right 7.059075e-02	k: 37750	n:540000
KS ci ratio: 2.255074e-01	ci left: 4.962235e-04	ci right 6.240488e-04	k: 301	n:540000
ALS2   540000 perm   269 sec   (2004 perm/sec)   p_kst 5.574074e-04   p_cons 6.990741e-02   p_joint 9.074074e-05

Joint ci ratio: 5.488838e-01	ci left: 6.747521e-05	ci right 1.198506e-04	k: 50	n:550000
Cons ci ratio: 1.927566e-02	ci left: 6.926189e-02	ci right 7.061174e-02	k: 38464	n:550000
KS ci ratio: 2.243961e-01	ci left: 4.923483e-04	ci right 6.184640e-04	k: 304	n:550000
ALS2   550000 perm   277 sec   (1984 perm/sec)   p_kst 5.527273e-04   p_cons 6.993455e-02   p_joint 9.090909e-05

Joint ci ratio: 5.488843e-01	ci left: 6.627028e-05	ci right 1.177104e-04	k: 50	n:560000
Cons ci ratio: 1.909527e-02	ci left: 6.931885e-02	ci right 7.065703e-02	k: 39192	n:560000
KS ci ratio: 2.222209e-01	ci left: 4.936714e-04	ci right 6.187326e-04	k: 310	n:560000
ALS2   560000 perm   285 sec   (1963 perm/sec)   p_kst 5.535714e-04   p_cons 6.998571e-02   p_joint 8.928571e-05

Joint ci ratio: 5.488848e-01	ci left: 6.510763e-05	ci right 1.156453e-04	k: 50	n:570000
Cons ci ratio: 1.892394e-02	ci left: 6.934593e-02	ci right 7.067248e-02	k: 39904	n:570000
KS ci ratio: 2.211573e-01	ci left: 4.899813e-04	ci right 6.134327e-04	k: 313	n:570000
ALS2   570000 perm   294 sec   (1941 perm/sec)   p_kst 5.491228e-04   p_cons 7.000702e-02   p_joint 8.771930e-05

Joint ci ratio: 5.435814e-01	ci left: 6.547111e-05	ci right 1.156115e-04	k: 51	n:580000
Cons ci ratio: 1.875912e-02	ci left: 6.935838e-02	ci right 7.067350e-02	k: 40608	n:580000
KS ci ratio: 2.190740e-01	ci left: 4.913079e-04	ci right 6.137705e-04	k: 319	n:580000
ALS2   580000 perm   302 sec   (1919 perm/sec)   p_kst 5.500000e-04   p_cons 7.001379e-02   p_joint 8.793103e-05

Joint ci ratio: 5.384288e-01	ci left: 6.582456e-05	ci right 1.155765e-04	k: 52	n:590000
Cons ci ratio: 1.859950e-02	ci left: 6.936372e-02	ci right 7.066763e-02	k: 41308	n:590000
KS ci ratio: 2.163854e-01	ci left: 4.958008e-04	ci right 6.176650e-04	k: 327	n:590000
ALS2   590000 perm   310 sec   (1901 perm/sec)   p_kst 5.542373e-04   p_cons 7.001356e-02   p_joint 8.813559e-05

Joint ci ratio: 5.334200e-01	ci left: 6.616841e-05	ci right 1.155406e-04	k: 53	n:600000
Cons ci ratio: 1.844649e-02	ci left: 6.935067e-02	ci right 7.064349e-02	k: 41997	n:600000
KS ci ratio: 2.154031e-01	ci left: 4.922670e-04	ci right 6.126407e-04	k: 330	n:600000
ALS2   600000 perm   318 sec   (1884 perm/sec)   p_kst 5.500000e-04   p_cons 6.999500e-02   p_joint 8.833333e-05

Joint ci ratio: 5.334204e-01	ci left: 6.508367e-05	ci right 1.136465e-04	k: 53	n:610000
Cons ci ratio: 1.828982e-02	ci left: 6.939032e-02	ci right 7.067278e-02	k: 42718	n:610000
KS ci ratio: 2.134768e-01	ci left: 4.935049e-04	ci right 6.129609e-04	k: 336	n:610000
ALS2   610000 perm   327 sec   (1867 perm/sec)   p_kst 5.508197e-04   p_cons 7.002951e-02   p_joint 8.688525e-05

Joint ci ratio: 5.334208e-01	ci left: 6.403392e-05	ci right 1.118135e-04	k: 53	n:620000
Cons ci ratio: 1.813326e-02	ci left: 6.945605e-02	ci right 7.072862e-02	k: 43456	n:620000
KS ci ratio: 2.125334e-01	ci left: 4.901256e-04	ci right 6.081710e-04	k: 339	n:620000
ALS2   620000 perm   335 sec   (1851 perm/sec)   p_kst 5.467742e-04   p_cons 7.009032e-02   p_joint 8.548387e-05

Joint ci ratio: 5.334211e-01	ci left: 6.301750e-05	ci right 1.100387e-04	k: 53	n:630000
Cons ci ratio: 1.799906e-02	ci left: 6.938695e-02	ci right 7.064875e-02	k: 44110	n:630000
KS ci ratio: 2.106825e-01	ci left: 4.913650e-04	ci right 6.085452e-04	k: 345	n:630000
ALS2   630000 perm   343 sec   (1836 perm/sec)   p_kst 5.476190e-04   p_cons 7.001587e-02   p_joint 8.412698e-05

Joint ci ratio: 5.238087e-01	ci left: 6.474052e-05	ci right 1.118580e-04	k: 55	n:640000
Cons ci ratio: 1.785278e-02	ci left: 6.942897e-02	ci right 7.068117e-02	k: 44834	n:640000
KS ci ratio: 2.077016e-01	ci left: 4.984941e-04	ci right 6.154788e-04	k: 355	n:640000
ALS2   640000 perm   351 sec   (1822 perm/sec)   p_kst 5.546875e-04   p_cons 7.005312e-02   p_joint 8.593750e-05

Joint ci ratio: 5.103170e-01	ci left: 6.775734e-05	ci right 1.153500e-04	k: 58	n:650000
Cons ci ratio: 1.771336e-02	ci left: 6.944523e-02	ci right 7.068784e-02	k: 45542	n:650000
KS ci ratio: 2.062583e-01	ci left: 4.981186e-04	ci right 6.141003e-04	k: 360	n:650000
ALS2   650000 perm   359 sec   (1808 perm/sec)   p_kst 5.538462e-04   p_cons 7.006462e-02   p_joint 8.923077e-05

Joint ci ratio: 5.103173e-01	ci left: 6.673070e-05	ci right 1.136023e-04	k: 58	n:660000
Cons ci ratio: 1.758022e-02	ci left: 6.943839e-02	ci right 7.067145e-02	k: 46235	n:660000
KS ci ratio: 2.059740e-01	ci left: 4.920081e-04	ci right 6.063892e-04	k: 361	n:660000
ALS2   660000 perm   368 sec   (1793 perm/sec)   p_kst 5.469697e-04   p_cons 7.005303e-02   p_joint 8.787879e-05

Joint ci ratio: 5.060468e-01	ci left: 6.703578e-05	ci right 1.135891e-04	k: 59	n:670000
Cons ci ratio: 1.744605e-02	ci left: 6.946152e-02	ci right 7.068548e-02	k: 46948	n:670000
KS ci ratio: 2.048456e-01	ci left: 4.903278e-04	ci right 6.036155e-04	k: 365	n:670000
ALS2   670000 perm   376 sec   (1780 perm/sec)   p_kst 5.447761e-04   p_cons 7.007164e-02   p_joint 8.805970e-05

Joint ci ratio: 5.018817e-01	ci left: 6.733348e-05	ci right 1.135749e-04	k: 60	n:680000
Cons ci ratio: 1.731411e-02	ci left: 6.948987e-02	ci right 7.070497e-02	k: 47665	n:680000
KS ci ratio: 2.029141e-01	ci left: 4.928857e-04	ci right 6.055577e-04	k: 372	n:680000
ALS2   680000 perm   385 sec   (1766 perm/sec)   p_kst 5.470588e-04   p_cons 7.009559e-02   p_joint 8.823529e-05

Joint ci ratio: 4.978178e-01	ci left: 6.762408e-05	ci right 1.135595e-04	k: 61	n:690000
Cons ci ratio: 1.717730e-02	ci left: 6.957661e-02	ci right 7.078352e-02	k: 48423	n:690000
KS ci ratio: 2.015677e-01	ci left: 4.926219e-04	ci right 6.043943e-04	k: 377	n:690000
ALS2   690000 perm   394 sec   (1753 perm/sec)   p_kst 5.463768e-04   p_cons 7.017826e-02   p_joint 8.840580e-05

Joint ci ratio: 4.978181e-01	ci left: 6.665802e-05	ci right 1.119373e-04	k: 61	n:700000
Cons ci ratio: 1.705730e-02	ci left: 6.955703e-02	ci right 7.075510e-02	k: 49108	n:700000
KS ci ratio: 1.997266e-01	ci left: 4.950821e-04	ci right 6.062618e-04	k: 384	n:700000
ALS2   700000 perm   402 sec   (1740 perm/sec)   p_kst 5.485714e-04   p_cons 7.015429e-02   p_joint 8.714286e-05

Joint ci ratio: 4.938513e-01	ci left: 6.695140e-05	ci right 1.119440e-04	k: 62	n:710000
Cons ci ratio: 1.694088e-02	ci left: 6.952962e-02	ci right 7.071896e-02	k: 49787	n:710000
KS ci ratio: 1.974318e-01	ci left: 5.001551e-04	ci right 6.110282e-04	k: 393	n:710000
ALS2   710000 perm   411 sec   (1728 perm/sec)   p_kst 5.535211e-04   p_cons 7.012254e-02   p_joint 8.732394e-05

Joint ci ratio: 4.861939e-01	ci left: 6.845593e-05	ci right 1.135077e-04	k: 64	n:720000
Cons ci ratio: 1.681821e-02	ci left: 6.956940e-02	ci right 7.075072e-02	k: 50514	n:720000
KS ci ratio: 1.952143e-01	ci left: 5.050942e-04	ci right 6.156552e-04	k: 402	n:720000
ALS2   720000 perm   420 sec   (1715 perm/sec)   p_kst 5.583333e-04   p_cons 7.015833e-02   p_joint 8.888889e-05

Joint ci ratio: 4.861942e-01	ci left: 6.751817e-05	ci right 1.119528e-04	k: 64	n:730000
Cons ci ratio: 1.671220e-02	ci left: 6.949896e-02	ci right 7.067158e-02	k: 51161	n:730000
KS ci ratio: 1.944921e-01	ci left: 5.020841e-04	ci right 6.115315e-04	k: 405	n:730000
ALS2   730000 perm   429 sec   (1702 perm/sec)   p_kst 5.547945e-04   p_cons 7.008356e-02   p_joint 8.767123e-05

Joint ci ratio: 4.861945e-01	ci left: 6.660575e-05	ci right 1.104400e-04	k: 64	n:740000
Cons ci ratio: 1.659973e-02	ci left: 6.949641e-02	ci right 7.066101e-02	k: 51857	n:740000
KS ci ratio: 1.933055e-01	ci left: 5.017280e-04	ci right 6.103519e-04	k: 410	n:740000
ALS2   740000 perm   438 sec   (1690 perm/sec)   p_kst 5.540541e-04   p_cons 7.007703e-02   p_joint 8.648649e-05

Joint ci ratio: 4.788825e-01	ci left: 6.805983e-05	ci right 1.119562e-04	k: 66	n:750000
Cons ci ratio: 1.648512e-02	ci left: 6.952848e-02	ci right 7.068551e-02	k: 52579	n:750000
KS ci ratio: 1.919097e-01	ci left: 5.026525e-04	ci right 6.105991e-04	k: 416	n:750000
ALS2   750000 perm   448 sec   (1675 perm/sec)   p_kst 5.546667e-04   p_cons 7.010533e-02   p_joint 8.800000e-05

Joint ci ratio: 4.753482e-01	ci left: 6.832179e-05	ci right 1.119561e-04	k: 67	n:760000
Cons ci ratio: 1.637780e-02	ci left: 6.952042e-02	ci right 7.066970e-02	k: 53271	n:760000
KS ci ratio: 1.898713e-01	ci left: 5.073150e-04	ci right 6.149721e-04	k: 425	n:760000
ALS2   760000 perm   457 sec   (1664 perm/sec)   p_kst 5.592105e-04   p_cons 7.009342e-02   p_joint 8.815789e-05

Joint ci ratio: 4.753485e-01	ci left: 6.743449e-05	ci right 1.105021e-04	k: 67	n:770000
Cons ci ratio: 1.627304e-02	ci left: 6.950870e-02	ci right 7.065038e-02	k: 53960	n:770000
KS ci ratio: 1.896494e-01	ci left: 5.019634e-04	ci right 6.083460e-04	k: 426	n:770000
ALS2   770000 perm   466 sec   (1652 perm/sec)   p_kst 5.532468e-04   p_cons 7.007792e-02   p_joint 8.701299e-05

Joint ci ratio: 4.753488e-01	ci left: 6.656993e-05	ci right 1.090854e-04	k: 67	n:780000
Cons ci ratio: 1.617075e-02	ci left: 6.949348e-02	ci right 7.062766e-02	k: 54646	n:780000
KS ci ratio: 1.883308e-01	ci left: 5.028563e-04	ci right 6.086025e-04	k: 432	n:780000
ALS2   780000 perm   476 sec   (1640 perm/sec)   p_kst 5.538462e-04   p_cons 7.005897e-02   p_joint 8.589744e-05

Joint ci ratio: 4.753491e-01	ci left: 6.572727e-05	ci right 1.077046e-04	k: 67	n:790000
Cons ci ratio: 1.606926e-02	ci left: 6.948750e-02	ci right 7.061439e-02	k: 55339	n:790000
KS ci ratio: 1.872528e-01	ci left: 5.025226e-04	ci right 6.075250e-04	k: 437	n:790000
ALS2   790000 perm   485 sec   (1629 perm/sec)   p_kst 5.531646e-04   p_cons 7.004937e-02   p_joint 8.481013e-05

Joint ci ratio: 4.718919e-01	ci left: 6.600641e-05	ci right 1.077565e-04	k: 68	n:800000
Cons ci ratio: 1.596645e-02	ci left: 6.950783e-02	ci right 7.062778e-02	k: 56053	n:800000
KS ci ratio: 1.859832e-01	ci left: 5.033907e-04	ci right 6.077809e-04	k: 443	n:800000
ALS2   800000 perm   495 sec   (1617 perm/sec)   p_kst 5.537500e-04   p_cons 7.006625e-02   p_joint 8.500000e-05

Joint ci ratio: 4.718922e-01	ci left: 6.519151e-05	ci right 1.064262e-04	k: 68	n:810000
Cons ci ratio: 1.586062e-02	ci left: 6.956828e-02	ci right 7.068171e-02	k: 56800	n:810000
KS ci ratio: 1.845341e-01	ci left: 5.054173e-04	ci right 6.093197e-04	k: 450	n:810000
ALS2   810000 perm   504 sec   (1606 perm/sec)   p_kst 5.555556e-04   p_cons 7.012346e-02   p_joint 8.395062e-05

Joint ci ratio: 4.685093e-01	ci left: 6.547145e-05	ci right 1.064914e-04	k: 69	n:820000
Cons ci ratio: 1.575835e-02	ci left: 6.961513e-02	ci right 7.072206e-02	k: 57537	n:820000
KS ci ratio: 1.831183e-01	ci left: 5.073975e-04	ci right 6.108178e-04	k: 457	n:820000
ALS2   820000 perm   514 sec   (1595 perm/sec)   p_kst 5.573171e-04   p_cons 7.016707e-02   p_joint 8.414634e-05

Joint ci ratio: 4.685096e-01	ci left: 6.468263e-05	ci right 1.052084e-04	k: 69	n:830000
Cons ci ratio: 1.565846e-02	ci left: 6.965727e-02	ci right 7.075778e-02	k: 58271	n:830000
KS ci ratio: 1.821269e-01	ci left: 5.070330e-04	ci right 6.097578e-04	k: 462	n:830000
ALS2   830000 perm   524 sec   (1584 perm/sec)   p_kst 5.566265e-04   p_cons 7.020602e-02   p_joint 8.313253e-05

Joint ci ratio: 4.685098e-01	ci left: 6.391259e-05	ci right 1.039559e-04	k: 69	n:840000
Cons ci ratio: 1.556030e-02	ci left: 6.969961e-02	ci right 7.079383e-02	k: 59006	n:840000
KS ci ratio: 1.805733e-01	ci left: 5.100884e-04	ci right 6.124543e-04	k: 470	n:840000
ALS2   840000 perm   534 sec   (1572 perm/sec)   p_kst 5.595238e-04   p_cons 7.024524e-02   p_joint 8.214286e-05

Joint ci ratio: 4.651987e-01	ci left: 6.419870e-05	ci right 1.040469e-04	k: 70	n:850000
Cons ci ratio: 1.546564e-02	ci left: 6.972691e-02	ci right 7.081484e-02	k: 59729	n:850000
KS ci ratio: 1.800012e-01	ci left: 5.074575e-04	ci right 6.089376e-04	k: 473	n:850000
ALS2   850000 perm   544 sec   (1562 perm/sec)   p_kst 5.564706e-04   p_cons 7.026941e-02   p_joint 8.235294e-05

Joint ci ratio: 4.651989e-01	ci left: 6.345220e-05	ci right 1.028370e-04	k: 70	n:860000
Cons ci ratio: 1.536831e-02	ci left: 6.979068e-02	ci right 7.087269e-02	k: 60484	n:860000
KS ci ratio: 1.788727e-01	ci left: 5.082202e-04	ci right 6.091467e-04	k: 479	n:860000
ALS2   860000 perm   555 sec   (1551 perm/sec)   p_kst 5.569767e-04   p_cons 7.033023e-02   p_joint 8.139535e-05

Joint ci ratio: 4.619570e-01	ci left: 6.373799e-05	ci right 1.029378e-04	k: 71	n:870000
Cons ci ratio: 1.527682e-02	ci left: 6.981863e-02	ci right 7.089458e-02	k: 61209	n:870000
KS ci ratio: 1.781321e-01	ci left: 5.067708e-04	ci right 6.069480e-04	k: 483	n:870000
ALS2   870000 perm   565 sec   (1541 perm/sec)   p_kst 5.551724e-04   p_cons 7.035517e-02   p_joint 8.160920e-05

Joint ci ratio: 4.556713e-01	ci left: 6.502367e-05	ci right 1.043018e-04	k: 73	n:880000
Cons ci ratio: 1.518615e-02	ci left: 6.985277e-02	ci right 7.092279e-02	k: 61940	n:880000
KS ci ratio: 1.772192e-01	ci left: 5.064412e-04	ci right 6.059851e-04	k: 488	n:880000
ALS2   880000 perm   575 sec   (1531 perm/sec)   p_kst 5.545455e-04   p_cons 7.038636e-02   p_joint 8.295455e-05

Joint ci ratio: 4.556715e-01	ci left: 6.429306e-05	ci right 1.031299e-04	k: 73	n:890000
Cons ci ratio: 1.509915e-02	ci left: 6.986824e-02	ci right 7.093231e-02	k: 62655	n:890000
KS ci ratio: 1.764989e-01	ci left: 5.050462e-04	ci right 6.038694e-04	k: 492	n:890000
ALS2   890000 perm   586 sec   (1520 perm/sec)   p_kst 5.528090e-04   p_cons 7.039888e-02   p_joint 8.202247e-05

Joint ci ratio: 4.556718e-01	ci left: 6.357869e-05	ci right 1.019840e-04	k: 73	n:900000
Cons ci ratio: 1.501274e-02	ci left: 6.989113e-02	ci right 7.094941e-02	k: 63377	n:900000
KS ci ratio: 1.757874e-01	ci left: 5.036831e-04	ci right 6.018000e-04	k: 496	n:900000
ALS2   900000 perm   596 sec   (1510 perm/sec)   p_kst 5.511111e-04   p_cons 7.041889e-02   p_joint 8.111111e-05

Joint ci ratio: 4.496358e-01	ci left: 6.482719e-05	ci right 1.033101e-04	k: 75	n:910000
Cons ci ratio: 1.492517e-02	ci left: 6.993654e-02	ci right 7.098928e-02	k: 64120	n:910000
KS ci ratio: 1.742167e-01	ci left: 5.076051e-04	ci right 6.055096e-04	k: 505	n:910000
ALS2   910000 perm   606 sec   (1501 perm/sec)   p_kst 5.549451e-04   p_cons 7.046154e-02   p_joint 8.241758e-05

Joint ci ratio: 4.496360e-01	ci left: 6.412254e-05	ci right 1.021871e-04	k: 75	n:920000
Cons ci ratio: 1.485044e-02	ci left: 6.988132e-02	ci right 7.092791e-02	k: 64771	n:920000
KS ci ratio: 1.738738e-01	ci left: 5.041668e-04	ci right 6.011966e-04	k: 507	n:920000
ALS2   920000 perm   617 sec   (1491 perm/sec)   p_kst 5.510870e-04   p_cons 7.040326e-02   p_joint 8.152174e-05

Joint ci ratio: 4.438337e-01	ci left: 6.534161e-05	ci right 1.034793e-04	k: 77	n:930000
Cons ci ratio: 1.476711e-02	ci left: 6.991302e-02	ci right 7.095417e-02	k: 65502	n:930000
KS ci ratio: 1.731934e-01	ci left: 5.028599e-04	ci right 5.992199e-04	k: 511	n:930000
ALS2   930000 perm   628 sec   (1482 perm/sec)   p_kst 5.494624e-04   p_cons 7.043226e-02   p_joint 8.279570e-05

Joint ci ratio: 4.410157e-01	ci left: 6.559177e-05	ci right 1.035601e-04	k: 78	n:940000
Cons ci ratio: 1.469066e-02	ci left: 6.989530e-02	ci right 7.093075e-02	k: 66187	n:940000
KS ci ratio: 1.723539e-01	ci left: 5.025994e-04	ci right 5.983941e-04	k: 516	n:940000
ALS2   940000 perm   639 sec   (1472 perm/sec)   p_kst 5.489362e-04   p_cons 7.041170e-02   p_joint 8.297872e-05

Joint ci ratio: 4.382506e-01	ci left: 6.583742e-05	ci right 1.036385e-04	k: 79	n:950000
Cons ci ratio: 1.461444e-02	ci left: 6.988636e-02	ci right 7.091626e-02	k: 66880	n:950000
KS ci ratio: 1.720218e-01	ci left: 4.993234e-04	ci right 5.942913e-04	k: 518	n:950000
ALS2   950000 perm   650 sec   (1462 perm/sec)   p_kst 5.452632e-04   p_cons 7.040000e-02   p_joint 8.315789e-05

Joint ci ratio: 4.355370e-01	ci left: 6.607869e-05	ci right 1.037145e-04	k: 80	n:960000
Cons ci ratio: 1.453813e-02	ci left: 6.988904e-02	ci right 7.091356e-02	k: 67584	n:960000
KS ci ratio: 1.713628e-01	ci left: 4.981097e-04	ci right 5.924463e-04	k: 522	n:960000
ALS2   960000 perm   660 sec   (1454 perm/sec)   p_kst 5.437500e-04   p_cons 7.040000e-02   p_joint 8.333333e-05

Joint ci ratio: 4.302573e-01	ci left: 6.723460e-05	ci right 1.049305e-04	k: 82	n:970000
Cons ci ratio: 1.446323e-02	ci left: 6.988962e-02	ci right 7.090882e-02	k: 68286	n:970000
KS ci ratio: 1.700669e-01	ci left: 5.008696e-04	ci right 5.949380e-04	k: 530	n:970000
ALS2   970000 perm   672 sec   (1445 perm/sec)   p_kst 5.463918e-04   p_cons 7.039794e-02   p_joint 8.453608e-05

Joint ci ratio: 4.276885e-01	ci left: 6.745875e-05	ci right 1.049897e-04	k: 83	n:980000
Cons ci ratio: 1.439216e-02	ci left: 6.986580e-02	ci right 7.087960e-02	k: 68964	n:980000
KS ci ratio: 1.692718e-01	ci left: 5.006441e-04	ci right 5.941857e-04	k: 535	n:980000
ALS2   980000 perm   683 sec   (1436 perm/sec)   p_kst 5.459184e-04   p_cons 7.037143e-02   p_joint 8.469388e-05

Joint ci ratio: 4.251652e-01	ci left: 6.767902e-05	ci right 1.050471e-04	k: 84	n:990000
Cons ci ratio: 1.432213e-02	ci left: 6.984246e-02	ci right 7.085096e-02	k: 69642	n:990000
KS ci ratio: 1.684878e-01	ci left: 5.004241e-04	ci right 5.934476e-04	k: 540	n:990000
ALS2   990000 perm   694 sec   (1427 perm/sec)   p_kst 5.454545e-04   p_cons 7.034545e-02   p_joint 8.484848e-05

Joint ci ratio: 4.226861e-01	ci left: 6.789553e-05	ci right 1.051028e-04	k: 85	n:1000000
Cons ci ratio: 1.424593e-02	ci left: 6.988539e-02	ci right 7.088910e-02	k: 70386	n:1000000
KS ci ratio: 1.666492e-01	ci left: 5.069168e-04	ci right 6.000157e-04	k: 552	n:1000000
ALS2   1000000 perm   705 sec   (1419 perm/sec)   p_kst 5.520000e-04   p_cons 7.038600e-02   p_joint 8.500000e-05

Joint ci ratio: 4.202498e-01	ci left: 6.810837e-05	ci right 1.051567e-04	k: 86	n:1010000
Cons ci ratio: 1.417253e-02	ci left: 6.991268e-02	ci right 7.091156e-02	k: 71115	n:1010000
KS ci ratio: 1.656042e-01	ci left: 5.085404e-04	ci right 6.012935e-04	k: 559	n:1010000
ALS2   1010000 perm   716 sec   (1410 perm/sec)   p_kst 5.534653e-04   p_cons 7.041089e-02   p_joint 8.514851e-05

Joint ci ratio: 4.202500e-01	ci left: 6.744063e-05	ci right 1.041257e-04	k: 86	n:1020000
Cons ci ratio: 1.410079e-02	ci left: 6.993457e-02	ci right 7.092866e-02	k: 71839	n:1020000
KS ci ratio: 1.653096e-01	ci left: 5.054342e-04	ci right 5.974405e-04	k: 561	n:1020000
ALS2   1020000 perm   728 sec   (1402 perm/sec)   p_kst 5.500000e-04   p_cons 7.043039e-02   p_joint 8.431373e-05

Joint ci ratio: 4.155010e-01	ci left: 6.852343e-05	ci right 1.052596e-04	k: 88	n:1030000
Cons ci ratio: 1.403200e-02	ci left: 6.993862e-02	ci right 7.092788e-02	k: 72545	n:1030000
KS ci ratio: 1.642895e-01	ci left: 5.070430e-04	ci right 5.987162e-04	k: 568	n:1030000
ALS2   1030000 perm   739 sec   (1393 perm/sec)   p_kst 5.514563e-04   p_cons 7.043204e-02   p_joint 8.543689e-05

Joint ci ratio: 4.155012e-01	ci left: 6.786455e-05	ci right 1.042475e-04	k: 88	n:1040000
Cons ci ratio: 1.396605e-02	ci left: 6.992535e-02	ci right 7.090974e-02	k: 73233	n:1040000
KS ci ratio: 1.634300e-01	ci left: 5.077002e-04	ci right 5.989649e-04	k: 574	n:1040000
ALS2   1040000 perm   751 sec   (1385 perm/sec)   p_kst 5.519231e-04   p_cons 7.041635e-02   p_joint 8.461538e-05

Joint ci ratio: 4.155014e-01	ci left: 6.721821e-05	ci right 1.032547e-04	k: 88	n:1050000
Cons ci ratio: 1.389627e-02	ci left: 6.995696e-02	ci right 7.093684e-02	k: 73968	n:1050000
KS ci ratio: 1.628646e-01	ci left: 5.065189e-04	ci right 5.972254e-04	k: 578	n:1050000
ALS2   1050000 perm   762 sec   (1377 perm/sec)   p_kst 5.504762e-04   p_cons 7.044571e-02   p_joint 8.380952e-05

Joint ci ratio: 4.042990e-01	ci left: 7.081472e-05	ci right 1.074813e-04	k: 93	n:1060000
Cons ci ratio: 1.382295e-02	ci left: 7.003125e-02	ci right 7.100695e-02	k: 74749	n:1060000
KS ci ratio: 1.613389e-01	ci left: 5.116970e-04	ci right 6.023891e-04	k: 589	n:1060000
ALS2   1060000 perm   774 sec   (1369 perm/sec)   p_kst 5.556604e-04   p_cons 7.051792e-02   p_joint 8.773585e-05

Joint ci ratio: 4.042992e-01	ci left: 7.015289e-05	ci right 1.064768e-04	k: 93	n:1070000
Cons ci ratio: 1.375655e-02	ci left: 7.004920e-02	ci right 7.102042e-02	k: 75471	n:1070000
KS ci ratio: 1.603901e-01	ci left: 5.131935e-04	ci right 6.035644e-04	k: 596	n:1070000
ALS2   1070000 perm   786 sec   (1361 perm/sec)   p_kst 5.570093e-04   p_cons 7.053364e-02   p_joint 8.691589e-05

Joint ci ratio: 4.042993e-01	ci left: 6.950333e-05	ci right 1.054909e-04	k: 93	n:1080000
Cons ci ratio: 1.368995e-02	ci left: 7.007790e-02	ci right 7.104478e-02	k: 76205	n:1080000
KS ci ratio: 1.598556e-01	ci left: 5.119970e-04	ci right 6.018279e-04	k: 600	n:1080000
ALS2   1080000 perm   798 sec   (1353 perm/sec)   p_kst 5.555556e-04   p_cons 7.056019e-02   p_joint 8.611111e-05

Joint ci ratio: 4.042995e-01	ci left: 6.886568e-05	ci right 1.045231e-04	k: 93	n:1090000
Cons ci ratio: 1.362430e-02	ci left: 7.010608e-02	ci right 7.106868e-02	k: 76939	n:1090000
KS ci ratio: 1.590635e-01	ci left: 5.125847e-04	ci right 6.020305e-04	k: 606	n:1090000
ALS2   1090000 perm   810 sec   (1346 perm/sec)   p_kst 5.559633e-04   p_cons 7.058624e-02   p_joint 8.532110e-05

Joint ci ratio: 4.042997e-01	ci left: 6.823962e-05	ci right 1.035729e-04	k: 93	n:1100000
Cons ci ratio: 1.356419e-02	ci left: 7.008936e-02	ci right 7.104745e-02	k: 77624	n:1100000
KS ci ratio: 1.584125e-01	ci left: 5.122897e-04	ci right 6.012834e-04	k: 611	n:1100000
ALS2   1100000 perm   822 sec   (1338 perm/sec)   p_kst 5.554545e-04   p_cons 7.056727e-02   p_joint 8.454545e-05

Joint ci ratio: 4.042998e-01	ci left: 6.762484e-05	ci right 1.026398e-04	k: 93	n:1110000
Cons ci ratio: 1.350135e-02	ci left: 7.010708e-02	ci right 7.106093e-02	k: 78347	n:1110000
KS ci ratio: 1.577693e-01	ci left: 5.120008e-04	ci right 6.005490e-04	k: 616	n:1110000
ALS2   1110000 perm   835 sec   (1330 perm/sec)   p_kst 5.549550e-04   p_cons 7.058288e-02   p_joint 8.378378e-05

Joint ci ratio: 4.043000e-01	ci left: 6.702104e-05	ci right 1.017234e-04	k: 93	n:1120000
Cons ci ratio: 1.344129e-02	ci left: 7.010579e-02	ci right 7.105536e-02	k: 79049	n:1120000
KS ci ratio: 1.572605e-01	ci left: 5.108600e-04	ci right 5.988991e-04	k: 620	n:1120000
ALS2   1120000 perm   847 sec   (1322 perm/sec)   p_kst 5.535714e-04   p_cons 7.057946e-02   p_joint 8.303571e-05

Joint ci ratio: 4.021664e-01	ci left: 6.722313e-05	ci right 1.017975e-04	k: 94	n:1130000
Cons ci ratio: 1.338482e-02	ci left: 7.007720e-02	ci right 7.102235e-02	k: 79720	n:1130000
KS ci ratio: 1.565062e-01	ci left: 5.114404e-04	ci right 5.991171e-04	k: 626	n:1130000
ALS2   1130000 perm   859 sec   (1315 perm/sec)   p_kst 5.539823e-04   p_cons 7.054867e-02   p_joint 8.318584e-05

Joint ci ratio: 4.021666e-01	ci left: 6.663345e-05	ci right 1.009045e-04	k: 94	n:1140000
Cons ci ratio: 1.332657e-02	ci left: 7.007359e-02	ci right 7.101456e-02	k: 80419	n:1140000
KS ci ratio: 1.557627e-01	ci left: 5.120116e-04	ci right 5.993303e-04	k: 632	n:1140000
ALS2   1140000 perm   872 sec   (1307 perm/sec)   p_kst 5.543860e-04   p_cons 7.054298e-02   p_joint 8.245614e-05

Joint ci ratio: 3.959628e-01	ci left: 6.840092e-05	ci right 1.028962e-04	k: 97	n:1150000
Cons ci ratio: 1.326836e-02	ci left: 7.007700e-02	ci right 7.101386e-02	k: 81126	n:1150000
KS ci ratio: 1.547875e-01	ci left: 5.142456e-04	ci right 6.013453e-04	k: 640	n:1150000
ALS2   1150000 perm   885 sec   (1299 perm/sec)   p_kst 5.565217e-04   p_cons 7.054435e-02   p_joint 8.434783e-05

Joint ci ratio: 3.939578e-01	ci left: 6.858770e-05	ci right 1.029565e-04	k: 98	n:1160000
Cons ci ratio: 1.321161e-02	ci left: 7.007347e-02	ci right 7.100626e-02	k: 81825	n:1160000
KS ci ratio: 1.538303e-01	ci left: 5.164428e-04	ci right 6.033239e-04	k: 648	n:1160000
ALS2   1160000 perm   898 sec   (1292 perm/sec)   p_kst 5.586207e-04   p_cons 7.053879e-02   p_joint 8.448276e-05

Joint ci ratio: 3.939580e-01	ci left: 6.800148e-05	ci right 1.020765e-04	k: 98	n:1170000
Cons ci ratio: 1.315669e-02	ci left: 7.005894e-02	ci right 7.098763e-02	k: 82511	n:1170000
KS ci ratio: 1.531241e-01	ci left: 5.169600e-04	ci right 6.034922e-04	k: 654	n:1170000
ALS2   1170000 perm   912 sec   (1283 perm/sec)   p_kst 5.589744e-04   p_cons 7.052222e-02   p_joint 8.376068e-05

Joint ci ratio: 3.900377e-01	ci left: 6.895305e-05	ci right 1.030726e-04	k: 100	n:1180000
Cons ci ratio: 1.309991e-02	ci left: 7.007001e-02	ci right 7.099481e-02	k: 83227	n:1180000
KS ci ratio: 1.521973e-01	ci left: 5.190997e-04	ci right 6.054163e-04	k: 662	n:1180000
ALS2   1180000 perm   925 sec   (1276 perm/sec)   p_kst 5.610169e-04   p_cons 7.053136e-02   p_joint 8.474576e-05

Joint ci ratio: 3.881210e-01	ci left: 6.913174e-05	ci right 1.031286e-04	k: 101	n:1190000
Cons ci ratio: 1.304578e-02	ci left: 7.006164e-02	ci right 7.098247e-02	k: 83920	n:1190000
KS ci ratio: 1.517404e-01	ci left: 5.179711e-04	ci right 6.038178e-04	k: 666	n:1190000
ALS2   1190000 perm   938 sec   (1269 perm/sec)   p_kst 5.596639e-04   p_cons 7.052101e-02   p_joint 8.487395e-05

Joint ci ratio: 3.843708e-01	ci left: 7.006047e-05	ci right 1.040969e-04	k: 103	n:1200000
Cons ci ratio: 1.298770e-02	ci left: 7.009994e-02	ci right 7.101714e-02	k: 84669	n:1200000
KS ci ratio: 1.509503e-01	ci left: 5.192671e-04	ci right 6.048401e-04	k: 673	n:1200000
ALS2   1200000 perm   951 sec   (1262 perm/sec)   p_kst 5.608333e-04   p_cons 7.055750e-02   p_joint 8.583333e-05

Joint ci ratio: 3.825361e-01	ci left: 7.022824e-05	ci right 1.041424e-04	k: 104	n:1210000
Cons ci ratio: 1.293478e-02	ci left: 7.009311e-02	ci right 7.100646e-02	k: 85364	n:1210000
KS ci ratio: 1.506156e-01	ci left: 5.173614e-04	ci right 6.024142e-04	k: 676	n:1210000
ALS2   1210000 perm   964 sec   (1255 perm/sec)   p_kst 5.586777e-04   p_cons 7.054876e-02   p_joint 8.595041e-05

Joint ci ratio: 3.807274e-01	ci left: 7.039364e-05	ci right 1.041867e-04	k: 105	n:1220000
Cons ci ratio: 1.288186e-02	ci left: 7.009295e-02	ci right 7.100253e-02	k: 86067	n:1220000
KS ci ratio: 1.500625e-01	ci left: 5.170649e-04	ci right 6.017289e-04	k: 681	n:1220000
ALS2   1220000 perm   977 sec   (1248 perm/sec)   p_kst 5.581967e-04   p_cons 7.054672e-02   p_joint 8.606557e-05

Joint ci ratio: 3.807275e-01	ci left: 6.982133e-05	ci right 1.033396e-04	k: 105	n:1230000
Cons ci ratio: 1.282998e-02	ci left: 7.008874e-02	ci right 7.099458e-02	k: 86765	n:1230000
KS ci ratio: 1.495155e-01	ci left: 5.167738e-04	ci right 6.010540e-04	k: 686	n:1230000
ALS2   1230000 perm   991 sec   (1241 perm/sec)   p_kst 5.577236e-04   p_cons 7.054065e-02   p_joint 8.536585e-05

Joint ci ratio: 3.789442e-01	ci left: 6.998770e-05	ci right 1.033894e-04	k: 106	n:1240000
Cons ci ratio: 1.277284e-02	ci left: 7.014492e-02	ci right 7.104741e-02	k: 87538	n:1240000
KS ci ratio: 1.491903e-01	ci left: 5.149352e-04	ci right 5.987166e-04	k: 689	n:1240000
ALS2   1240000 perm   1004 sec   (1235 perm/sec)   p_kst 5.556452e-04   p_cons 7.059516e-02   p_joint 8.548387e-05

Joint ci ratio: 3.771857e-01	ci left: 7.015178e-05	ci right 1.034379e-04	k: 107	n:1250000
Cons ci ratio: 1.271924e-02	ci left: 7.017148e-02	ci right 7.107051e-02	k: 88275	n:1250000
KS ci ratio: 1.487598e-01	ci left: 5.138964e-04	ci right 5.972461e-04	k: 693	n:1250000
ALS2   1250000 perm   1017 sec   (1229 perm/sec)   p_kst 5.544000e-04   p_cons 7.062000e-02   p_joint 8.560000e-05

Joint ci ratio: 3.771859e-01	ci left: 6.959502e-05	ci right 1.026170e-04	k: 107	n:1260000
Cons ci ratio: 1.266853e-02	ci left: 7.017469e-02	ci right 7.107014e-02	k: 88983	n:1260000
KS ci ratio: 1.486530e-01	ci left: 5.105819e-04	ci right 5.933293e-04	k: 694	n:1260000
ALS2   1260000 perm   1031 sec   (1222 perm/sec)   p_kst 5.507937e-04   p_cons 7.062143e-02   p_joint 8.492063e-05

Joint ci ratio: 3.737410e-01	ci left: 7.047322e-05	ci right 1.035317e-04	k: 109	n:1270000
Cons ci ratio: 1.262076e-02	ci left: 7.015351e-02	ci right 7.104530e-02	k: 89660	n:1270000
KS ci ratio: 1.470738e-01	ci left: 5.179358e-04	ci right 6.009049e-04	k: 709	n:1270000
ALS2   1270000 perm   1045 sec   (1216 perm/sec)   p_kst 5.582677e-04   p_cons 7.059843e-02   p_joint 8.582677e-05

Joint ci ratio: 3.703888e-01	ci left: 7.133906e-05	ci right 1.044308e-04	k: 111	n:1280000
Cons ci ratio: 1.257466e-02	ci left: 7.012099e-02	ci right 7.100908e-02	k: 90322	n:1280000
KS ci ratio: 1.466613e-01	ci left: 5.168996e-04	ci right 5.994501e-04	k: 713	n:1280000
ALS2   1280000 perm   1058 sec   (1209 perm/sec)   p_kst 5.570313e-04   p_cons 7.056406e-02   p_joint 8.671875e-05

Joint ci ratio: 3.687463e-01	ci left: 7.148924e-05	ci right 1.044682e-04	k: 112	n:1290000
Cons ci ratio: 1.252558e-02	ci left: 7.012530e-02	ci right 7.100996e-02	k: 91031	n:1290000
KS ci ratio: 1.459476e-01	ci left: 5.181203e-04	ci right 6.004280e-04	k: 720	n:1290000
ALS2   1290000 perm   1072 sec   (1203 perm/sec)   p_kst 5.581395e-04   p_cons 7.056667e-02   p_joint 8.682171e-05

Joint ci ratio: 3.671254e-01	ci left: 7.163744e-05	ci right 1.045046e-04	k: 113	n:1300000
Cons ci ratio: 1.247824e-02	ci left: 7.011729e-02	ci right 7.099847e-02	k: 91724	n:1300000
KS ci ratio: 1.451444e-01	ci left: 5.200646e-04	ci right 6.021871e-04	k: 728	n:1300000
ALS2   1300000 perm   1086 sec   (1197 perm/sec)   p_kst 5.600000e-04   p_cons 7.055692e-02   p_joint 8.692308e-05

Joint ci ratio: 3.655257e-01	ci left: 7.178368e-05	ci right 1.045402e-04	k: 114	n:1310000
Cons ci ratio: 1.242926e-02	ci left: 7.013223e-02	ci right 7.101012e-02	k: 92447	n:1310000
KS ci ratio: 1.444525e-01	ci left: 5.212446e-04	ci right 6.031272e-04	k: 735	n:1310000
ALS2   1310000 perm   1100 sec   (1191 perm/sec)   p_kst 5.610687e-04   p_cons 7.057023e-02   p_joint 8.702290e-05

Joint ci ratio: 3.623879e-01	ci left: 7.261647e-05	ci right 1.054013e-04	k: 116	n:1320000
Cons ci ratio: 1.238207e-02	ci left: 7.013412e-02	ci right 7.100867e-02	k: 93153	n:1320000
KS ci ratio: 1.433847e-01	ci left: 5.253291e-04	ci right 6.071911e-04	k: 746	n:1320000
ALS2   1320000 perm   1114 sec   (1185 perm/sec)   p_kst 5.651515e-04   p_cons 7.057045e-02   p_joint 8.787879e-05

Joint ci ratio: 3.608491e-01	ci left: 7.275405e-05	ci right 1.054287e-04	k: 117	n:1330000
Cons ci ratio: 1.233520e-02	ci left: 7.013823e-02	ci right 7.100950e-02	k: 93862	n:1330000
KS ci ratio: 1.429072e-01	ci left: 5.250040e-04	ci right 6.065197e-04	k: 751	n:1330000
ALS2   1330000 perm   1128 sec   (1179 perm/sec)   p_kst 5.646617e-04   p_cons 7.057293e-02   p_joint 8.796992e-05

Joint ci ratio: 3.593297e-01	ci left: 7.288987e-05	ci right 1.054554e-04	k: 118	n:1340000
Cons ci ratio: 1.228809e-02	ci left: 7.015047e-02	ci right 7.101855e-02	k: 94582	n:1340000
KS ci ratio: 1.424345e-01	ci left: 5.246842e-04	ci right 6.058579e-04	k: 756	n:1340000
ALS2   1340000 perm   1142 sec   (1173 perm/sec)   p_kst 5.641791e-04   p_cons 7.058358e-02   p_joint 8.805970e-05

Joint ci ratio: 3.593298e-01	ci left: 7.234994e-05	ci right 1.046743e-04	k: 118	n:1350000
Cons ci ratio: 1.223951e-02	ci left: 7.018396e-02	ci right 7.104899e-02	k: 95331	n:1350000
KS ci ratio: 1.417804e-01	ci left: 5.257985e-04	ci right 6.067395e-04	k: 763	n:1350000
ALS2   1350000 perm   1157 sec   (1167 perm/sec)   p_kst 5.651852e-04   p_cons 7.061556e-02   p_joint 8.740741e-05

Joint ci ratio: 3.578295e-01	ci left: 7.248701e-05	ci right 1.047059e-04	k: 119	n:1360000
Cons ci ratio: 1.219376e-02	ci left: 7.019277e-02	ci right 7.105465e-02	k: 96047	n:1360000
KS ci ratio: 1.408613e-01	ci left: 5.290254e-04	ci right 6.098908e-04	k: 773	n:1360000
ALS2   1360000 perm   1171 sec   (1161 perm/sec)   p_kst 5.683824e-04   p_cons 7.062279e-02   p_joint 8.750000e-05

Joint ci ratio: 3.548842e-01	ci left: 7.328709e-05	ci right 1.055316e-04	k: 121	n:1370000
Cons ci ratio: 1.214750e-02	ci left: 7.021237e-02	ci right 7.107120e-02	k: 96778	n:1370000
KS ci ratio: 1.404086e-01	ci left: 5.286851e-04	ci right 6.092171e-04	k: 778	n:1370000
ALS2   1370000 perm   1185 sec   (1156 perm/sec)   p_kst 5.678832e-04   p_cons 7.064088e-02   p_joint 8.832117e-05

Joint ci ratio: 3.548843e-01	ci left: 7.275602e-05	ci right 1.047669e-04	k: 121	n:1380000
Cons ci ratio: 1.210451e-02	ci left: 7.020207e-02	ci right 7.105771e-02	k: 97468	n:1380000
KS ci ratio: 1.401391e-01	ci left: 5.269516e-04	ci right 6.070526e-04	k: 781	n:1380000
ALS2   1380000 perm   1200 sec   (1150 perm/sec)   p_kst 5.659420e-04   p_cons 7.062899e-02   p_joint 8.768116e-05

Joint ci ratio: 3.534387e-01	ci left: 7.288802e-05	ci right 1.047964e-04	k: 122	n:1390000
Cons ci ratio: 1.205873e-02	ci left: 7.022707e-02	ci right 7.107976e-02	k: 98207	n:1390000
KS ci ratio: 1.396046e-01	ci left: 5.273261e-04	ci right 6.071528e-04	k: 787	n:1390000
ALS2   1390000 perm   1215 sec   (1144 perm/sec)   p_kst 5.661871e-04   p_cons 7.065252e-02   p_joint 8.776978e-05

Joint ci ratio: 3.534388e-01	ci left: 7.236738e-05	ci right 1.040478e-04	k: 122	n:1400000
Cons ci ratio: 1.201562e-02	ci left: 7.022821e-02	ci right 7.107785e-02	k: 98913	n:1400000
KS ci ratio: 1.392517e-01	ci left: 5.263170e-04	ci right 6.057728e-04	k: 791	n:1400000
ALS2   1400000 perm   1230 sec   (1138 perm/sec)   p_kst 5.650000e-04   p_cons 7.065214e-02   p_joint 8.714286e-05

Joint ci ratio: 3.520108e-01	ci left: 7.250053e-05	ci right 1.040817e-04	k: 123	n:1410000
Cons ci ratio: 1.197116e-02	ci left: 7.024915e-02	ci right 7.109587e-02	k: 99647	n:1410000
KS ci ratio: 1.390764e-01	ci left: 5.239532e-04	ci right 6.029444e-04	k: 793	n:1410000
ALS2   1410000 perm   1245 sec   (1132 perm/sec)   p_kst 5.624113e-04   p_cons 7.067163e-02   p_joint 8.723404e-05

Joint ci ratio: 3.505999e-01	ci left: 7.263205e-05	ci right 1.041148e-04	k: 124	n:1420000
Cons ci ratio: 1.192648e-02	ci left: 7.027753e-02	ci right 7.112141e-02	k: 100392	n:1420000
KS ci ratio: 1.388145e-01	ci left: 5.223026e-04	ci right 6.008844e-04	k: 796	n:1420000
ALS2   1420000 perm   1260 sec   (1127 perm/sec)   p_kst 5.605634e-04   p_cons 7.069859e-02   p_joint 8.732394e-05

Joint ci ratio: 3.506000e-01	ci left: 7.212413e-05	ci right 1.033868e-04	k: 124	n:1430000
Cons ci ratio: 1.188174e-02	ci left: 7.031179e-02	ci right 7.115289e-02	k: 101146	n:1430000
KS ci ratio: 1.382088e-01	ci left: 5.233756e-04	ci right 6.017470e-04	k: 803	n:1430000
ALS2   1430000 perm   1278 sec   (1119 perm/sec)   p_kst 5.615385e-04   p_cons 7.073147e-02   p_joint 8.671329e-05

Joint ci ratio: 3.506001e-01	ci left: 7.162326e-05	ci right 1.026688e-04	k: 124	n:1440000
Cons ci ratio: 1.184162e-02	ci left: 7.029987e-02	ci right 7.113797e-02	k: 101834	n:1440000
KS ci ratio: 1.377811e-01	ci left: 5.230934e-04	ci right 6.011603e-04	k: 808	n:1440000
ALS2   1440000 perm   1294 sec   (1113 perm/sec)   p_kst 5.611111e-04   p_cons 7.071806e-02   p_joint 8.611111e-05

Joint ci ratio: 3.478284e-01	ci left: 7.238765e-05	ci right 1.034606e-04	k: 126	n:1450000
Cons ci ratio: 1.180500e-02	ci left: 7.025373e-02	ci right 7.108867e-02	k: 102472	n:1450000
KS ci ratio: 1.371048e-01	ci left: 5.248134e-04	ci right 6.027211e-04	k: 816	n:1450000
ALS2   1450000 perm   1309 sec   (1107 perm/sec)   p_kst 5.627586e-04   p_cons 7.067034e-02   p_joint 8.689655e-05

Joint ci ratio: 3.464670e-01	ci left: 7.251706e-05	ci right 1.034963e-04	k: 127	n:1460000
Cons ci ratio: 1.176589e-02	ci left: 7.023965e-02	ci right 7.107164e-02	k: 103156	n:1460000
KS ci ratio: 1.361085e-01	ci left: 5.291572e-04	ci right 6.070927e-04	k: 828	n:1460000
ALS2   1460000 perm   1325 sec   (1102 perm/sec)   p_kst 5.671233e-04   p_cons 7.065479e-02   p_joint 8.698630e-05

Joint ci ratio: 3.451215e-01	ci left: 7.264494e-05	ci right 1.035314e-04	k: 128	n:1470000
Cons ci ratio: 1.172657e-02	ci left: 7.023255e-02	ci right 7.106166e-02	k: 103850	n:1470000
KS ci ratio: 1.356999e-01	ci left: 5.288432e-04	ci right 6.064798e-04	k: 833	n:1470000
ALS2   1470000 perm   1340 sec   (1097 perm/sec)   p_kst 5.666667e-04   p_cons 7.064626e-02   p_joint 8.707483e-05

Joint ci ratio: 3.411769e-01	ci left: 7.400647e-05	ci right 1.050329e-04	k: 131	n:1480000
Cons ci ratio: 1.168475e-02	ci left: 7.025790e-02	ci right 7.108433e-02	k: 104592	n:1480000
KS ci ratio: 1.354567e-01	ci left: 5.272282e-04	ci right 6.044777e-04	k: 836	n:1480000
ALS2   1480000 perm   1355 sec   (1092 perm/sec)   p_kst 5.648649e-04   p_cons 7.067027e-02   p_joint 8.851351e-05

Joint ci ratio: 3.398918e-01	ci left: 7.412354e-05	ci right 1.050563e-04	k: 132	n:1490000
Cons ci ratio: 1.164534e-02	ci left: 7.026082e-02	ci right 7.108448e-02	k: 105301	n:1490000
KS ci ratio: 1.351342e-01	ci left: 5.262834e-04	ci right 6.031962e-04	k: 840	n:1490000
ALS2   1490000 perm   1371 sec   (1087 perm/sec)   p_kst 5.637584e-04   p_cons 7.067181e-02   p_joint 8.859060e-05

Joint ci ratio: 3.386212e-01	ci left: 7.423926e-05	ci right 1.050792e-04	k: 133	n:1500000
Cons ci ratio: 1.160673e-02	ci left: 7.025905e-02	ci right 7.107994e-02	k: 106003	n:1500000
KS ci ratio: 1.345753e-01	ci left: 5.272841e-04	ci right 6.039989e-04	k: 847	n:1500000
ALS2   1500000 perm   1387 sec   (1082 perm/sec)   p_kst 5.646667e-04   p_cons 7.066867e-02   p_joint 8.866667e-05

Joint ci ratio: 3.386213e-01	ci left: 7.374760e-05	ci right 1.043833e-04	k: 133	n:1510000
Cons ci ratio: 1.156921e-02	ci left: 7.024939e-02	ci right 7.106749e-02	k: 106693	n:1510000
KS ci ratio: 1.338666e-01	ci left: 5.295523e-04	ci right 6.061591e-04	k: 856	n:1510000
ALS2   1510000 perm   1403 sec   (1077 perm/sec)   p_kst 5.668874e-04   p_cons 7.065762e-02   p_joint 8.807947e-05

Joint ci ratio: 3.348930e-01	ci left: 7.506924e-05	ci right 1.058365e-04	k: 136	n:1520000
Cons ci ratio: 1.153008e-02	ci left: 7.026216e-02	ci right 7.107763e-02	k: 107417	n:1520000
KS ci ratio: 1.331690e-01	ci left: 5.317917e-04	ci right 6.082899e-04	k: 865	n:1520000
ALS2   1520000 perm   1419 sec   (1072 perm/sec)   p_kst 5.690789e-04   p_cons 7.066908e-02   p_joint 8.947368e-05

Joint ci ratio: 3.348931e-01	ci left: 7.457859e-05	ci right 1.051447e-04	k: 136	n:1530000
Cons ci ratio: 1.149124e-02	ci left: 7.027608e-02	ci right 7.108894e-02	k: 108143	n:1530000
KS ci ratio: 1.328626e-01	ci left: 5.308434e-04	ci right 6.070155e-04	k: 869	n:1530000
ALS2   1530000 perm   1435 sec   (1066 perm/sec)   p_kst 5.679739e-04   p_cons 7.068170e-02   p_joint 8.888889e-05

Joint ci ratio: 3.324749e-01	ci left: 7.528422e-05	ci right 1.058691e-04	k: 138	n:1540000
Cons ci ratio: 1.145431e-02	ci left: 7.027234e-02	ci right 7.108253e-02	k: 108842	n:1540000
KS ci ratio: 1.321054e-01	ci left: 5.336747e-04	ci right 6.097824e-04	k: 879	n:1540000
ALS2   1540000 perm   1451 sec   (1061 perm/sec)   p_kst 5.707792e-04   p_cons 7.067662e-02   p_joint 8.961039e-05

Joint ci ratio: 3.312854e-01	ci left: 7.538993e-05	ci right 1.058848e-04	k: 139	n:1550000
Cons ci ratio: 1.141757e-02	ci left: 7.027057e-02	ci right 7.107813e-02	k: 109544	n:1550000
KS ci ratio: 1.318062e-01	ci left: 5.327270e-04	ci right 6.085141e-04	k: 883	n:1550000
ALS2   1550000 perm   1469 sec   (1055 perm/sec)   p_kst 5.696774e-04   p_cons 7.067355e-02   p_joint 8.967742e-05

Joint ci ratio: 3.289440e-01	ci left: 7.608247e-05	ci right 1.065940e-04	k: 141	n:1560000
Cons ci ratio: 1.138318e-02	ci left: 7.024582e-02	ci right 7.105064e-02	k: 110210	n:1560000
KS ci ratio: 1.307016e-01	ci left: 5.386119e-04	ci right 6.145442e-04	k: 898	n:1560000
ALS2   1560000 perm   1487 sec   (1049 perm/sec)   p_kst 5.756410e-04   p_cons 7.064744e-02   p_joint 9.038462e-05

Joint ci ratio: 3.277918e-01	ci left: 7.618231e-05	ci right 1.066043e-04	k: 142	n:1570000
Cons ci ratio: 1.134932e-02	ci left: 7.021885e-02	ci right 7.102095e-02	k: 110872	n:1570000
KS ci ratio: 1.300521e-01	ci left: 5.407268e-04	ci right 6.165492e-04	k: 907	n:1570000
ALS2   1570000 perm   1503 sec   (1045 perm/sec)   p_kst 5.777070e-04   p_cons 7.061911e-02   p_joint 9.044586e-05

Joint ci ratio: 3.277919e-01	ci left: 7.570014e-05	ci right 1.059296e-04	k: 142	n:1580000
Cons ci ratio: 1.131341e-02	ci left: 7.021936e-02	ci right 7.101892e-02	k: 111577	n:1580000
KS ci ratio: 1.299093e-01	ci left: 5.385291e-04	ci right 6.139540e-04	k: 909	n:1580000
ALS2   1580000 perm   1519 sec   (1040 perm/sec)   p_kst 5.753165e-04   p_cons 7.061835e-02   p_joint 8.987342e-05

Joint ci ratio: 3.266518e-01	ci left: 7.580131e-05	ci right 1.059438e-04	k: 143	n:1590000
Cons ci ratio: 1.127892e-02	ci left: 7.020733e-02	ci right 7.100430e-02	k: 112262	n:1590000
KS ci ratio: 1.296248e-01	ci left: 5.375762e-04	ci right 6.126900e-04	k: 913	n:1590000
ALS2   1590000 perm   1536 sec   (1035 perm/sec)   p_kst 5.742138e-04   p_cons 7.060503e-02   p_joint 8.993711e-05

Joint ci ratio: 3.255234e-01	ci left: 7.590140e-05	ci right 1.059576e-04	k: 144	n:1600000
Cons ci ratio: 1.123977e-02	ci left: 7.025343e-02	ci right 7.104813e-02	k: 113040	n:1600000
KS ci ratio: 1.290611e-01	ci left: 5.390546e-04	ci right 6.140224e-04	k: 921	n:1600000
ALS2   1600000 perm   1553 sec   (1030 perm/sec)   p_kst 5.756250e-04   p_cons 7.065000e-02   p_joint 9.000000e-05

Joint ci ratio: 3.255235e-01	ci left: 7.542996e-05	ci right 1.052995e-04	k: 144	n:1610000
Cons ci ratio: 1.120378e-02	ci left: 7.026674e-02	ci right 7.105903e-02	k: 113766	n:1610000
KS ci ratio: 1.286432e-01	ci left: 5.393130e-04	ci right 6.140553e-04	k: 927	n:1610000
ALS2   1610000 perm   1569 sec   (1026 perm/sec)   p_kst 5.757764e-04   p_cons 7.066211e-02   p_joint 8.944099e-05

Joint ci ratio: 3.233014e-01	ci left: 7.609839e-05	ci right 1.059842e-04	k: 146	n:1620000
Cons ci ratio: 1.116954e-02	ci left: 7.026327e-02	ci right 7.105308e-02	k: 114465	n:1620000
KS ci ratio: 1.281607e-01	ci left: 5.401661e-04	ci right 6.147245e-04	k: 934	n:1620000
ALS2   1620000 perm   1586 sec   (1021 perm/sec)   p_kst 5.765432e-04   p_cons 7.065741e-02   p_joint 9.012346e-05

Joint ci ratio: 3.200518e-01	ci left: 7.732344e-05	ci right 1.073226e-04	k: 149	n:1630000
Cons ci ratio: 1.113521e-02	ci left: 7.026474e-02	ci right 7.105213e-02	k: 115172	n:1630000
KS ci ratio: 1.275481e-01	ci left: 5.421971e-04	ci right 6.166512e-04	k: 943	n:1630000
ALS2   1630000 perm   1603 sec   (1017 perm/sec)   p_kst 5.785276e-04   p_cons 7.065767e-02   p_joint 9.141104e-05

Joint ci ratio: 3.200519e-01	ci left: 7.685195e-05	ci right 1.066682e-04	k: 149	n:1640000
Cons ci ratio: 1.110082e-02	ci left: 7.027045e-02	ci right 7.105546e-02	k: 115886	n:1640000
KS ci ratio: 1.272788e-01	ci left: 5.412523e-04	ci right 6.154078e-04	k: 947	n:1640000
ALS2   1640000 perm   1620 sec   (1012 perm/sec)   p_kst 5.774390e-04   p_cons 7.066220e-02   p_joint 9.085366e-05

Joint ci ratio: 3.179392e-01	ci left: 7.750127e-05	ci right 1.073306e-04	k: 151	n:1650000
Cons ci ratio: 1.106824e-02	ci left: 7.025857e-02	ci right 7.104112e-02	k: 116571	n:1650000
KS ci ratio: 1.268780e-01	ci left: 5.414928e-04	ci right 6.154300e-04	k: 953	n:1650000
ALS2   1650000 perm   1637 sec   (1008 perm/sec)   p_kst 5.775758e-04   p_cons 7.064909e-02   p_joint 9.151515e-05

Joint ci ratio: 3.179393e-01	ci left: 7.703439e-05	ci right 1.066840e-04	k: 151	n:1660000
Cons ci ratio: 1.103548e-02	ci left: 7.025224e-02	ci right 7.103239e-02	k: 117265	n:1660000
KS ci ratio: 1.265468e-01	ci left: 5.411473e-04	ci right 6.148301e-04	k: 958	n:1660000
ALS2   1660000 perm   1654 sec   (1003 perm/sec)   p_kst 5.771084e-04   p_cons 7.064157e-02   p_joint 9.096386e-05

Joint ci ratio: 3.179394e-01	ci left: 7.657310e-05	ci right 1.060452e-04	k: 151	n:1670000
Cons ci ratio: 1.100186e-02	ci left: 7.025973e-02	ci right 7.103757e-02	k: 117982	n:1670000
KS ci ratio: 1.260874e-01	ci left: 5.419661e-04	ci right 6.154724e-04	k: 965	n:1670000
ALS2   1670000 perm   1671 sec   (999 perm/sec)   p_kst 5.778443e-04   p_cons 7.064790e-02   p_joint 9.041916e-05

Joint ci ratio: 3.168987e-01	ci left: 7.666513e-05	ci right 1.060565e-04	k: 152	n:1680000
Cons ci ratio: 1.096865e-02	ci left: 7.026594e-02	ci right 7.104149e-02	k: 118697	n:1680000
KS ci ratio: 1.258272e-01	ci left: 5.410460e-04	ci right 6.142648e-04	k: 969	n:1680000
ALS2   1680000 perm   1689 sec   (995 perm/sec)   p_kst 5.767857e-04   p_cons 7.065298e-02   p_joint 9.047619e-05

Joint ci ratio: 3.168988e-01	ci left: 7.621149e-05	ci right 1.054289e-04	k: 152	n:1690000
Cons ci ratio: 1.093810e-02	ci left: 7.024375e-02	ci right 7.101689e-02	k: 119364	n:1690000
KS ci ratio: 1.254399e-01	ci left: 5.412833e-04	ci right 6.142920e-04	k: 975	n:1690000
ALS2   1690000 perm   1706 sec   (990 perm/sec)   p_kst 5.769231e-04   p_cons 7.062959e-02   p_joint 8.994083e-05

Joint ci ratio: 3.168989e-01	ci left: 7.576319e-05	ci right 1.048087e-04	k: 152	n:1700000
Cons ci ratio: 1.090658e-02	ci left: 7.023650e-02	ci right 7.100731e-02	k: 120056	n:1700000
KS ci ratio: 1.253758e-01	ci left: 5.386690e-04	ci right 6.112852e-04	k: 976	n:1700000
ALS2   1700000 perm   1724 sec   (986 perm/sec)   p_kst 5.741176e-04   p_cons 7.062118e-02   p_joint 8.941176e-05

Joint ci ratio: 3.168989e-01	ci left: 7.532012e-05	ci right 1.041958e-04	k: 152	n:1710000
Cons ci ratio: 1.087053e-02	ci left: 7.028709e-02	ci right 7.105589e-02	k: 120847	n:1710000
KS ci ratio: 1.249926e-01	ci left: 5.389178e-04	ci right 6.113290e-04	k: 982	n:1710000
ALS2   1710000 perm   1741 sec   (982 perm/sec)   p_kst 5.742690e-04   p_cons 7.067076e-02   p_joint 8.888889e-05

Joint ci ratio: 3.168990e-01	ci left: 7.488221e-05	ci right 1.035900e-04	k: 152	n:1720000
Cons ci ratio: 1.083950e-02	ci left: 7.028083e-02	ci right 7.104736e-02	k: 121541	n:1720000
KS ci ratio: 1.246760e-01	ci left: 5.386008e-04	ci right 6.107725e-04	k: 987	n:1720000
ALS2   1720000 perm   1759 sec   (978 perm/sec)   p_kst 5.738372e-04   p_cons 7.066337e-02   p_joint 8.837209e-05

Joint ci ratio: 3.168991e-01	ci left: 7.444936e-05	ci right 1.029913e-04	k: 152	n:1730000
Cons ci ratio: 1.080958e-02	ci left: 7.026427e-02	ci right 7.102849e-02	k: 122217	n:1730000
KS ci ratio: 1.244244e-01	ci left: 5.377275e-04	ci right 6.096262e-04	k: 991	n:1730000
ALS2   1730000 perm   1777 sec   (974 perm/sec)   p_kst 5.728324e-04   p_cons 7.064566e-02   p_joint 8.786127e-05

Joint ci ratio: 3.168992e-01	ci left: 7.402149e-05	ci right 1.023994e-04	k: 152	n:1740000
Cons ci ratio: 1.077935e-02	ci left: 7.025479e-02	ci right 7.101675e-02	k: 122905	n:1740000
KS ci ratio: 1.242993e-01	ci left: 5.357508e-04	ci right 6.073078e-04	k: 993	n:1740000
ALS2   1740000 perm   1795 sec   (969 perm/sec)   p_kst 5.706897e-04   p_cons 7.063506e-02   p_joint 8.735632e-05

Joint ci ratio: 3.128359e-01	ci left: 7.570364e-05	ci right 1.042799e-04	k: 156	n:1750000
Cons ci ratio: 1.075002e-02	ci left: 7.023744e-02	ci right 7.099713e-02	k: 123579	n:1750000
KS ci ratio: 1.236786e-01	ci left: 5.382265e-04	ci right 6.097288e-04	k: 1003	n:1750000
ALS2   1750000 perm   1813 sec   (965 perm/sec)   p_kst 5.731429e-04   p_cons 7.061657e-02   p_joint 8.914286e-05

Joint ci ratio: 3.118444e-01	ci left: 7.579716e-05	ci right 1.043000e-04	k: 157	n:1760000
Cons ci ratio: 1.071963e-02	ci left: 7.023615e-02	ci right 7.099367e-02	k: 124281	n:1760000
KS ci ratio: 1.234330e-01	ci left: 5.373708e-04	ci right 6.086074e-04	k: 1007	n:1760000
ALS2   1760000 perm   1831 sec   (961 perm/sec)   p_kst 5.721591e-04   p_cons 7.061420e-02   p_joint 8.920455e-05

Joint ci ratio: 3.118444e-01	ci left: 7.536893e-05	ci right 1.037108e-04	k: 157	n:1770000
Cons ci ratio: 1.068996e-02	ci left: 7.022925e-02	ci right 7.098458e-02	k: 124973	n:1770000
KS ci ratio: 1.231280e-01	ci left: 5.370726e-04	ci right 6.080809e-04	k: 1012	n:1770000
ALS2   1770000 perm   1849 sec   (957 perm/sec)   p_kst 5.717514e-04   p_cons 7.060621e-02   p_joint 8.870056e-05

Joint ci ratio: 3.108622e-01	ci left: 7.546341e-05	ci right 1.037337e-04	k: 158	n:1780000
Cons ci ratio: 1.065888e-02	ci left: 7.024260e-02	ci right 7.099587e-02	k: 125701	n:1780000
KS ci ratio: 1.224049e-01	ci left: 5.405899e-04	ci right 6.116131e-04	k: 1024	n:1780000
ALS2   1780000 perm   1868 sec   (953 perm/sec)   p_kst 5.752809e-04   p_cons 7.061854e-02   p_joint 8.876404e-05

Joint ci ratio: 3.108623e-01	ci left: 7.504183e-05	ci right 1.031542e-04	k: 158	n:1790000
Cons ci ratio: 1.062967e-02	ci left: 7.023631e-02	ci right 7.098743e-02	k: 126394	n:1790000
KS ci ratio: 1.219891e-01	ci left: 5.413609e-04	ci right 6.122264e-04	k: 1031	n:1790000
ALS2   1790000 perm   1886 sec   (949 perm/sec)   p_kst 5.759777e-04   p_cons 7.061117e-02   p_joint 8.826816e-05

Joint ci ratio: 3.089254e-01	ci left: 7.564965e-05	ci right 1.037783e-04	k: 160	n:1800000
Cons ci ratio: 1.059777e-02	ci left: 7.026611e-02	ci right 7.101528e-02	k: 127152	n:1800000
KS ci ratio: 1.215774e-01	ci left: 5.421238e-04	ci right 6.128324e-04	k: 1038	n:1800000
ALS2   1800000 perm   1904 sec   (945 perm/sec)   p_kst 5.766667e-04   p_cons 7.064000e-02   p_joint 8.888889e-05

Joint ci ratio: 3.079704e-01	ci left: 7.574142e-05	ci right 1.038001e-04	k: 161	n:1810000
Cons ci ratio: 1.056918e-02	ci left: 7.025810e-02	ci right 7.100515e-02	k: 127842	n:1810000
KS ci ratio: 1.211699e-01	ci left: 5.428787e-04	ci right 6.134313e-04	k: 1045	n:1810000
ALS2   1810000 perm   1923 sec   (941 perm/sec)   p_kst 5.773481e-04   p_cons 7.063094e-02   p_joint 8.895028e-05

Joint ci ratio: 3.079705e-01	ci left: 7.532526e-05	ci right 1.032297e-04	k: 161	n:1820000
Cons ci ratio: 1.053902e-02	ci left: 7.027266e-02	ci right 7.101772e-02	k: 128573	n:1820000
KS ci ratio: 1.209966e-01	ci left: 5.414942e-04	ci right 6.117591e-04	k: 1048	n:1820000
ALS2   1820000 perm   1941 sec   (937 perm/sec)   p_kst 5.758242e-04   p_cons 7.064451e-02   p_joint 8.846154e-05

Joint ci ratio: 3.060868e-01	ci left: 7.592236e-05	ci right 1.038425e-04	k: 163	n:1830000
Cons ci ratio: 1.051174e-02	ci left: 7.025435e-02	ci right 7.099728e-02	k: 129244	n:1830000
KS ci ratio: 1.206520e-01	ci left: 5.417148e-04	ci right 6.117939e-04	k: 1054	n:1830000
ALS2   1830000 perm   1960 sec   (934 perm/sec)   p_kst 5.759563e-04   p_cons 7.062514e-02   p_joint 8.907104e-05

Joint ci ratio: 3.051578e-01	ci left: 7.601154e-05	ci right 1.038631e-04	k: 164	n:1840000
Cons ci ratio: 1.048445e-02	ci left: 7.023896e-02	ci right 7.097978e-02	k: 129920	n:1840000
KS ci ratio: 1.204240e-01	ci left: 5.408791e-04	ci right 6.107084e-04	k: 1058	n:1840000
ALS2   1840000 perm   1979 sec   (930 perm/sec)   p_kst 5.750000e-04   p_cons 7.060870e-02   p_joint 8.913043e-05

Joint ci ratio: 3.051579e-01	ci left: 7.560067e-05	ci right 1.033017e-04	k: 164	n:1850000
Cons ci ratio: 1.045676e-02	ci left: 7.023128e-02	ci right 7.097006e-02	k: 130610	n:1850000
KS ci ratio: 1.201972e-01	ci left: 5.400525e-04	ci right 6.096345e-04	k: 1062	n:1850000
ALS2   1850000 perm   1998 sec   (926 perm/sec)   p_kst 5.740541e-04   p_cons 7.060000e-02   p_joint 8.864865e-05

Joint ci ratio: 3.024208e-01	ci left: 7.668420e-05	ci right 1.044818e-04	k: 167	n:1860000
Cons ci ratio: 1.042819e-02	ci left: 7.023764e-02	ci right 7.097445e-02	k: 131326	n:1860000
KS ci ratio: 1.194687e-01	ci left: 5.439288e-04	ci right 6.135554e-04	k: 1075	n:1860000
ALS2   1860000 perm   2017 sec   (922 perm/sec)   p_kst 5.779570e-04   p_cons 7.060538e-02   p_joint 8.978495e-05

Joint ci ratio: 3.024209e-01	ci left: 7.627412e-05	ci right 1.039231e-04	k: 167	n:1870000
Cons ci ratio: 1.039959e-02	ci left: 7.024713e-02	ci right 7.098201e-02	k: 132048	n:1870000
KS ci ratio: 1.190270e-01	ci left: 5.451706e-04	ci right 6.146800e-04	k: 1083	n:1870000
ALS2   1870000 perm   2036 sec   (919 perm/sec)   p_kst 5.791444e-04   p_cons 7.061390e-02   p_joint 8.930481e-05

Joint ci ratio: 3.015248e-01	ci left: 7.636003e-05	ci right 1.039424e-04	k: 168	n:1880000
Cons ci ratio: 1.037304e-02	ci left: 7.023370e-02	ci right 7.096656e-02	k: 132727	n:1880000
KS ci ratio: 1.185358e-01	ci left: 5.469158e-04	ci right 6.163398e-04	k: 1092	n:1880000
ALS2   1880000 perm   2055 sec   (915 perm/sec)   p_kst 5.808511e-04   p_cons 7.059947e-02   p_joint 8.936170e-05

Joint ci ratio: 2.997563e-01	ci left: 7.693441e-05	ci right 1.045302e-04	k: 170	n:1890000
Cons ci ratio: 1.034552e-02	ci left: 7.023520e-02	ci right 7.096611e-02	k: 133434	n:1890000
KS ci ratio: 1.182118e-01	ci left: 5.471026e-04	ci right 6.163473e-04	k: 1098	n:1890000
ALS2   1890000 perm   2075 sec   (911 perm/sec)   p_kst 5.809524e-04   p_cons 7.060000e-02   p_joint 8.994709e-05

Joint ci ratio: 2.988836e-01	ci left: 7.701629e-05	ci right 1.045457e-04	k: 171	n:1900000
Cons ci ratio: 1.031983e-02	ci left: 7.021621e-02	ci right 7.094510e-02	k: 134102	n:1900000
KS ci ratio: 1.177306e-01	ci left: 5.488202e-04	ci right 6.179799e-04	k: 1107	n:1900000
ALS2   1900000 perm   2095 sec   (907 perm/sec)   p_kst 5.826316e-04   p_cons 7.058000e-02   p_joint 9.000000e-05

Joint ci ratio: 2.971608e-01	ci left: 7.758191e-05	ci right 1.051235e-04	k: 173	n:1910000
Cons ci ratio: 1.029171e-02	ci left: 7.023085e-02	ci right 7.095789e-02	k: 134834	n:1910000
KS ci ratio: 1.174131e-01	ci left: 5.489958e-04	ci right 6.179781e-04	k: 1113	n:1910000
ALS2   1910000 perm   2114 sec   (903 perm/sec)   p_kst 5.827225e-04   p_cons 7.059372e-02   p_joint 9.057592e-05

Joint ci ratio: 2.938027e-01	ci left: 7.910677e-05	ci right 1.068133e-04	k: 177	n:1920000
Cons ci ratio: 1.026694e-02	ci left: 7.020533e-02	ci right 7.093035e-02	k: 135489	n:1920000
KS ci ratio: 1.169937e-01	ci left: 5.501810e-04	ci right 6.190482e-04	k: 1121	n:1920000
ALS2   1920000 perm   2135 sec   (899 perm/sec)   p_kst 5.838542e-04   p_cons 7.056719e-02   p_joint 9.218750e-05

Joint ci ratio: 2.938028e-01	ci left: 7.869689e-05	ci right 1.062599e-04	k: 177	n:1930000
Cons ci ratio: 1.024022e-02	ci left: 7.020747e-02	ci right 7.093061e-02	k: 136197	n:1930000
KS ci ratio: 1.165788e-01	ci left: 5.513543e-04	ci right 6.201068e-04	k: 1129	n:1930000
ALS2   1930000 perm   2155 sec   (896 perm/sec)   p_kst 5.849741e-04   p_cons 7.056839e-02   p_joint 9.170984e-05

Joint ci ratio: 2.929810e-01	ci left: 7.876877e-05	ci right 1.062654e-04	k: 178	n:1940000
Cons ci ratio: 1.021394e-02	ci left: 7.020650e-02	ci right 7.092777e-02	k: 136899	n:1940000
KS ci ratio: 1.162705e-01	ci left: 5.515150e-04	ci right 6.200931e-04	k: 1135	n:1940000
ALS2   1940000 perm   2175 sec   (892 perm/sec)   p_kst 5.850515e-04   p_cons 7.056649e-02   p_joint 9.175258e-05

Joint ci ratio: 2.929810e-01	ci left: 7.836483e-05	ci right 1.057205e-04	k: 178	n:1950000
Cons ci ratio: 1.018723e-02	ci left: 7.021374e-02	ci right 7.093318e-02	k: 137617	n:1950000
KS ci ratio: 1.160664e-01	ci left: 5.506784e-04	ci right 6.190241e-04	k: 1139	n:1950000
ALS2   1950000 perm   2195 sec   (888 perm/sec)   p_kst 5.841026e-04   p_cons 7.057282e-02   p_joint 9.128205e-05

Joint ci ratio: 2.921661e-01	ci left: 7.843777e-05	ci right 1.057287e-04	k: 179	n:1960000
Cons ci ratio: 1.016084e-02	ci left: 7.021937e-02	ci right 7.093700e-02	k: 138332	n:1960000
KS ci ratio: 1.158127e-01	ci left: 5.503459e-04	ci right 6.184907e-04	k: 1144	n:1960000
ALS2   1960000 perm   2214 sec   (885 perm/sec)   p_kst 5.836735e-04   p_cons 7.057755e-02   p_joint 9.132653e-05

Joint ci ratio: 2.921661e-01	ci left: 7.803961e-05	ci right 1.051920e-04	k: 179	n:1970000
Cons ci ratio: 1.013501e-02	ci left: 7.022040e-02	ci right 7.093620e-02	k: 139038	n:1970000
KS ci ratio: 1.153102e-01	ci left: 5.524817e-04	ci right 6.205740e-04	k: 1154	n:1970000
ALS2   1970000 perm   2235 sec   (882 perm/sec)   p_kst 5.857868e-04   p_cons 7.057766e-02   p_joint 9.086294e-05

Joint ci ratio: 2.921662e-01	ci left: 7.764547e-05	ci right 1.046607e-04	k: 179	n:1980000
Cons ci ratio: 1.010844e-02	ci left: 7.023350e-02	ci right 7.094755e-02	k: 139768	n:1980000
KS ci ratio: 1.152106e-01	ci left: 5.506723e-04	ci right 6.184790e-04	k: 1156	n:1980000
ALS2   1980000 perm   2255 sec   (878 perm/sec)   p_kst 5.838384e-04   p_cons 7.058990e-02   p_joint 9.040404e-05

Joint ci ratio: 2.913580e-01	ci left: 7.772103e-05	ci right 1.046739e-04	k: 180	n:1990000
Cons ci ratio: 1.008293e-02	ci left: 7.023545e-02	ci right 7.094771e-02	k: 140476	n:1990000
KS ci ratio: 1.147650e-01	ci left: 5.522977e-04	ci right 6.200237e-04	k: 1165	n:1990000
ALS2   1990000 perm   2275 sec   (875 perm/sec)   p_kst 5.854271e-04   p_cons 7.059095e-02   p_joint 9.045226e-05

Joint ci ratio: 2.913580e-01	ci left: 7.733242e-05	ci right 1.041506e-04	k: 180	n:2000000
Cons ci ratio: 1.005738e-02	ci left: 7.024038e-02	ci right 7.095087e-02	k: 141190	n:2000000
KS ci ratio: 1.143732e-01	ci left: 5.534216e-04	ci right 6.210381e-04	k: 1173	n:2000000
ALS2   2000000 perm   2295 sec   (871 perm/sec)   p_kst 5.865000e-04   p_cons 7.059500e-02   p_joint 9.000000e-05

Joint ci ratio: 2.905565e-01	ci left: 7.740889e-05	ci right 1.041661e-04	k: 181	n:2010000
Cons ci ratio: 1.003035e-02	ci left: 7.026709e-02	ci right 7.097593e-02	k: 141948	n:2010000
KS ci ratio: 1.139373e-01	ci left: 5.550180e-04	ci right 6.225537e-04	k: 1182	n:2010000
ALS2   2010000 perm   2316 sec   (868 perm/sec)   p_kst 5.880597e-04   p_cons 7.062090e-02   p_joint 9.004975e-05

Joint ci ratio: 2.905566e-01	ci left: 7.702568e-05	ci right 1.036505e-04	k: 181	n:2020000
Cons ci ratio: 1.000558e-02	ci left: 7.026688e-02	ci right 7.097396e-02	k: 142652	n:2020000
KS ci ratio: 1.137452e-01	ci left: 5.541942e-04	ci right 6.215084e-04	k: 1186	n:2020000
ALS2   2020000 perm   2336 sec   (865 perm/sec)   p_kst 5.871287e-04   p_cons 7.061980e-02   p_joint 8.960396e-05

Joint ci ratio: 2.905566e-01	ci left: 7.664624e-05	ci right 1.031399e-04	k: 181	n:2030000
Cons ci ratio: 9.980085e-03	ci left: 7.027846e-02	ci right 7.098385e-02	k: 143380	n:2030000
KS ci ratio: 1.136018e-01	ci left: 5.529000e-04	ci right 6.199666e-04	k: 1189	n:2030000
ALS2   2030000 perm   2357 sec   (861 perm/sec)   p_kst 5.857143e-04   p_cons 7.063054e-02   p_joint 8.916256e-05

Joint ci ratio: 2.889731e-01	ci left: 7.717967e-05	ci right 1.036857e-04	k: 183	n:2040000
Cons ci ratio: 9.954008e-03	ci left: 7.030021e-02	ci right 7.100395e-02	k: 144129	n:2040000
KS ci ratio: 1.134114e-01	ci left: 5.520948e-04	ci right 6.189440e-04	k: 1193	n:2040000
ALS2   2040000 perm   2377 sec   (858 perm/sec)   p_kst 5.848039e-04   p_cons 7.065147e-02   p_joint 8.970588e-05

Joint ci ratio: 2.889732e-01	ci left: 7.680318e-05	ci right 1.031799e-04	k: 183	n:2050000
Cons ci ratio: 9.929830e-03	ci left: 7.029935e-02	ci right 7.100137e-02	k: 144832	n:2050000
KS ci ratio: 1.131747e-01	ci left: 5.517716e-04	ci right 6.184329e-04	k: 1198	n:2050000
ALS2   2050000 perm   2398 sec   (855 perm/sec)   p_kst 5.843902e-04   p_cons 7.064976e-02   p_joint 8.926829e-05

Joint ci ratio: 2.889733e-01	ci left: 7.643035e-05	ci right 1.026791e-04	k: 183	n:2060000
Cons ci ratio: 9.906780e-03	ci left: 7.028592e-02	ci right 7.098616e-02	k: 145509	n:2060000
KS ci ratio: 1.129395e-01	ci left: 5.514516e-04	ci right 6.179266e-04	k: 1203	n:2060000
ALS2   2060000 perm   2418 sec   (852 perm/sec)   p_kst 5.839806e-04   p_cons 7.063544e-02   p_joint 8.883495e-05

Joint ci ratio: 2.881912e-01	ci left: 7.650925e-05	ci right 1.027010e-04	k: 184	n:2070000
Cons ci ratio: 9.884435e-03	ci left: 7.026538e-02	ci right 7.096384e-02	k: 146171	n:2070000
KS ci ratio: 1.124732e-01	ci left: 5.534824e-04	ci right 6.199084e-04	k: 1213	n:2070000
ALS2   2070000 perm   2439 sec   (849 perm/sec)   p_kst 5.859903e-04   p_cons 7.061401e-02   p_joint 8.888889e-05

Joint ci ratio: 2.866458e-01	ci left: 7.703365e-05	ci right 1.032379e-04	k: 186	n:2080000
Cons ci ratio: 9.860000e-03	ci left: 7.027479e-02	ci right 7.097160e-02	k: 146895	n:2080000
KS ci ratio: 1.122424e-01	ci left: 5.531577e-04	ci right 6.193995e-04	k: 1218	n:2080000
ALS2   2080000 perm   2460 sec   (846 perm/sec)   p_kst 5.855769e-04   p_cons 7.062260e-02   p_joint 8.942308e-05

Joint ci ratio: 2.843737e-01	ci left: 7.799771e-05	ci right 1.042818e-04	k: 189	n:2090000
Cons ci ratio: 9.837683e-03	ci left: 7.025833e-02	ci right 7.095339e-02	k: 147565	n:2090000
KS ci ratio: 1.120587e-01	ci left: 5.523712e-04	ci right 6.184034e-04	k: 1222	n:2090000
ALS2   2090000 perm   2480 sec   (843 perm/sec)   p_kst 5.846890e-04   p_cons 7.060526e-02   p_joint 9.043062e-05

Joint ci ratio: 2.836283e-01	ci left: 7.806857e-05	ci right 1.042953e-04	k: 190	n:2100000
Cons ci ratio: 9.814768e-03	ci left: 7.025200e-02	ci right 7.094537e-02	k: 148256	n:2100000
KS ci ratio: 1.118304e-01	ci left: 5.520551e-04	ci right 6.179062e-04	k: 1227	n:2100000
ALS2   2100000 perm   2501 sec   (840 perm/sec)   p_kst 5.842857e-04   p_cons 7.059810e-02   p_joint 9.047619e-05

Joint ci ratio: 2.828887e-01	ci left: 7.813885e-05	ci right 1.043085e-04	k: 191	n:2110000
Cons ci ratio: 9.791765e-03	ci left: 7.024905e-02	ci right 7.094076e-02	k: 148954	n:2110000
KS ci ratio: 1.114678e-01	ci left: 5.531243e-04	ci right 6.188750e-04	k: 1235	n:2110000
ALS2   2110000 perm   2522 sec   (836 perm/sec)   p_kst 5.853081e-04   p_cons 7.059431e-02   p_joint 9.052133e-05

Joint ci ratio: 2.821549e-01	ci left: 7.820855e-05	ci right 1.043215e-04	k: 192	n:2120000
Cons ci ratio: 9.768396e-03	ci left: 7.025318e-02	ci right 7.094327e-02	k: 149667	n:2120000
KS ci ratio: 1.111982e-01	ci left: 5.532666e-04	ci right 6.188648e-04	k: 1241	n:2120000
ALS2   2120000 perm   2544 sec   (833 perm/sec)   p_kst 5.853774e-04   p_cons 7.059764e-02   p_joint 9.056604e-05

Joint ci ratio: 2.821549e-01	ci left: 7.784137e-05	ci right 1.038317e-04	k: 192	n:2130000
Cons ci ratio: 9.744044e-03	ci left: 7.027274e-02	ci right 7.096129e-02	k: 150413	n:2130000
KS ci ratio: 1.109751e-01	ci left: 5.529513e-04	ci right 6.183719e-04	k: 1246	n:2130000
ALS2   2130000 perm   2565 sec   (830 perm/sec)   p_kst 5.849765e-04   p_cons 7.061643e-02   p_joint 9.014085e-05

Joint ci ratio: 2.821550e-01	ci left: 7.747762e-05	ci right 1.033466e-04	k: 192	n:2140000
Cons ci ratio: 9.720980e-03	ci left: 7.027720e-02	ci right 7.096415e-02	k: 151127	n:2140000
KS ci ratio: 1.107533e-01	ci left: 5.526391e-04	ci right 6.178836e-04	k: 1251	n:2140000
ALS2   2140000 perm   2587 sec   (827 perm/sec)   p_kst 5.845794e-04   p_cons 7.062009e-02   p_joint 8.971963e-05

Joint ci ratio: 2.821550e-01	ci left: 7.711726e-05	ci right 1.028659e-04	k: 192	n:2150000
Cons ci ratio: 9.698697e-03	ci left: 7.027326e-02	ci right 7.095859e-02	k: 151823	n:2150000
KS ci ratio: 1.106209e-01	ci left: 5.514254e-04	ci right 6.164437e-04	k: 1254	n:2150000
ALS2   2150000 perm   2608 sec   (824 perm/sec)   p_kst 5.832558e-04   p_cons 7.061535e-02   p_joint 8.930233e-05

Joint ci ratio: 2.821551e-01	ci left: 7.676023e-05	ci right 1.023896e-04	k: 192	n:2160000
Cons ci ratio: 9.676431e-03	ci left: 7.027121e-02	ci right 7.095494e-02	k: 152523	n:2160000
KS ci ratio: 1.104451e-01	ci left: 5.506731e-04	ci right 6.154928e-04	k: 1258	n:2160000
ALS2   2160000 perm   2629 sec   (822 perm/sec)   p_kst 5.824074e-04   p_cons 7.061250e-02   p_joint 8.888889e-05

Joint ci ratio: 2.821552e-01	ci left: 7.640650e-05	ci right 1.019178e-04	k: 192	n:2170000
Cons ci ratio: 9.655164e-03	ci left: 7.025769e-02	ci right 7.093977e-02	k: 153198	n:2170000
KS ci ratio: 1.102265e-01	ci left: 5.503760e-04	ci right 6.150241e-04	k: 1263	n:2170000
ALS2   2170000 perm   2650 sec   (819 perm/sec)   p_kst 5.820276e-04   p_cons 7.059816e-02   p_joint 8.847926e-05

Joint ci ratio: 2.821552e-01	ci left: 7.605601e-05	ci right 1.014503e-04	k: 192	n:2180000
Cons ci ratio: 9.632657e-03	ci left: 7.026305e-02	ci right 7.094359e-02	k: 153914	n:2180000
KS ci ratio: 1.099658e-01	ci left: 5.505279e-04	ci right 6.150310e-04	k: 1269	n:2180000
ALS2   2180000 perm   2672 sec   (816 perm/sec)   p_kst 5.821101e-04   p_cons 7.060275e-02   p_joint 8.807339e-05

Joint ci ratio: 2.799874e-01	ci left: 7.698204e-05	ci right 1.024532e-04	k: 195	n:2190000
Cons ci ratio: 9.610005e-03	ci left: 7.027247e-02	ci right 7.095149e-02	k: 154639	n:2190000
KS ci ratio: 1.097500e-01	ci left: 5.502344e-04	ci right 6.145684e-04	k: 1274	n:2190000
ALS2   2190000 perm   2693 sec   (813 perm/sec)   p_kst 5.817352e-04   p_cons 7.061142e-02   p_joint 8.904110e-05

Joint ci ratio: 2.792759e-01	ci left: 7.705480e-05	ci right 1.024738e-04	k: 196	n:2200000
Cons ci ratio: 9.588309e-03	ci left: 7.027092e-02	ci right 7.094839e-02	k: 155340	n:2200000
KS ci ratio: 1.095783e-01	ci left: 5.495016e-04	ci right 6.136430e-04	k: 1278	n:2200000
ALS2   2200000 perm   2715 sec   (810 perm/sec)   p_kst 5.809091e-04   p_cons 7.060909e-02   p_joint 8.909091e-05

Joint ci ratio: 2.785697e-01	ci left: 7.712698e-05	ci right 1.024942e-04	k: 197	n:2210000
Cons ci ratio: 9.567749e-03	ci left: 7.025585e-02	ci right 7.093171e-02	k: 156011	n:2210000
KS ci ratio: 1.092796e-01	ci left: 5.500960e-04	ci right 6.141204e-04	k: 1285	n:2210000
ALS2   2210000 perm   2738 sec   (807 perm/sec)   p_kst 5.814480e-04   p_cons 7.059321e-02   p_joint 8.914027e-05

Joint ci ratio: 2.771733e-01	ci left: 7.761770e-05	ci right 1.029960e-04	k: 199	n:2220000
Cons ci ratio: 9.547715e-03	ci left: 7.023551e-02	ci right 7.090975e-02	k: 156670	n:2220000
KS ci ratio: 1.089834e-01	ci left: 5.506851e-04	ci right 6.145933e-04	k: 1292	n:2220000
ALS2   2220000 perm   2760 sec   (804 perm/sec)   p_kst 5.819820e-04   p_cons 7.057207e-02   p_joint 8.963964e-05

Joint ci ratio: 2.771734e-01	ci left: 7.726963e-05	ci right 1.025342e-04	k: 199	n:2230000
Cons ci ratio: 9.526404e-03	ci left: 7.023460e-02	ci right 7.090732e-02	k: 157372	n:2230000
KS ci ratio: 1.087314e-01	ci left: 5.508330e-04	ci right 6.146011e-04	k: 1298	n:2230000
ALS2   2230000 perm   2782 sec   (802 perm/sec)   p_kst 5.820628e-04   p_cons 7.057040e-02   p_joint 8.923767e-05

Joint ci ratio: 2.764830e-01	ci left: 7.734012e-05	ci right 1.025538e-04	k: 200	n:2240000
Cons ci ratio: 9.502973e-03	ci left: 7.026488e-02	ci right 7.093623e-02	k: 158144	n:2240000
KS ci ratio: 1.086061e-01	ci left: 5.496768e-04	ci right 6.132330e-04	k: 1301	n:2240000
ALS2   2240000 perm   2804 sec   (799 perm/sec)   p_kst 5.808036e-04   p_cons 7.060000e-02   p_joint 8.928571e-05

Joint ci ratio: 2.751176e-01	ci left: 7.782382e-05	ci right 1.030482e-04	k: 202	n:2250000
Cons ci ratio: 9.482121e-03	ci left: 7.026164e-02	ci right 7.093147e-02	k: 158841	n:2250000
KS ci ratio: 1.082326e-01	ci left: 5.511254e-04	ci right 6.146159e-04	k: 1310	n:2250000
ALS2   2250000 perm   2826 sec   (796 perm/sec)   p_kst 5.822222e-04   p_cons 7.059600e-02   p_joint 8.977778e-05

Joint ci ratio: 2.751176e-01	ci left: 7.747946e-05	ci right 1.025922e-04	k: 202	n:2260000
Cons ci ratio: 9.460927e-03	ci left: 7.026504e-02	ci right 7.093340e-02	k: 159553	n:2260000
KS ci ratio: 1.081502e-01	ci left: 5.495477e-04	ci right 6.128053e-04	k: 1312	n:2260000
ALS2   2260000 perm   2849 sec   (793 perm/sec)   p_kst 5.805310e-04   p_cons 7.059867e-02   p_joint 8.938053e-05

Joint ci ratio: 2.737723e-01	ci left: 7.795858e-05	ci right 1.030818e-04	k: 204	n:2270000
Cons ci ratio: 9.438955e-03	ci left: 7.028117e-02	ci right 7.094812e-02	k: 160294	n:2270000
KS ci ratio: 1.078631e-01	ci left: 5.501272e-04	ci right 6.132727e-04	k: 1319	n:2270000
ALS2   2270000 perm   2871 sec   (791 perm/sec)   p_kst 5.810573e-04   p_cons 7.061410e-02   p_joint 8.986784e-05

Joint ci ratio: 2.737723e-01	ci left: 7.761665e-05	ci right 1.026297e-04	k: 204	n:2280000
Cons ci ratio: 9.416853e-03	ci left: 7.030109e-02	ci right 7.096667e-02	k: 161044	n:2280000
KS ci ratio: 1.076187e-01	ci left: 5.502751e-04	ci right 6.132853e-04	k: 1325	n:2280000
ALS2   2280000 perm   2893 sec   (788 perm/sec)   p_kst 5.811404e-04   p_cons 7.063333e-02   p_joint 8.947368e-05

Joint ci ratio: 2.724465e-01	ci left: 7.809128e-05	ci right 1.031145e-04	k: 206	n:2290000
Cons ci ratio: 9.394812e-03	ci left: 7.032215e-02	ci right 7.098636e-02	k: 161797	n:2290000
KS ci ratio: 1.073761e-01	ci left: 5.504218e-04	ci right 6.132977e-04	k: 1331	n:2290000
ALS2   2290000 perm   2916 sec   (785 perm/sec)   p_kst 5.812227e-04   p_cons 7.065371e-02   p_joint 8.995633e-05

Joint ci ratio: 2.724465e-01	ci left: 7.775175e-05	ci right 1.026662e-04	k: 206	n:2300000
Cons ci ratio: 9.374073e-03	ci left: 7.032698e-02	ci right 7.098976e-02	k: 162513	n:2300000
KS ci ratio: 1.072554e-01	ci left: 5.492979e-04	ci right 6.119706e-04	k: 1334	n:2300000
ALS2   2300000 perm   2938 sec   (783 perm/sec)   p_kst 5.800000e-04   p_cons 7.065783e-02   p_joint 8.956522e-05

Joint ci ratio: 2.724466e-01	ci left: 7.741516e-05	ci right 1.022218e-04	k: 206	n:2310000
Cons ci ratio: 9.353378e-03	ci left: 7.033306e-02	ci right 7.099442e-02	k: 163232	n:2310000
KS ci ratio: 1.070951e-01	ci left: 5.486052e-04	ci right 6.110994e-04	k: 1338	n:2310000
ALS2   2310000 perm   2960 sec   (780 perm/sec)   p_kst 5.792208e-04   p_cons 7.066320e-02   p_joint 8.917749e-05

Joint ci ratio: 2.724466e-01	ci left: 7.708148e-05	ci right 1.017812e-04	k: 206	n:2320000
Cons ci ratio: 9.333983e-03	ci left: 7.032275e-02	ci right 7.098263e-02	k: 163913	n:2320000
KS ci ratio: 1.070153e-01	ci left: 5.470795e-04	ci right 6.093505e-04	k: 1340	n:2320000
ALS2   2320000 perm   2983 sec   (778 perm/sec)   p_kst 5.775862e-04   p_cons 7.065216e-02   p_joint 8.879310e-05

Joint ci ratio: 2.711399e-01	ci left: 7.755054e-05	ci right 1.022611e-04	k: 208	n:2330000
Cons ci ratio: 9.314465e-03	ci left: 7.031595e-02	ci right 7.097439e-02	k: 164602	n:2330000
KS ci ratio: 1.066975e-01	ci left: 5.480732e-04	ci right 6.102605e-04	k: 1348	n:2330000
ALS2   2330000 perm   3006 sec   (775 perm/sec)   p_kst 5.785408e-04   p_cons 7.064464e-02   p_joint 8.927039e-05

Joint ci ratio: 2.711399e-01	ci left: 7.721912e-05	ci right 1.018240e-04	k: 208	n:2340000
Cons ci ratio: 9.294645e-03	ci left: 7.031518e-02	ci right 7.097220e-02	k: 165305	n:2340000
KS ci ratio: 1.063825e-01	ci left: 5.490588e-04	ci right 6.111624e-04	k: 1356	n:2340000
ALS2   2340000 perm   3029 sec   (772 perm/sec)   p_kst 5.794872e-04   p_cons 7.064316e-02   p_joint 8.888889e-05

Joint ci ratio: 2.698518e-01	ci left: 7.768389e-05	ci right 1.022994e-04	k: 210	n:2350000
Cons ci ratio: 9.274952e-03	ci left: 7.031442e-02	ci right 7.097004e-02	k: 166008	n:2350000
KS ci ratio: 1.062261e-01	ci left: 5.483792e-04	ci right 6.103090e-04	k: 1360	n:2350000
ALS2   2350000 perm   3053 sec   (770 perm/sec)   p_kst 5.787234e-04   p_cons 7.064170e-02   p_joint 8.936170e-05

Joint ci ratio: 2.692146e-01	ci left: 7.774982e-05	ci right 1.023182e-04	k: 211	n:2360000
Cons ci ratio: 9.254756e-03	ci left: 7.032255e-02	ci right 7.097681e-02	k: 166732	n:2360000
KS ci ratio: 1.060315e-01	ci left: 5.481180e-04	ci right 6.098979e-04	k: 1365	n:2360000
ALS2   2360000 perm   3076 sec   (767 perm/sec)   p_kst 5.783898e-04   p_cons 7.064915e-02   p_joint 8.940678e-05

Joint ci ratio: 2.692146e-01	ci left: 7.742176e-05	ci right 1.018865e-04	k: 211	n:2370000
Cons ci ratio: 9.236175e-03	ci left: 7.030956e-02	ci right 7.096237e-02	k: 167406	n:2370000
KS ci ratio: 1.058766e-01	ci left: 5.474483e-04	ci right 6.090569e-04	k: 1369	n:2370000
ALS2   2370000 perm   3099 sec   (765 perm/sec)   p_kst 5.776371e-04   p_cons 7.063544e-02   p_joint 8.902954e-05

Joint ci ratio: 2.692147e-01	ci left: 7.709645e-05	ci right 1.014584e-04	k: 211	n:2380000
Cons ci ratio: 9.216348e-03	ci left: 7.031597e-02	ci right 7.096743e-02	k: 168126	n:2380000
KS ci ratio: 1.057610e-01	ci left: 5.463752e-04	ci right 6.077917e-04	k: 1372	n:2380000
ALS2   2380000 perm   3122 sec   (762 perm/sec)   p_kst 5.764706e-04   p_cons 7.064118e-02   p_joint 8.865546e-05

Joint ci ratio: 2.692147e-01	ci left: 7.677387e-05	ci right 1.010339e-04	k: 211	n:2390000
Cons ci ratio: 9.198056e-03	ci left: 7.030228e-02	ci right 7.095232e-02	k: 168798	n:2390000
KS ci ratio: 1.055689e-01	ci left: 5.461259e-04	ci right 6.073960e-04	k: 1377	n:2390000
ALS2   2390000 perm   3146 sec   (760 perm/sec)   p_kst 5.761506e-04   p_cons 7.062678e-02   p_joint 8.828452e-05

Joint ci ratio: 2.685820e-01	ci left: 7.684256e-05	ci right 1.010576e-04	k: 212	n:2400000
Cons ci ratio: 9.178182e-03	ci left: 7.031282e-02	ci right 7.096155e-02	k: 169528	n:2400000
KS ci ratio: 1.053018e-01	ci left: 5.466901e-04	ci right 6.078587e-04	k: 1384	n:2400000
ALS2   2400000 perm   3169 sec   (757 perm/sec)   p_kst 5.766667e-04   p_cons 7.063667e-02   p_joint 8.833333e-05

Joint ci ratio: 2.679537e-01	ci left: 7.691075e-05	ci right 1.010811e-04	k: 213	n:2410000
Cons ci ratio: 9.159739e-03	ci left: 7.030465e-02	ci right 7.095199e-02	k: 170213	n:2410000
KS ci ratio: 1.050367e-01	ci left: 5.472499e-04	ci right 6.083174e-04	k: 1391	n:2410000
ALS2   2410000 perm   3193 sec   (755 perm/sec)   p_kst 5.771784e-04   p_cons 7.062780e-02   p_joint 8.838174e-05

Joint ci ratio: 2.673298e-01	ci left: 7.697843e-05	ci right 1.011042e-04	k: 214	n:2420000
Cons ci ratio: 9.140112e-03	ci left: 7.031510e-02	ci right 7.096114e-02	k: 170943	n:2420000
KS ci ratio: 1.047735e-01	ci left: 5.478052e-04	ci right 6.087721e-04	k: 1398	n:2420000
ALS2   2420000 perm   3217 sec   (752 perm/sec)   p_kst 5.776860e-04   p_cons 7.063760e-02   p_joint 8.842975e-05

Joint ci ratio: 2.667103e-01	ci left: 7.704563e-05	ci right 1.011272e-04	k: 215	n:2430000
Cons ci ratio: 9.121554e-03	ci left: 7.031191e-02	ci right 7.095660e-02	k: 171640	n:2430000
KS ci ratio: 1.046241e-01	ci left: 5.471538e-04	ci right 6.079561e-04	k: 1402	n:2430000
ALS2   2430000 perm   3240 sec   (750 perm/sec)   p_kst 5.769547e-04   p_cons 7.063374e-02   p_joint 8.847737e-05

Joint ci ratio: 2.667104e-01	ci left: 7.672986e-05	ci right 1.007127e-04	k: 215	n:2440000
Cons ci ratio: 9.103478e-03	ci left: 7.030344e-02	ci right 7.094676e-02	k: 172324	n:2440000
KS ci ratio: 1.044382e-01	ci left: 5.469070e-04	ci right 6.075672e-04	k: 1407	n:2440000
ALS2   2440000 perm   3264 sec   (747 perm/sec)   p_kst 5.766393e-04   p_cons 7.062459e-02   p_joint 8.811475e-05

Joint ci ratio: 2.667104e-01	ci left: 7.641668e-05	ci right 1.003017e-04	k: 215	n:2450000
Cons ci ratio: 9.085029e-03	ci left: 7.030195e-02	ci right 7.094396e-02	k: 173025	n:2450000
KS ci ratio: 1.043642e-01	ci left: 5.454697e-04	ci right 6.059250e-04	k: 1409	n:2450000
ALS2   2450000 perm   3288 sec   (745 perm/sec)   p_kst 5.751020e-04   p_cons 7.062245e-02   p_joint 8.775510e-05

Joint ci ratio: 2.654841e-01	ci left: 7.686482e-05	ci right 1.007610e-04	k: 217	n:2460000
Cons ci ratio: 9.064839e-03	ci left: 7.032726e-02	ci right 7.096806e-02	k: 173792	n:2460000
KS ci ratio: 1.040326e-01	ci left: 5.468155e-04	ci right 6.072157e-04	k: 1418	n:2460000
ALS2   2460000 perm   3312 sec   (743 perm/sec)   p_kst 5.764228e-04   p_cons 7.064715e-02   p_joint 8.821138e-05

Joint ci ratio: 2.654841e-01	ci left: 7.655363e-05	ci right 1.003531e-04	k: 217	n:2470000
Cons ci ratio: 9.046958e-03	ci left: 7.032085e-02	ci right 7.096032e-02	k: 174481	n:2470000
KS ci ratio: 1.039595e-01	ci left: 5.453904e-04	ci right 6.055881e-04	k: 1420	n:2470000
ALS2   2470000 perm   3336 sec   (740 perm/sec)   p_kst 5.748988e-04   p_cons 7.064008e-02   p_joint 8.785425e-05

Joint ci ratio: 2.648773e-01	ci left: 7.662137e-05	ci right 1.003784e-04	k: 218	n:2480000
Cons ci ratio: 9.028267e-03	ci left: 7.032777e-02	ci right 7.096598e-02	k: 175203	n:2480000
KS ci ratio: 1.035955e-01	ci left: 5.471188e-04	ci right 6.072831e-04	k: 1430	n:2480000
ALS2   2480000 perm   3360 sec   (738 perm/sec)   p_kst 5.766129e-04   p_cons 7.064637e-02   p_joint 8.790323e-05

Joint ci ratio: 2.642746e-01	ci left: 7.668862e-05	ci right 1.004035e-04	k: 219	n:2490000
Cons ci ratio: 9.011538e-03	ci left: 7.030778e-02	ci right 7.094462e-02	k: 175858	n:2490000
KS ci ratio: 1.033790e-01	ci left: 5.472688e-04	ci right 6.073162e-04	k: 1436	n:2490000
ALS2   2490000 perm   3384 sec   (736 perm/sec)   p_kst 5.767068e-04   p_cons 7.062570e-02   p_joint 8.795181e-05

Joint ci ratio: 2.642747e-01	ci left: 7.638187e-05	ci right 1.000019e-04	k: 219	n:2500000
Cons ci ratio: 8.992737e-03	ci left: 7.031949e-02	ci right 7.095510e-02	k: 176592	n:2500000
KS ci ratio: 1.030924e-01	ci left: 5.481972e-04	ci right 6.081695e-04	k: 1444	n:2500000
ALS2   2500000 perm   3409 sec   (733 perm/sec)   p_kst 5.776000e-04   p_cons 7.063680e-02   p_joint 8.760000e-05

Joint ci ratio: 2.636761e-01	ci left: 7.644960e-05	ci right 1.000282e-04	k: 220	n:2510000
Cons ci ratio: 8.974679e-03	ci left: 7.032197e-02	ci right 7.095631e-02	k: 177303	n:2510000
KS ci ratio: 1.029145e-01	ci left: 5.479538e-04	ci right 6.077898e-04	k: 1449	n:2510000
ALS2   2510000 perm   3433 sec   (731 perm/sec)   p_kst 5.772908e-04   p_cons 7.063865e-02   p_joint 8.764940e-05

Joint ci ratio: 2.630815e-01	ci left: 7.651686e-05	ci right 1.000542e-04	k: 221	n:2520000
Cons ci ratio: 8.957542e-03	ci left: 7.031254e-02	ci right 7.094559e-02	k: 177984	n:2520000
KS ci ratio: 1.026669e-01	ci left: 5.484858e-04	ci right 6.082271e-04	k: 1456	n:2520000
ALS2   2520000 perm   3457 sec   (729 perm/sec)   p_kst 5.777778e-04   p_cons 7.062857e-02   p_joint 8.769841e-05

Joint ci ratio: 2.630816e-01	ci left: 7.621442e-05	ci right 9.965872e-05	k: 221	n:2530000
Cons ci ratio: 8.939910e-03	ci left: 7.031187e-02	ci right 7.094366e-02	k: 178687	n:2530000
KS ci ratio: 1.024212e-01	ci left: 5.490137e-04	ci right 6.086608e-04	k: 1463	n:2530000
ALS2   2530000 perm   3482 sec   (727 perm/sec)   p_kst 5.782609e-04   p_cons 7.062727e-02   p_joint 8.735178e-05

Joint ci ratio: 2.624910e-01	ci left: 7.628213e-05	ci right 9.968594e-05	k: 222	n:2540000
Cons ci ratio: 8.920831e-03	ci left: 7.033399e-02	ci right 7.096462e-02	k: 179448	n:2540000
KS ci ratio: 1.023165e-01	ci left: 5.480031e-04	ci right 6.074758e-04	k: 1466	n:2540000
ALS2   2540000 perm   3506 sec   (724 perm/sec)   p_kst 5.771654e-04   p_cons 7.064882e-02   p_joint 8.740157e-05

Joint ci ratio: 2.619045e-01	ci left: 7.634937e-05	ci right 9.971289e-05	k: 223	n:2550000
Cons ci ratio: 8.904372e-03	ci left: 7.031916e-02	ci right 7.094849e-02	k: 180115	n:2550000
KS ci ratio: 1.021079e-01	ci left: 5.481468e-04	ci right 6.075067e-04	k: 1472	n:2550000
ALS2   2550000 perm   3531 sec   (722 perm/sec)   p_kst 5.772549e-04   p_cons 7.063333e-02   p_joint 8.745098e-05

Joint ci ratio: 2.619045e-01	ci left: 7.605113e-05	ci right 9.932339e-05	k: 223	n:2560000
Cons ci ratio: 8.886946e-03	ci left: 7.032003e-02	ci right 7.094813e-02	k: 180822	n:2560000
KS ci ratio: 1.019695e-01	ci left: 5.475282e-04	ci right 6.067360e-04	k: 1476	n:2560000
ALS2   2560000 perm   3556 sec   (720 perm/sec)   p_kst 5.765625e-04   p_cons 7.063359e-02   p_joint 8.710938e-05

Joint ci ratio: 2.619046e-01	ci left: 7.575521e-05	ci right 9.893692e-05	k: 223	n:2570000
Cons ci ratio: 8.869990e-03	ci left: 7.031546e-02	ci right 7.094232e-02	k: 181515	n:2570000
KS ci ratio: 1.019006e-01	ci left: 5.461561e-04	ci right 6.051732e-04	k: 1478	n:2570000
ALS2   2570000 perm   3582 sec   (718 perm/sec)   p_kst 5.750973e-04   p_cons 7.062840e-02   p_joint 8.677043e-05

Joint ci ratio: 2.613219e-01	ci left: 7.582376e-05	ci right 9.896640e-05	k: 224	n:2580000
Cons ci ratio: 8.852739e-03	ci left: 7.031673e-02	ci right 7.094237e-02	k: 182223	n:2580000
KS ci ratio: 1.015919e-01	ci left: 5.474389e-04	ci right 6.064046e-04	k: 1487	n:2580000
ALS2   2580000 perm   3606 sec   (715 perm/sec)   p_kst 5.763566e-04   p_cons 7.062907e-02   p_joint 8.682171e-05

Joint ci ratio: 2.607431e-01	ci left: 7.589185e-05	ci right 9.899559e-05	k: 225	n:2590000
Cons ci ratio: 8.836965e-03	ci left: 7.029757e-02	ci right 7.092192e-02	k: 182878	n:2590000
KS ci ratio: 1.014557e-01	ci left: 5.468304e-04	ci right 6.056469e-04	k: 1491	n:2590000
ALS2   2590000 perm   3631 sec   (713 perm/sec)   p_kst 5.756757e-04   p_cons 7.060927e-02   p_joint 8.687259e-05

Joint ci ratio: 2.607431e-01	ci left: 7.559995e-05	ci right 9.861484e-05	k: 225	n:2600000
Cons ci ratio: 8.820991e-03	ci left: 7.028278e-02	ci right 7.090587e-02	k: 183544	n:2600000
KS ci ratio: 1.013539e-01	ci left: 5.458518e-04	ci right 6.045006e-04	k: 1494	n:2600000
ALS2   2600000 perm   3656 sec   (711 perm/sec)   p_kst 5.746154e-04   p_cons 7.059385e-02   p_joint 8.653846e-05

Joint ci ratio: 2.601682e-01	ci left: 7.566843e-05	ci right 9.864511e-05	k: 226	n:2610000
Cons ci ratio: 8.803484e-03	ci left: 7.029220e-02	ci right 7.091412e-02	k: 184273	n:2610000
KS ci ratio: 1.012186e-01	ci left: 5.452541e-04	ci right 6.037559e-04	k: 1498	n:2610000
ALS2   2610000 perm   3682 sec   (709 perm/sec)   p_kst 5.739464e-04   p_cons 7.060268e-02   p_joint 8.659004e-05

Joint ci ratio: 2.601682e-01	ci left: 7.537962e-05	ci right 9.826860e-05	k: 226	n:2620000
Cons ci ratio: 8.786719e-03	ci left: 7.029202e-02	ci right 7.091275e-02	k: 184977	n:2620000
KS ci ratio: 1.010167e-01	ci left: 5.454052e-04	ci right 6.037995e-04	k: 1504	n:2620000
ALS2   2620000 perm   3707 sec   (707 perm/sec)   p_kst 5.740458e-04   p_cons 7.060191e-02   p_joint 8.625954e-05

Joint ci ratio: 2.601683e-01	ci left: 7.509300e-05	ci right 9.789496e-05	k: 226	n:2630000
Cons ci ratio: 8.769186e-03	ci left: 7.030474e-02	ci right 7.092434e-02	k: 185715	n:2630000
KS ci ratio: 1.006494e-01	ci left: 5.474084e-04	ci right 6.057916e-04	k: 1515	n:2630000
ALS2   2630000 perm   3733 sec   (705 perm/sec)   p_kst 5.760456e-04   p_cons 7.061407e-02   p_joint 8.593156e-05

Joint ci ratio: 2.595971e-01	ci left: 7.516267e-05	ci right 9.792755e-05	k: 227	n:2640000
Cons ci ratio: 8.753172e-03	ci left: 7.029620e-02	ci right 7.091459e-02	k: 186397	n:2640000
KS ci ratio: 1.004838e-01	ci left: 5.471812e-04	ci right 6.054385e-04	k: 1520	n:2640000
ALS2   2640000 perm   3760 sec   (702 perm/sec)   p_kst 5.757576e-04   p_cons 7.060492e-02   p_joint 8.598485e-05

Joint ci ratio: 2.595971e-01	ci left: 7.487904e-05	ci right 9.755802e-05	k: 227	n:2650000
Cons ci ratio: 8.735939e-03	ci left: 7.030731e-02	ci right 7.092457e-02	k: 187131	n:2650000
KS ci ratio: 1.003191e-01	ci left: 5.469558e-04	ci right 6.050880e-04	k: 1525	n:2650000
ALS2   2650000 perm   3786 sec   (700 perm/sec)   p_kst 5.754717e-04   p_cons 7.061547e-02   p_joint 8.566038e-05

Joint ci ratio: 2.584659e-01	ci left: 7.530061e-05	ci right 9.799184e-05	k: 229	n:2660000
Cons ci ratio: 8.719407e-03	ci left: 7.030933e-02	ci right 7.092544e-02	k: 187841	n:2660000
KS ci ratio: 1.001225e-01	ci left: 5.470987e-04	ci right 6.051253e-04	k: 1531	n:2660000
ALS2   2660000 perm   3813 sec   (698 perm/sec)   p_kst 5.755639e-04   p_cons 7.061692e-02   p_joint 8.609023e-05

Joint ci ratio: 2.579059e-01	ci left: 7.536888e-05	ci right 9.802355e-05	k: 230	n:2670000
Cons ci ratio: 8.702968e-03	ci left: 7.031134e-02	ci right 7.092630e-02	k: 188551	n:2670000
KS ci ratio: 9.992697e-02	ci left: 5.472406e-04	ci right 6.051623e-04	k: 1537	n:2670000
ALS2   2670000 perm   3839 sec   (695 perm/sec)   p_kst 5.756554e-04   p_cons 7.061835e-02   p_joint 8.614232e-05

Joint ci ratio: 2.579059e-01	ci left: 7.508765e-05	ci right 9.765779e-05	k: 230	n:2680000
Cons ci ratio: 8.686449e-03	ci left: 7.031594e-02	ci right 7.092976e-02	k: 189268	n:2680000
KS ci ratio: 9.976494e-02	ci left: 5.470177e-04	ci right 6.048165e-04	k: 1542	n:2680000
ALS2   2680000 perm   3865 sec   (693 perm/sec)   p_kst 5.753731e-04   p_cons 7.062239e-02   p_joint 8.582090e-05

Joint ci ratio: 2.579059e-01	ci left: 7.480851e-05	ci right 9.729475e-05	k: 230	n:2690000
Cons ci ratio: 8.670073e-03	ci left: 7.031977e-02	ci right 7.093246e-02	k: 189983	n:2690000
KS ci ratio: 9.970042e-02	ci left: 5.457091e-04	ci right 6.033302e-04	k: 1544	n:2690000
ALS2   2690000 perm   3891 sec   (691 perm/sec)   p_kst 5.739777e-04   p_cons 7.062565e-02   p_joint 8.550186e-05

Joint ci ratio: 2.579060e-01	ci left: 7.453144e-05	ci right 9.693440e-05	k: 230	n:2700000
Cons ci ratio: 8.653520e-03	ci left: 7.032763e-02	ci right 7.093922e-02	k: 190709	n:2700000
KS ci ratio: 9.963602e-02	ci left: 5.444103e-04	ci right 6.018549e-04	k: 1546	n:2700000
ALS2   2700000 perm   3917 sec   (689 perm/sec)   p_kst 5.725926e-04   p_cons 7.063296e-02   p_joint 8.518519e-05

Joint ci ratio: 2.567967e-01	ci left: 7.494683e-05	ci right 9.736222e-05	k: 232	n:2710000
Cons ci ratio: 8.636844e-03	ci left: 7.033875e-02	ci right 7.094925e-02	k: 191444	n:2710000
KS ci ratio: 9.941134e-02	ci left: 5.449201e-04	ci right 6.022813e-04	k: 1553	n:2710000
ALS2   2710000 perm   3944 sec   (687 perm/sec)   p_kst 5.730627e-04   p_cons 7.064354e-02   p_joint 8.560886e-05

Joint ci ratio: 2.562473e-01	ci left: 7.501530e-05	ci right 9.739550e-05	k: 233	n:2720000
Cons ci ratio: 8.621036e-03	ci left: 7.033805e-02	ci right 7.094742e-02	k: 192147	n:2720000
KS ci ratio: 9.915640e-02	ci left: 5.457849e-04	ci right 6.030812e-04	k: 1561	n:2720000
ALS2   2720000 perm   3971 sec   (685 perm/sec)   p_kst 5.738971e-04   p_cons 7.064228e-02   p_joint 8.566176e-05

Joint ci ratio: 2.546203e-01	ci left: 7.576908e-05	ci right 9.820784e-05	k: 236	n:2730000
Cons ci ratio: 8.605098e-03	ci left: 7.034065e-02	ci right 7.094891e-02	k: 192859	n:2730000
KS ci ratio: 9.893494e-02	ci left: 5.462863e-04	ci right 6.034997e-04	k: 1568	n:2730000
ALS2   2730000 perm   3996 sec   (683 perm/sec)   p_kst 5.743590e-04   p_cons 7.064432e-02   p_joint 8.644689e-05

Joint ci ratio: 2.530238e-01	ci left: 7.651779e-05	ci right 9.901380e-05	k: 239	n:2740000
Cons ci ratio: 8.590633e-03	ci left: 7.032210e-02	ci right 7.092917e-02	k: 193513	n:2740000
KS ci ratio: 9.880910e-02	ci left: 5.457163e-04	ci right 6.027931e-04	k: 1572	n:2740000
ALS2   2740000 perm   4023 sec   (681 perm/sec)   p_kst 5.737226e-04   p_cons 7.062518e-02   p_joint 8.722628e-05

Joint ci ratio: 2.514570e-01	ci left: 7.726150e-05	ci right 9.981347e-05	k: 242	n:2750000
Cons ci ratio: 8.575623e-03	ci left: 7.031312e-02	ci right 7.091905e-02	k: 194193	n:2750000
KS ci ratio: 9.858995e-02	ci left: 5.462145e-04	ci right 6.032094e-04	k: 1579	n:2750000
ALS2   2750000 perm   4049 sec   (679 perm/sec)   p_kst 5.741818e-04   p_cons 7.061564e-02   p_joint 8.800000e-05

Joint ci ratio: 2.514570e-01	ci left: 7.698157e-05	ci right 9.945183e-05	k: 242	n:2760000
Cons ci ratio: 8.560526e-03	ci left: 7.030675e-02	ci right 7.091155e-02	k: 194880	n:2760000
KS ci ratio: 9.843434e-02	ci left: 5.460024e-04	ci right 6.028800e-04	k: 1584	n:2760000
ALS2   2760000 perm   4076 sec   (677 perm/sec)   p_kst 5.739130e-04   p_cons 7.060870e-02   p_joint 8.768116e-05

Joint ci ratio: 2.509412e-01	ci left: 7.704194e-05	ci right 9.947649e-05	k: 243	n:2770000
Cons ci ratio: 8.545180e-03	ci left: 7.030546e-02	ci right 7.090916e-02	k: 195581	n:2770000
KS ci ratio: 9.831039e-02	ci left: 5.454398e-04	ci right 6.021831e-04	k: 1588	n:2770000
ALS2   2770000 perm   4103 sec   (675 perm/sec)   p_kst 5.732852e-04   p_cons 7.060686e-02   p_joint 8.772563e-05

Joint ci ratio: 2.509412e-01	ci left: 7.676481e-05	ci right 9.911866e-05	k: 243	n:2780000
Cons ci ratio: 8.529916e-03	ci left: 7.030418e-02	ci right 7.090679e-02	k: 196282	n:2780000
KS ci ratio: 9.827956e-02	ci left: 5.438286e-04	ci right 6.003856e-04	k: 1589	n:2780000
ALS2   2780000 perm   4130 sec   (673 perm/sec)   p_kst 5.715827e-04   p_cons 7.060504e-02   p_joint 8.741007e-05

Joint ci ratio: 2.504286e-01	ci left: 7.682558e-05	ci right 9.914429e-05	k: 244	n:2790000
Cons ci ratio: 8.513919e-03	ci left: 7.031543e-02	ci right 7.091700e-02	k: 197018	n:2790000
KS ci ratio: 9.806391e-02	ci left: 5.443268e-04	ci right 6.008042e-04	k: 1596	n:2790000
ALS2   2790000 perm   4157 sec   (671 perm/sec)   p_kst 5.720430e-04   p_cons 7.061577e-02   p_joint 8.745520e-05

Joint ci ratio: 2.504286e-01	ci left: 7.655120e-05	ci right 9.879021e-05	k: 244	n:2800000
Cons ci ratio: 8.498289e-03	ci left: 7.032233e-02	ci right 7.092284e-02	k: 197742	n:2800000
KS ci ratio: 9.788021e-02	ci left: 5.444731e-04	ci right 6.008538e-04	k: 1602	n:2800000
ALS2   2800000 perm   4184 sec   (669 perm/sec)   p_kst 5.721429e-04   p_cons 7.062214e-02   p_joint 8.714286e-05

Joint ci ratio: 2.489092e-01	ci left: 7.727960e-05	ci right 9.957291e-05	k: 247	n:2810000
Cons ci ratio: 8.482332e-03	ci left: 7.033557e-02	ci right 7.093507e-02	k: 198484	n:2810000
KS ci ratio: 9.763683e-02	ci left: 5.453129e-04	ci right 6.016321e-04	k: 1610	n:2810000
ALS2   2810000 perm   4211 sec   (667 perm/sec)   p_kst 5.729537e-04   p_cons 7.063488e-02   p_joint 8.790036e-05

Joint ci ratio: 2.479115e-01	ci left: 7.767063e-05	ci right 9.997309e-05	k: 249	n:2820000
Cons ci ratio: 8.467561e-03	ci left: 7.033173e-02	ci right 7.093014e-02	k: 199178	n:2820000
KS ci ratio: 9.736519e-02	ci left: 5.464928e-04	ci right 6.027679e-04	k: 1619	n:2820000
ALS2   2820000 perm   4239 sec   (665 perm/sec)   p_kst 5.741135e-04   p_cons 7.063050e-02   p_joint 8.829787e-05

Joint ci ratio: 2.479116e-01	ci left: 7.739618e-05	ci right 9.961983e-05	k: 249	n:2830000
Cons ci ratio: 8.451753e-03	ci left: 7.034520e-02	ci right 7.094261e-02	k: 199921	n:2830000
KS ci ratio: 9.718538e-02	ci left: 5.466303e-04	ci right 6.028097e-04	k: 1625	n:2830000
ALS2   2830000 perm   4266 sec   (663 perm/sec)   p_kst 5.742049e-04   p_cons 7.064346e-02   p_joint 8.798587e-05

Joint ci ratio: 2.469258e-01	ci left: 7.778422e-05	ci right 1.000169e-04	k: 251	n:2840000
Cons ci ratio: 8.437594e-03	ci left: 7.033433e-02	ci right 7.093063e-02	k: 200595	n:2840000
KS ci ratio: 9.685821e-02	ci left: 5.484848e-04	ci right 6.046543e-04	k: 1636	n:2840000
ALS2   2840000 perm   4294 sec   (661 perm/sec)   p_kst 5.760563e-04   p_cons 7.063204e-02   p_joint 8.838028e-05

Joint ci ratio: 2.469258e-01	ci left: 7.751129e-05	ci right 9.966592e-05	k: 251	n:2850000
Cons ci ratio: 8.423033e-03	ci left: 7.033088e-02	ci right 7.092613e-02	k: 201290	n:2850000
KS ci ratio: 9.668119e-02	ci left: 5.486146e-04	ci right 6.046889e-04	k: 1642	n:2850000
ALS2   2850000 perm   4322 sec   (659 perm/sec)   p_kst 5.761404e-04   p_cons 7.062807e-02   p_joint 8.807018e-05

Joint ci ratio: 2.464373e-01	ci left: 7.756831e-05	ci right 9.968866e-05	k: 252	n:2860000
Cons ci ratio: 8.408480e-03	ci left: 7.032851e-02	ci right 7.092271e-02	k: 201988	n:2860000
KS ci ratio: 9.650514e-02	ci left: 5.487436e-04	ci right 6.047231e-04	k: 1648	n:2860000
ALS2   2860000 perm   4350 sec   (658 perm/sec)   p_kst 5.762238e-04   p_cons 7.062517e-02   p_joint 8.811189e-05

Joint ci ratio: 2.464374e-01	ci left: 7.729804e-05	ci right 9.934131e-05	k: 252	n:2870000
Cons ci ratio: 8.393735e-03	ci left: 7.033033e-02	ci right 7.092349e-02	k: 202698	n:2870000
KS ci ratio: 9.644673e-02	ci left: 5.475117e-04	ci right 6.033298e-04	k: 1650	n:2870000
ALS2   2870000 perm   4378 sec   (656 perm/sec)   p_kst 5.749129e-04   p_cons 7.062648e-02   p_joint 8.780488e-05

Joint ci ratio: 2.464374e-01	ci left: 7.702964e-05	ci right 9.899638e-05	k: 252	n:2880000
Cons ci ratio: 8.379178e-03	ci left: 7.033041e-02	ci right 7.092254e-02	k: 203403	n:2880000
KS ci ratio: 9.615589e-02	ci left: 5.489992e-04	ci right 6.047907e-04	k: 1660	n:2880000
ALS2   2880000 perm   4405 sec   (654 perm/sec)   p_kst 5.763889e-04   p_cons 7.062604e-02   p_joint 8.750000e-05

Joint ci ratio: 2.464375e-01	ci left: 7.676310e-05	ci right 9.865383e-05	k: 252	n:2890000
Cons ci ratio: 8.364101e-03	ci left: 7.033981e-02	ci right 7.093095e-02	k: 204135	n:2890000
KS ci ratio: 9.604035e-02	ci left: 5.484504e-04	ci right 6.041153e-04	k: 1664	n:2890000
ALS2   2890000 perm   4433 sec   (652 perm/sec)   p_kst 5.757785e-04   p_cons 7.063495e-02   p_joint 8.719723e-05

Joint ci ratio: 2.464375e-01	ci left: 7.649840e-05	ci right 9.831365e-05	k: 252	n:2900000
Cons ci ratio: 8.350926e-03	ci left: 7.032058e-02	ci right 7.091062e-02	k: 204784	n:2900000
KS ci ratio: 9.586777e-02	ci left: 5.485785e-04	ci right 6.041508e-04	k: 1670	n:2900000
ALS2   2900000 perm   4461 sec   (650 perm/sec)   p_kst 5.758621e-04   p_cons 7.061517e-02   p_joint 8.689655e-05

Joint ci ratio: 2.449892e-01	ci left: 7.720298e-05	ci right 9.907008e-05	k: 255	n:2910000
Cons ci ratio: 8.335499e-03	ci left: 7.033784e-02	ci right 7.092693e-02	k: 205539	n:2910000
KS ci ratio: 9.566757e-02	ci left: 5.490412e-04	ci right 6.045377e-04	k: 1677	n:2910000
ALS2   2910000 perm   4489 sec   (648 perm/sec)   p_kst 5.762887e-04   p_cons 7.063196e-02   p_joint 8.762887e-05

Joint ci ratio: 2.440377e-01	ci left: 7.758155e-05	ci right 9.945761e-05	k: 257	n:2920000
Cons ci ratio: 8.321937e-03	ci left: 7.032696e-02	ci right 7.091499e-02	k: 206212	n:2920000
KS ci ratio: 9.552537e-02	ci left: 5.488323e-04	ci right 6.042207e-04	k: 1682	n:2920000
ALS2   2920000 perm   4517 sec   (646 perm/sec)   p_kst 5.760274e-04   p_cons 7.062055e-02   p_joint 8.801370e-05

Joint ci ratio: 2.440378e-01	ci left: 7.731677e-05	ci right 9.911816e-05	k: 257	n:2930000
Cons ci ratio: 8.307318e-03	ci left: 7.033386e-02	ci right 7.092091e-02	k: 206937	n:2930000
KS ci ratio: 9.546873e-02	ci left: 5.476255e-04	ci right 6.028574e-04	k: 1684	n:2930000
ALS2   2930000 perm   4546 sec   (645 perm/sec)   p_kst 5.747440e-04   p_cons 7.062696e-02   p_joint 8.771331e-05

Joint ci ratio: 2.435662e-01	ci left: 7.737314e-05	ci right 9.914190e-05	k: 258	n:2940000
Cons ci ratio: 8.293291e-03	ci left: 7.033257e-02	ci right 7.091862e-02	k: 207638	n:2940000
KS ci ratio: 9.515854e-02	ci left: 5.494151e-04	ci right 6.046375e-04	k: 1695	n:2940000
ALS2   2940000 perm   4575 sec   (643 perm/sec)   p_kst 5.765306e-04   p_cons 7.062517e-02   p_joint 8.775510e-05

Joint ci ratio: 2.435662e-01	ci left: 7.711086e-05	ci right 9.880583e-05	k: 258	n:2950000
Cons ci ratio: 8.279014e-03	ci left: 7.033636e-02	ci right 7.092143e-02	k: 208354	n:2950000
KS ci ratio: 9.499066e-02	ci left: 5.495382e-04	ci right 6.046701e-04	k: 1701	n:2950000
ALS2   2950000 perm   4603 sec   (641 perm/sec)   p_kst 5.766102e-04   p_cons 7.062847e-02   p_joint 8.745763e-05

Joint ci ratio: 2.430974e-01	ci left: 7.716759e-05	ci right 9.883042e-05	k: 259	n:2960000
Cons ci ratio: 8.264684e-03	ci left: 7.034216e-02	ci right 7.092625e-02	k: 209076	n:2960000
KS ci ratio: 9.485145e-02	ci left: 5.493308e-04	ci right 6.043566e-04	k: 1706	n:2960000
ALS2   2960000 perm   4631 sec   (639 perm/sec)   p_kst 5.763514e-04   p_cons 7.063378e-02   p_joint 8.750000e-05

Joint ci ratio: 2.426312e-01	ci left: 7.722398e-05	ci right 9.885481e-05	k: 260	n:2970000
Cons ci ratio: 8.250956e-03	ci left: 7.033951e-02	ci right 7.092261e-02	k: 209773	n:2970000
KS ci ratio: 9.468519e-02	ci left: 5.494535e-04	ci right 6.043898e-04	k: 1712	n:2970000
ALS2   2970000 perm   4659 sec   (637 perm/sec)   p_kst 5.764310e-04   p_cons 7.063064e-02   p_joint 8.754209e-05

Joint ci ratio: 2.426312e-01	ci left: 7.696484e-05	ci right 9.852308e-05	k: 260	n:2980000
Cons ci ratio: 8.237676e-03	ci left: 7.033085e-02	ci right 7.091294e-02	k: 210452	n:2980000
KS ci ratio: 9.463002e-02	ci left: 5.482649e-04	ci right 6.030487e-04	k: 1714	n:2980000
ALS2   2980000 perm   4688 sec   (636 perm/sec)   p_kst 5.751678e-04   p_cons 7.062148e-02   p_joint 8.724832e-05

Joint ci ratio: 2.426313e-01	ci left: 7.670743e-05	ci right 9.819358e-05	k: 260	n:2990000
Cons ci ratio: 8.224103e-03	ci left: 7.032793e-02	ci right 7.090902e-02	k: 211148	n:2990000
KS ci ratio: 9.441004e-02	ci left: 5.490436e-04	ci right 6.037706e-04	k: 1722	n:2990000
ALS2   2990000 perm   4718 sec   (634 perm/sec)   p_kst 5.759197e-04   p_cons 7.061806e-02   p_joint 8.695652e-05

Joint ci ratio: 2.421678e-01	ci left: 7.676483e-05	ci right 9.821980e-05	k: 261	n:3000000
Cons ci ratio: 8.209888e-03	ci left: 7.033634e-02	ci right 7.091649e-02	k: 211878	n:3000000
KS ci ratio: 9.424608e-02	ci left: 5.491663e-04	ci right 6.038052e-04	k: 1728	n:3000000
ALS2   3000000 perm   4746 sec   (632 perm/sec)   p_kst 5.760000e-04   p_cons 7.062600e-02   p_joint 8.700000e-05

Joint ci ratio: 2.421678e-01	ci left: 7.650979e-05	ci right 9.789349e-05	k: 261	n:3010000
Cons ci ratio: 8.195871e-03	ci left: 7.034270e-02	ci right 7.092191e-02	k: 212602	n:3010000
KS ci ratio: 9.411012e-02	ci left: 5.489638e-04	ci right 6.034994e-04	k: 1733	n:3010000
ALS2   3010000 perm   4775 sec   (630 perm/sec)   p_kst 5.757475e-04   p_cons 7.063189e-02   p_joint 8.671096e-05

Joint ci ratio: 2.421679e-01	ci left: 7.625645e-05	ci right 9.756935e-05	k: 261	n:3020000
Cons ci ratio: 8.183577e-03	ci left: 7.032258e-02	ci right 7.090076e-02	k: 213246	n:3020000
KS ci ratio: 9.405595e-02	ci left: 5.477927e-04	ci right 6.021789e-04	k: 1735	n:3020000
ALS2   3020000 perm   4804 sec   (629 perm/sec)   p_kst 5.745033e-04   p_cons 7.061126e-02   p_joint 8.642384e-05

Joint ci ratio: 2.417070e-01	ci left: 7.631480e-05	ci right 9.759734e-05	k: 262	n:3030000
Cons ci ratio: 8.170167e-03	ci left: 7.032137e-02	ci right 7.089859e-02	k: 213947	n:3030000
KS ci ratio: 9.383994e-02	ci left: 5.485631e-04	ci right 6.028938e-04	k: 1743	n:3030000
ALS2   3030000 perm   4833 sec   (627 perm/sec)   p_kst 5.752475e-04   p_cons 7.060957e-02   p_joint 8.646865e-05

Joint ci ratio: 2.417071e-01	ci left: 7.606377e-05	ci right 9.727629e-05	k: 262	n:3040000
Cons ci ratio: 8.156945e-03	ci left: 7.031821e-02	ci right 7.089445e-02	k: 214642	n:3040000
KS ci ratio: 9.370572e-02	ci left: 5.483648e-04	ci right 6.025939e-04	k: 1748	n:3040000
ALS2   3040000 perm   4863 sec   (625 perm/sec)   p_kst 5.750000e-04   p_cons 7.060592e-02   p_joint 8.618421e-05

Joint ci ratio: 2.412488e-01	ci left: 7.612241e-05	ci right 9.730502e-05	k: 263	n:3050000
Cons ci ratio: 8.142932e-03	ci left: 7.032880e-02	ci right 7.090414e-02	k: 215379	n:3050000
KS ci ratio: 9.349212e-02	ci left: 5.491284e-04	ci right 6.033025e-04	k: 1756	n:3050000
ALS2   3050000 perm   4892 sec   (623 perm/sec)   p_kst 5.757377e-04   p_cons 7.061607e-02   p_joint 8.622951e-05

Joint ci ratio: 2.407932e-01	ci left: 7.618071e-05	ci right 9.733353e-05	k: 264	n:3060000
Cons ci ratio: 8.129842e-03	ci left: 7.032563e-02	ci right 7.090002e-02	k: 216074	n:3060000
KS ci ratio: 9.320074e-02	ci left: 5.508447e-04	ci right 6.050096e-04	k: 1767	n:3060000
ALS2   3060000 perm   4921 sec   (622 perm/sec)   p_kst 5.774510e-04   p_cons 7.061242e-02   p_joint 8.627451e-05

Joint ci ratio: 2.398896e-01	ci left: 7.654480e-05	ci right 9.770710e-05	k: 266	n:3070000
Cons ci ratio: 8.115908e-03	ci left: 7.033711e-02	ci right 7.091060e-02	k: 216814	n:3070000
KS ci ratio: 9.312181e-02	ci left: 5.500049e-04	ci right 6.040388e-04	k: 1770	n:3070000
ALS2   3070000 perm   4951 sec   (620 perm/sec)   p_kst 5.765472e-04   p_cons 7.062345e-02   p_joint 8.664495e-05

Joint ci ratio: 2.398897e-01	ci left: 7.629628e-05	ci right 9.738987e-05	k: 266	n:3080000
Cons ci ratio: 8.103709e-03	ci left: 7.032162e-02	ci right 7.089412e-02	k: 217471	n:3080000
KS ci ratio: 9.288604e-02	ci left: 5.510733e-04	ci right 6.050677e-04	k: 1779	n:3080000
ALS2   3080000 perm   4980 sec   (618 perm/sec)   p_kst 5.775974e-04   p_cons 7.060747e-02   p_joint 8.636364e-05

Joint ci ratio: 2.398897e-01	ci left: 7.604936e-05	ci right 9.707470e-05	k: 266	n:3090000
Cons ci ratio: 8.091365e-03	ci left: 7.030946e-02	ci right 7.088099e-02	k: 218138	n:3090000
KS ci ratio: 9.280791e-02	ci left: 5.502382e-04	ci right 6.041029e-04	k: 1782	n:3090000
ALS2   3090000 perm   5010 sec   (617 perm/sec)   p_kst 5.766990e-04   p_cons 7.059482e-02   p_joint 8.608414e-05

Joint ci ratio: 2.398897e-01	ci left: 7.580404e-05	ci right 9.676155e-05	k: 266	n:3100000
Cons ci ratio: 8.078025e-03	ci left: 7.031445e-02	ci right 7.088506e-02	k: 218858	n:3100000
KS ci ratio: 9.278197e-02	ci left: 5.487783e-04	ci right 6.024843e-04	k: 1783	n:3100000
ALS2   3100000 perm   5040 sec   (615 perm/sec)   p_kst 5.751613e-04   p_cons 7.059935e-02   p_joint 8.580645e-05

Joint ci ratio: 2.398898e-01	ci left: 7.556030e-05	ci right 9.645042e-05	k: 266	n:3110000
Cons ci ratio: 8.064553e-03	ci left: 7.032261e-02	ci right 7.089234e-02	k: 219588	n:3110000
KS ci ratio: 9.262633e-02	ci left: 5.488983e-04	ci right 6.025210e-04	k: 1789	n:3110000
ALS2   3110000 perm   5071 sec   (613 perm/sec)   p_kst 5.752412e-04   p_cons 7.060707e-02   p_joint 8.553055e-05

Joint ci ratio: 2.389963e-01	ci left: 7.592069e-05	ci right 9.682070e-05	k: 268	n:3120000
Cons ci ratio: 8.051542e-03	ci left: 7.032432e-02	ci right 7.089314e-02	k: 220298	n:3120000
KS ci ratio: 9.239430e-02	ci left: 5.499569e-04	ci right 6.035412e-04	k: 1798	n:3120000
ALS2   3120000 perm   5101 sec   (612 perm/sec)   p_kst 5.762821e-04   p_cons 7.060833e-02   p_joint 8.589744e-05

Joint ci ratio: 2.389963e-01	ci left: 7.567813e-05	ci right 9.651137e-05	k: 268	n:3130000
Cons ci ratio: 8.038926e-03	ci left: 7.032060e-02	ci right 7.088850e-02	k: 220991	n:3130000
KS ci ratio: 9.231740e-02	ci left: 5.491361e-04	ci right 6.025936e-04	k: 1801	n:3130000
ALS2   3130000 perm   5131 sec   (610 perm/sec)   p_kst 5.753994e-04   p_cons 7.060415e-02   p_joint 8.562300e-05

Joint ci ratio: 2.389963e-01	ci left: 7.543711e-05	ci right 9.620401e-05	k: 268	n:3140000
Cons ci ratio: 8.025804e-03	ci left: 7.032613e-02	ci right 7.089313e-02	k: 221713	n:3140000
KS ci ratio: 9.218960e-02	ci left: 5.489429e-04	ci right 6.023036e-04	k: 1806	n:3140000
ALS2   3140000 perm   5161 sec   (608 perm/sec)   p_kst 5.751592e-04   p_cons 7.060924e-02   p_joint 8.535032e-05

Joint ci ratio: 2.389964e-01	ci left: 7.519763e-05	ci right 9.589860e-05	k: 268	n:3150000
Cons ci ratio: 8.012882e-03	ci left: 7.032940e-02	ci right 7.089552e-02	k: 222428	n:3150000
KS ci ratio: 9.213868e-02	ci left: 5.478205e-04	ci right 6.010410e-04	k: 1808	n:3150000
ALS2   3150000 perm   5191 sec   (607 perm/sec)   p_kst 5.739683e-04   p_cons 7.061206e-02   p_joint 8.507937e-05

Joint ci ratio: 2.381128e-01	ci left: 7.555475e-05	ci right 9.626579e-05	k: 270	n:3160000
Cons ci ratio: 7.999829e-03	ci left: 7.033581e-02	ci right 7.090105e-02	k: 223153	n:3160000
KS ci ratio: 9.196091e-02	ci left: 5.482511e-04	ci right 6.014052e-04	k: 1815	n:3160000
ALS2   3160000 perm   5221 sec   (605 perm/sec)   p_kst 5.743671e-04   p_cons 7.061804e-02   p_joint 8.544304e-05

Joint ci ratio: 2.376747e-01	ci left: 7.561306e-05	ci right 9.629634e-05	k: 271	n:3170000
Cons ci ratio: 7.986418e-03	ci left: 7.034911e-02	ci right 7.091350e-02	k: 223900	n:3170000
KS ci ratio: 9.178416e-02	ci left: 5.486791e-04	ci right 6.017669e-04	k: 1822	n:3170000
ALS2   3170000 perm   5252 sec   (604 perm/sec)   p_kst 5.747634e-04   p_cons 7.063091e-02   p_joint 8.548896e-05

Joint ci ratio: 2.372390e-01	ci left: 7.567104e-05	ci right 9.632666e-05	k: 272	n:3180000
Cons ci ratio: 7.974009e-03	ci left: 7.034694e-02	ci right 7.091044e-02	k: 224598	n:3180000
KS ci ratio: 9.145854e-02	ci left: 5.509481e-04	ci right 6.040562e-04	k: 1835	n:3180000
ALS2   3180000 perm   5282 sec   (602 perm/sec)   p_kst 5.770440e-04   p_cons 7.062830e-02   p_joint 8.553459e-05

Joint ci ratio: 2.372390e-01	ci left: 7.543383e-05	ci right 9.602469e-05	k: 272	n:3190000
Cons ci ratio: 7.961164e-03	ci left: 7.035293e-02	ci right 7.091556e-02	k: 225322	n:3190000
KS ci ratio: 9.125990e-02	ci left: 5.516715e-04	ci right 6.047277e-04	k: 1843	n:3190000
ALS2   3190000 perm   5313 sec   (600 perm/sec)   p_kst 5.777429e-04   p_cons 7.063386e-02   p_joint 8.526646e-05

Joint ci ratio: 2.372390e-01	ci left: 7.519810e-05	ci right 9.572462e-05	k: 272	n:3200000
Cons ci ratio: 7.949365e-03	ci left: 7.034266e-02	ci right 7.090437e-02	k: 225994	n:3200000
KS ci ratio: 9.113644e-02	ci left: 5.514744e-04	ci right 6.044361e-04	k: 1848	n:3200000
ALS2   3200000 perm   5343 sec   (599 perm/sec)   p_kst 5.775000e-04   p_cons 7.062312e-02   p_joint 8.500000e-05

Joint ci ratio: 2.372391e-01	ci left: 7.496383e-05	ci right 9.542641e-05	k: 272	n:3210000
Cons ci ratio: 7.937091e-03	ci left: 7.034116e-02	ci right 7.090199e-02	k: 226694	n:3210000
KS ci ratio: 9.108724e-02	ci left: 5.503653e-04	ci right 6.031904e-04	k: 1850	n:3210000
ALS2   3210000 perm   5375 sec   (597 perm/sec)   p_kst 5.763240e-04   p_cons 7.062118e-02   p_joint 8.473520e-05

Joint ci ratio: 2.368057e-01	ci left: 7.502314e-05	ci right 9.545902e-05	k: 273	n:3220000
Cons ci ratio: 7.923955e-03	ci left: 7.035486e-02	ci right 7.091486e-02	k: 227443	n:3220000
KS ci ratio: 9.101355e-02	ci left: 5.495665e-04	ci right 6.022700e-04	k: 1853	n:3220000
ALS2   3220000 perm   5406 sec   (596 perm/sec)   p_kst 5.754658e-04   p_cons 7.063447e-02   p_joint 8.478261e-05

Joint ci ratio: 2.368058e-01	ci left: 7.479087e-05	ci right 9.516349e-05	k: 273	n:3230000
Cons ci ratio: 7.911629e-03	ci left: 7.035611e-02	ci right 7.091525e-02	k: 228152	n:3230000
KS ci ratio: 9.086664e-02	ci left: 5.496804e-04	ci right 6.023052e-04	k: 1859	n:3230000
ALS2   3230000 perm   5437 sec   (594 perm/sec)   p_kst 5.755418e-04   p_cons 7.063529e-02   p_joint 8.452012e-05

Joint ci ratio: 2.368058e-01	ci left: 7.456004e-05	ci right 9.486977e-05	k: 273	n:3240000
Cons ci ratio: 7.899269e-03	ci left: 7.035890e-02	ci right 7.091718e-02	k: 228866	n:3240000
KS ci ratio: 9.079348e-02	ci left: 5.488888e-04	ci right 6.013932e-04	k: 1862	n:3240000
ALS2   3240000 perm   5468 sec   (593 perm/sec)   p_kst 5.746914e-04   p_cons 7.063765e-02   p_joint 8.425926e-05

Joint ci ratio: 2.368058e-01	ci left: 7.433062e-05	ci right 9.457787e-05	k: 273	n:3250000
Cons ci ratio: 7.887372e-03	ci left: 7.035491e-02	ci right 7.091232e-02	k: 229558	n:3250000
KS ci ratio: 9.062337e-02	ci left: 5.493049e-04	ci right 6.017455e-04	k: 1869	n:3250000
ALS2   3250000 perm   5499 sec   (591 perm/sec)   p_kst 5.750769e-04   p_cons 7.063323e-02   p_joint 8.400000e-05

Joint ci ratio: 2.368059e-01	ci left: 7.410261e-05	ci right 9.428775e-05	k: 273	n:3260000
Cons ci ratio: 7.875382e-03	ci left: 7.035340e-02	ci right 7.090994e-02	k: 230258	n:3260000
KS ci ratio: 9.055081e-02	ci left: 5.485193e-04	ci right 6.008407e-04	k: 1872	n:3260000
ALS2   3260000 perm   5531 sec   (589 perm/sec)   p_kst 5.742331e-04   p_cons 7.063129e-02   p_joint 8.374233e-05

Joint ci ratio: 2.363749e-01	ci left: 7.416368e-05	ci right 9.432332e-05	k: 274	n:3270000
Cons ci ratio: 7.863868e-03	ci left: 7.034487e-02	ci right 7.090054e-02	k: 230935	n:3270000
KS ci ratio: 9.047841e-02	ci left: 5.477385e-04	ci right 5.999415e-04	k: 1875	n:3270000
ALS2   3270000 perm   5562 sec   (588 perm/sec)   p_kst 5.733945e-04   p_cons 7.062232e-02   p_joint 8.379205e-05

Joint ci ratio: 2.363749e-01	ci left: 7.393757e-05	ci right 9.403575e-05	k: 274	n:3280000
Cons ci ratio: 7.851730e-03	ci left: 7.034766e-02	ci right 7.090249e-02	k: 231649	n:3280000
KS ci ratio: 9.033407e-02	ci left: 5.478565e-04	ci right 5.999830e-04	k: 1881	n:3280000
ALS2   3280000 perm   5594 sec   (586 perm/sec)   p_kst 5.734756e-04   p_cons 7.062470e-02   p_joint 8.353659e-05

Joint ci ratio: 2.363750e-01	ci left: 7.371284e-05	ci right 9.374993e-05	k: 274	n:3290000
Cons ci ratio: 7.839974e-03	ci left: 7.034498e-02	ci right 7.089894e-02	k: 232345	n:3290000
KS ci ratio: 9.023825e-02	ci left: 5.473796e-04	ci right 5.994026e-04	k: 1885	n:3290000
ALS2   3290000 perm   5625 sec   (585 perm/sec)   p_kst 5.729483e-04   p_cons 7.062158e-02   p_joint 8.328267e-05

Joint ci ratio: 2.363750e-01	ci left: 7.348946e-05	ci right 9.346584e-05	k: 274	n:3300000
Cons ci ratio: 7.827675e-03	ci left: 7.035229e-02	ci right 7.090544e-02	k: 233074	n:3300000
KS ci ratio: 9.011888e-02	ci left: 5.472019e-04	ci right 5.991355e-04	k: 1890	n:3300000
ALS2   3300000 perm   5657 sec   (583 perm/sec)   p_kst 5.727273e-04   p_cons 7.062848e-02   p_joint 8.303030e-05

Joint ci ratio: 2.363750e-01	ci left: 7.326744e-05	ci right 9.318346e-05	k: 274	n:3310000
Cons ci ratio: 7.815559e-03	ci left: 7.035744e-02	ci right 7.090977e-02	k: 233796	n:3310000
KS ci ratio: 9.009512e-02	ci left: 5.458440e-04	ci right 5.976344e-04	k: 1891	n:3310000
ALS2   3310000 perm   5688 sec   (582 perm/sec)   p_kst 5.712991e-04   p_cons 7.063323e-02   p_joint 8.277946e-05

Joint ci ratio: 2.363751e-01	ci left: 7.304675e-05	ci right 9.290279e-05	k: 274	n:3320000
Cons ci ratio: 7.803768e-03	ci left: 7.035806e-02	ci right 7.090956e-02	k: 234503	n:3320000
KS ci ratio: 9.000006e-02	ci left: 5.453775e-04	ci right 5.970663e-04	k: 1895	n:3320000
ALS2   3320000 perm   5721 sec   (580 perm/sec)   p_kst 5.707831e-04   p_cons 7.063343e-02   p_joint 8.253012e-05

Joint ci ratio: 2.355201e-01	ci left: 7.339249e-05	ci right 9.325984e-05	k: 276	n:3330000
Cons ci ratio: 7.792743e-03	ci left: 7.034668e-02	ci right 7.089731e-02	k: 235170	n:3330000
KS ci ratio: 8.988163e-02	ci left: 5.452075e-04	ci right 5.968085e-04	k: 1900	n:3330000
ALS2   3330000 perm   5752 sec   (579 perm/sec)   p_kst 5.705706e-04   p_cons 7.062162e-02   p_joint 8.288288e-05

Joint ci ratio: 2.350962e-01	ci left: 7.345451e-05	ci right 9.329764e-05	k: 277	n:3340000
Cons ci ratio: 7.779404e-03	ci left: 7.037512e-02	ci right 7.092502e-02	k: 235970	n:3340000
KS ci ratio: 8.981083e-02	ci left: 5.444532e-04	ci right 5.959401e-04	k: 1903	n:3340000
ALS2   3340000 perm   5784 sec   (577 perm/sec)   p_kst 5.697605e-04   p_cons 7.064970e-02   p_joint 8.293413e-05

Joint ci ratio: 2.342550e-01	ci left: 7.379716e-05	ci right 9.365119e-05	k: 279	n:3350000
Cons ci ratio: 7.767476e-03	ci left: 7.038075e-02	ci right 7.092985e-02	k: 236694	n:3350000
KS ci ratio: 8.962271e-02	ci left: 5.451624e-04	ci right 5.966028e-04	k: 1911	n:3350000
ALS2   3350000 perm   5817 sec   (576 perm/sec)   p_kst 5.704478e-04   p_cons 7.065493e-02   p_joint 8.328358e-05

Joint ci ratio: 2.334228e-01	ci left: 7.413789e-05	ci right 9.400251e-05	k: 281	n:3360000
Cons ci ratio: 7.756867e-03	ci left: 7.036495e-02	ci right 7.091317e-02	k: 237346	n:3360000
KS ci ratio: 8.952914e-02	ci left: 5.447037e-04	ci right 5.960443e-04	k: 1915	n:3360000
ALS2   3360000 perm   5849 sec   (574 perm/sec)   p_kst 5.699405e-04   p_cons 7.063869e-02   p_joint 8.363095e-05

Joint ci ratio: 2.330100e-01	ci left: 7.419730e-05	ci right 9.403761e-05	k: 282	n:3370000
Cons ci ratio: 7.744779e-03	ci left: 7.037501e-02	ci right 7.092246e-02	k: 238085	n:3370000
KS ci ratio: 8.941255e-02	ci left: 5.445379e-04	ci right 5.957925e-04	k: 1920	n:3370000
ALS2   3370000 perm   5882 sec   (573 perm/sec)   p_kst 5.697329e-04   p_cons 7.064837e-02   p_joint 8.367953e-05

Joint ci ratio: 2.325994e-01	ci left: 7.425638e-05	ci right 9.407248e-05	k: 283	n:3380000
Cons ci ratio: 7.734142e-03	ci left: 7.036140e-02	ci right 7.090798e-02	k: 238744	n:3380000
KS ci ratio: 8.931963e-02	ci left: 5.440838e-04	ci right 5.952397e-04	k: 1924	n:3380000
ALS2   3380000 perm   5914 sec   (572 perm/sec)   p_kst 5.692308e-04   p_cons 7.063432e-02   p_joint 8.372781e-05

Joint ci ratio: 2.321910e-01	ci left: 7.431515e-05	ci right 9.410711e-05	k: 284	n:3390000
Cons ci ratio: 7.722420e-03	ci left: 7.036700e-02	ci right 7.091279e-02	k: 239468	n:3390000
KS ci ratio: 8.918075e-02	ci left: 5.442092e-04	ci right 5.952932e-04	k: 1930	n:3390000
ALS2   3390000 perm   5946 sec   (570 perm/sec)   p_kst 5.693215e-04   p_cons 7.063953e-02   p_joint 8.377581e-05

Joint ci ratio: 2.301805e-01	ci left: 7.548201e-05	ci right 9.538592e-05	k: 289	n:3400000
Cons ci ratio: 7.710802e-03	ci left: 7.037169e-02	ci right 7.091669e-02	k: 240189	n:3400000
KS ci ratio: 8.901953e-02	ci left: 5.446216e-04	ci right 5.956470e-04	k: 1937	n:3400000
ALS2   3400000 perm   5978 sec   (569 perm/sec)   p_kst 5.697059e-04   p_cons 7.064382e-02   p_joint 8.500000e-05

Joint ci ratio: 2.301805e-01	ci left: 7.526065e-05	ci right 9.510620e-05	k: 289	n:3410000
Cons ci ratio: 7.700029e-03	ci left: 7.036288e-02	ci right 7.090706e-02	k: 240864	n:3410000
KS ci ratio: 8.881350e-02	ci left: 5.456051e-04	ci right 5.965982e-04	k: 1946	n:3410000
ALS2   3410000 perm   6011 sec   (567 perm/sec)   p_kst 5.706745e-04   p_cons 7.063460e-02   p_joint 8.475073e-05

Joint ci ratio: 2.297847e-01	ci left: 7.531614e-05	ci right 9.513732e-05	k: 290	n:3420000
Cons ci ratio: 7.688118e-03	ci left: 7.037427e-02	ci right 7.091769e-02	k: 241608	n:3420000
KS ci ratio: 8.874520e-02	ci left: 5.448674e-04	ci right 5.957504e-04	k: 1949	n:3420000
ALS2   3420000 perm   6044 sec   (566 perm/sec)   p_kst 5.698830e-04   p_cons 7.064561e-02   p_joint 8.479532e-05

Joint ci ratio: 2.289990e-01	ci left: 7.564615e-05	ci right 9.547649e-05	k: 292	n:3430000
Cons ci ratio: 7.676894e-03	ci left: 7.037482e-02	ci right 7.091745e-02	k: 242315	n:3430000
KS ci ratio: 8.863165e-02	ci left: 5.447043e-04	ci right 5.955036e-04	k: 1954	n:3430000
ALS2   3430000 perm   6077 sec   (564 perm/sec)   p_kst 5.696793e-04   p_cons 7.064577e-02   p_joint 8.513120e-05

Joint ci ratio: 2.282214e-01	ci left: 7.597435e-05	ci right 9.581358e-05	k: 294	n:3440000
Cons ci ratio: 7.665481e-03	ci left: 7.037944e-02	ci right 7.092129e-02	k: 243036	n:3440000
KS ci ratio: 8.847338e-02	ci left: 5.451107e-04	ci right 5.958524e-04	k: 1961	n:3440000
ALS2   3440000 perm   6110 sec   (563 perm/sec)   p_kst 5.700581e-04   p_cons 7.065000e-02   p_joint 8.546512e-05

Joint ci ratio: 2.278356e-01	ci left: 7.602743e-05	ci right 9.584224e-05	k: 295	n:3450000
Cons ci ratio: 7.654524e-03	ci left: 7.037708e-02	ci right 7.091813e-02	k: 243733	n:3450000
KS ci ratio: 8.842837e-02	ci left: 5.440975e-04	ci right 5.947179e-04	k: 1963	n:3450000
ALS2   3450000 perm   6142 sec   (562 perm/sec)   p_kst 5.689855e-04   p_cons 7.064725e-02   p_joint 8.550725e-05

Joint ci ratio: 2.274517e-01	ci left: 7.608024e-05	ci right 9.587071e-05	k: 296	n:3460000
Cons ci ratio: 7.642739e-03	ci left: 7.038974e-02	ci right 7.093005e-02	k: 244482	n:3460000
KS ci ratio: 8.833848e-02	ci left: 5.436555e-04	ci right 5.941806e-04	k: 1967	n:3460000
ALS2   3460000 perm   6176 sec   (560 perm/sec)   p_kst 5.684971e-04   p_cons 7.065954e-02   p_joint 8.554913e-05

Joint ci ratio: 2.270697e-01	ci left: 7.613277e-05	ci right 9.589899e-05	k: 297	n:3470000
Cons ci ratio: 7.631662e-03	ci left: 7.039111e-02	ci right 7.093065e-02	k: 245192	n:3470000
KS ci ratio: 8.822648e-02	ci left: 5.434979e-04	ci right 5.939410e-04	k: 1972	n:3470000
ALS2   3470000 perm   6209 sec   (559 perm/sec)   p_kst 5.682997e-04   p_cons 7.066052e-02   p_joint 8.559078e-05

Joint ci ratio: 2.270697e-01	ci left: 7.591399e-05	ci right 9.562341e-05	k: 297	n:3480000
Cons ci ratio: 7.620515e-03	ci left: 7.039448e-02	ci right 7.093325e-02	k: 245909	n:3480000
KS ci ratio: 8.811491e-02	ci left: 5.433412e-04	ci right 5.937028e-04	k: 1977	n:3480000
ALS2   3480000 perm   6242 sec   (557 perm/sec)   p_kst 5.681034e-04   p_cons 7.066351e-02   p_joint 8.534483e-05

Joint ci ratio: 2.270698e-01	ci left: 7.569647e-05	ci right 9.534942e-05	k: 297	n:3490000
Cons ci ratio: 7.609717e-03	ci left: 7.039268e-02	ci right 7.093067e-02	k: 246608	n:3490000
KS ci ratio: 8.807044e-02	ci left: 5.423448e-04	ci right 5.925873e-04	k: 1979	n:3490000
ALS2   3490000 perm   6275 sec   (556 perm/sec)   p_kst 5.670487e-04   p_cons 7.066132e-02   p_joint 8.510029e-05

Joint ci ratio: 2.270698e-01	ci left: 7.548020e-05	ci right 9.507700e-05	k: 297	n:3500000
Cons ci ratio: 7.598964e-03	ci left: 7.039089e-02	ci right 7.092810e-02	k: 247307	n:3500000
KS ci ratio: 8.798164e-02	ci left: 5.419129e-04	ci right 5.920622e-04	k: 1983	n:3500000
ALS2   3500000 perm   6309 sec   (555 perm/sec)   p_kst 5.665714e-04   p_cons 7.065914e-02   p_joint 8.485714e-05

Joint ci ratio: 2.266898e-01	ci left: 7.553386e-05	ci right 9.510719e-05	k: 298	n:3510000
Cons ci ratio: 7.587730e-03	ci left: 7.039822e-02	ci right 7.093469e-02	k: 248038	n:3510000
KS ci ratio: 8.787099e-02	ci left: 5.417622e-04	ci right 5.918313e-04	k: 1988	n:3510000
ALS2   3510000 perm   6342 sec   (553 perm/sec)   p_kst 5.663818e-04   p_cons 7.066610e-02   p_joint 8.490028e-05

Joint ci ratio: 2.266898e-01	ci left: 7.531928e-05	ci right 9.483700e-05	k: 298	n:3520000
Cons ci ratio: 7.577315e-03	ci left: 7.039217e-02	ci right 7.092786e-02	k: 248722	n:3520000
KS ci ratio: 8.769478e-02	ci left: 5.424459e-04	ci right 5.924725e-04	k: 1996	n:3520000
ALS2   3520000 perm   6375 sec   (552 perm/sec)   p_kst 5.670455e-04   p_cons 7.065966e-02   p_joint 8.465909e-05

Joint ci ratio: 2.259354e-01	ci left: 7.564036e-05	ci right 9.516697e-05	k: 300	n:3530000
Cons ci ratio: 7.566161e-03	ci left: 7.039973e-02	ci right 7.093468e-02	k: 249454	n:3530000
KS ci ratio: 8.754147e-02	ci left: 5.428488e-04	ci right 5.928206e-04	k: 2003	n:3530000
ALS2   3530000 perm   6409 sec   (551 perm/sec)   p_kst 5.674221e-04   p_cons 7.066686e-02   p_joint 8.498584e-05

Joint ci ratio: 2.259354e-01	ci left: 7.542669e-05	ci right 9.489814e-05	k: 300	n:3540000
Cons ci ratio: 7.555217e-03	ci left: 7.040443e-02	ci right 7.093864e-02	k: 250176	n:3540000
KS ci ratio: 8.738896e-02	ci left: 5.432495e-04	ci right 5.931666e-04	k: 2010	n:3540000
ALS2   3540000 perm   6444 sec   (549 perm/sec)   p_kst 5.677966e-04   p_cons 7.067119e-02   p_joint 8.474576e-05

Joint ci ratio: 2.259354e-01	ci left: 7.521422e-05	ci right 9.463082e-05	k: 300	n:3550000
Cons ci ratio: 7.544143e-03	ci left: 7.041220e-02	ci right 7.094568e-02	k: 250909	n:3550000
KS ci ratio: 8.730220e-02	ci left: 5.428214e-04	ci right 5.926470e-04	k: 2014	n:3550000
ALS2   3550000 perm   6480 sec   (548 perm/sec)   p_kst 5.673239e-04   p_cons 7.067859e-02   p_joint 8.450704e-05

Joint ci ratio: 2.259355e-01	ci left: 7.500294e-05	ci right 9.436501e-05	k: 300	n:3560000
Cons ci ratio: 7.532989e-03	ci left: 7.042217e-02	ci right 7.095493e-02	k: 251650	n:3560000
KS ci ratio: 8.725895e-02	ci left: 5.418461e-04	ci right 5.915564e-04	k: 2016	n:3560000
ALS2   3560000 perm   6513 sec   (547 perm/sec)   p_kst 5.662921e-04   p_cons 7.068820e-02   p_joint 8.426966e-05

Joint ci ratio: 2.259355e-01	ci left: 7.479285e-05	ci right 9.410068e-05	k: 300	n:3570000
Cons ci ratio: 7.522510e-03	ci left: 7.042118e-02	ci right 7.095319e-02	k: 252352	n:3570000
KS ci ratio: 8.715101e-02	ci left: 5.416983e-04	ci right 5.913304e-04	k: 2021	n:3570000
ALS2   3570000 perm   6548 sec   (545 perm/sec)   p_kst 5.661064e-04   p_cons 7.068683e-02   p_joint 8.403361e-05

Joint ci ratio: 2.255611e-01	ci left: 7.484747e-05	ci right 9.413293e-05	k: 301	n:3580000
Cons ci ratio: 7.511834e-03	ci left: 7.042437e-02	ci right 7.095565e-02	k: 253069	n:3580000
KS ci ratio: 8.695765e-02	ci left: 5.426445e-04	ci right 5.922474e-04	k: 2030	n:3580000
ALS2   3580000 perm   6582 sec   (544 perm/sec)   p_kst 5.670391e-04   p_cons 7.068966e-02   p_joint 8.407821e-05

Joint ci ratio: 2.251886e-01	ci left: 7.490180e-05	ci right 9.416497e-05	k: 302	n:3590000
Cons ci ratio: 7.501077e-03	ci left: 7.042978e-02	ci right 7.096033e-02	k: 253794	n:3590000
KS ci ratio: 8.682949e-02	ci left: 5.427679e-04	ci right 5.923053e-04	k: 2036	n:3590000
ALS2   3590000 perm   6616 sec   (543 perm/sec)   p_kst 5.671309e-04   p_cons 7.069471e-02   p_joint 8.412256e-05

Joint ci ratio: 2.244490e-01	ci left: 7.521802e-05	ci right 9.449019e-05	k: 304	n:3600000
Cons ci ratio: 7.490461e-03	ci left: 7.043349e-02	ci right 7.096332e-02	k: 254513	n:3600000
KS ci ratio: 8.665946e-02	ci left: 5.434342e-04	ci right 5.929304e-04	k: 2044	n:3600000
ALS2   3600000 perm   6650 sec   (541 perm/sec)   p_kst 5.677778e-04   p_cons 7.069806e-02   p_joint 8.444444e-05

Joint ci ratio: 2.240820e-01	ci left: 7.527110e-05	ci right 9.452099e-05	k: 305	n:3610000
Cons ci ratio: 7.480899e-03	ci left: 7.041948e-02	ci right 7.094852e-02	k: 255168	n:3610000
KS ci ratio: 8.653260e-02	ci left: 5.435549e-04	ci right 5.929859e-04	k: 2050	n:3610000
ALS2   3610000 perm   6684 sec   (540 perm/sec)   p_kst 5.678670e-04   p_cons 7.068366e-02   p_joint 8.448753e-05

Joint ci ratio: 2.237167e-01	ci left: 7.532392e-05	ci right 9.455159e-05	k: 306	n:3620000
Cons ci ratio: 7.470572e-03	ci left: 7.041961e-02	ci right 7.094793e-02	k: 255874	n:3620000
KS ci ratio: 8.632237e-02	ci left: 5.447562e-04	ci right 5.941700e-04	k: 2060	n:3620000
ALS2   3620000 perm   6719 sec   (539 perm/sec)   p_kst 5.690608e-04   p_cons 7.068343e-02   p_joint 8.453039e-05

Joint ci ratio: 2.233532e-01	ci left: 7.537648e-05	ci right 9.458200e-05	k: 307	n:3630000
Cons ci ratio: 7.460930e-03	ci left: 7.040847e-02	ci right 7.093602e-02	k: 256539	n:3630000
KS ci ratio: 8.628056e-02	ci left: 5.437945e-04	ci right 5.930960e-04	k: 2062	n:3630000
ALS2   3630000 perm   6753 sec   (538 perm/sec)   p_kst 5.680441e-04   p_cons 7.067190e-02   p_joint 8.457300e-05

Joint ci ratio: 2.226315e-01	ci left: 7.568816e-05	ci right 9.490224e-05	k: 309	n:3640000
Cons ci ratio: 7.450483e-03	ci left: 7.041220e-02	ci right 7.093903e-02	k: 257258	n:3640000
KS ci ratio: 8.611372e-02	ci left: 5.444510e-04	ci right 5.937118e-04	k: 2070	n:3640000
ALS2   3640000 perm   6789 sec   (536 perm/sec)   p_kst 5.686813e-04   p_cons 7.067527e-02   p_joint 8.489011e-05

Joint ci ratio: 2.222733e-01	ci left: 7.573951e-05	ci right 9.493145e-05	k: 310	n:3650000
Cons ci ratio: 7.440716e-03	ci left: 7.040470e-02	ci right 7.093078e-02	k: 257936	n:3650000
KS ci ratio: 8.598925e-02	ci left: 5.445678e-04	ci right 5.937643e-04	k: 2076	n:3650000
ALS2   3650000 perm   6824 sec   (535 perm/sec)   p_kst 5.687671e-04   p_cons 7.066740e-02   p_joint 8.493151e-05

Joint ci ratio: 2.222733e-01	ci left: 7.553257e-05	ci right 9.467208e-05	k: 310	n:3660000
Cons ci ratio: 7.429565e-03	ci left: 7.042233e-02	ci right 7.094775e-02	k: 258706	n:3660000
KS ci ratio: 8.594792e-02	ci left: 5.436146e-04	ci right 5.927002e-04	k: 2078	n:3660000
ALS2   3660000 perm   6858 sec   (534 perm/sec)   p_kst 5.677596e-04   p_cons 7.068470e-02   p_joint 8.469945e-05

Joint ci ratio: 2.219168e-01	ci left: 7.558408e-05	ci right 9.470173e-05	k: 311	n:3670000
Cons ci ratio: 7.419003e-03	ci left: 7.043034e-02	ci right 7.095507e-02	k: 259441	n:3670000
KS ci ratio: 8.580358e-02	ci left: 5.439998e-04	ci right 5.930336e-04	k: 2085	n:3670000
ALS2   3670000 perm   6894 sec   (532 perm/sec)   p_kst 5.681199e-04   p_cons 7.069237e-02   p_joint 8.474114e-05

Joint ci ratio: 2.219169e-01	ci left: 7.537869e-05	ci right 9.444439e-05	k: 311	n:3680000
Cons ci ratio: 7.409329e-03	ci left: 7.042340e-02	ci right 7.094739e-02	k: 260121	n:3680000
KS ci ratio: 8.572145e-02	ci left: 5.435852e-04	ci right 5.925323e-04	k: 2089	n:3680000
ALS2   3680000 perm   6929 sec   (531 perm/sec)   p_kst 5.676630e-04   p_cons 7.068505e-02   p_joint 8.451087e-05

Joint ci ratio: 2.215621e-01	ci left: 7.543036e-05	ci right 9.447447e-05	k: 312	n:3690000
Cons ci ratio: 7.399799e-03	ci left: 7.041459e-02	ci right 7.093784e-02	k: 260794	n:3690000
KS ci ratio: 8.557824e-02	ci left: 5.439684e-04	ci right 5.928642e-04	k: 2096	n:3690000
ALS2   3690000 perm   6965 sec   (530 perm/sec)   p_kst 5.680217e-04   p_cons 7.067588e-02   p_joint 8.455285e-05

Joint ci ratio: 2.208575e-01	ci left: 7.573709e-05	ci right 9.478957e-05	k: 314	n:3700000
Cons ci ratio: 7.389774e-03	ci left: 7.041528e-02	ci right 7.093782e-02	k: 261502	n:3700000
KS ci ratio: 8.541544e-02	ci left: 5.446142e-04	ci right 5.934702e-04	k: 2104	n:3700000
ALS2   3700000 perm   7000 sec   (529 perm/sec)   p_kst 5.686486e-04   p_cons 7.067622e-02   p_joint 8.486486e-05

Joint ci ratio: 2.208576e-01	ci left: 7.553294e-05	ci right 9.453408e-05	k: 314	n:3710000
Cons ci ratio: 7.379653e-03	ci left: 7.041839e-02	ci right 7.094023e-02	k: 262219	n:3710000
KS ci ratio: 8.533442e-02	ci left: 5.442014e-04	ci right 5.929718e-04	k: 2108	n:3710000
ALS2   3710000 perm   7035 sec   (527 perm/sec)   p_kst 5.681941e-04   p_cons 7.067898e-02   p_joint 8.463612e-05

Joint ci ratio: 2.201597e-01	ci left: 7.583784e-05	ci right 9.484723e-05	k: 316	n:3720000
Cons ci ratio: 7.369528e-03	ci left: 7.042228e-02	ci right 7.094344e-02	k: 262939	n:3720000
KS ci ratio: 8.503246e-02	ci left: 5.466849e-04	ci right 5.954958e-04	k: 2123	n:3720000
ALS2   3720000 perm   7070 sec   (526 perm/sec)   p_kst 5.706989e-04   p_cons 7.068253e-02   p_joint 8.494624e-05

Joint ci ratio: 2.201597e-01	ci left: 7.563452e-05	ci right 9.459295e-05	k: 316	n:3730000
Cons ci ratio: 7.359355e-03	ci left: 7.042776e-02	ci right 7.094824e-02	k: 263665	n:3730000
KS ci ratio: 8.497250e-02	ci left: 5.460064e-04	ci right 5.947207e-04	k: 2126	n:3730000
ALS2   3730000 perm   7106 sec   (525 perm/sec)   p_kst 5.699732e-04   p_cons 7.068767e-02   p_joint 8.471850e-05

Joint ci ratio: 2.201598e-01	ci left: 7.543229e-05	ci right 9.434003e-05	k: 316	n:3740000
Cons ci ratio: 7.348685e-03	ci left: 7.044282e-02	ci right 7.096265e-02	k: 264427	n:3740000
KS ci ratio: 8.485290e-02	ci left: 5.461167e-04	ci right 5.947689e-04	k: 2132	n:3740000
ALS2   3740000 perm   7140 sec   (524 perm/sec)   p_kst 5.700535e-04   p_cons 7.070241e-02   p_joint 8.449198e-05

Joint ci ratio: 2.198133e-01	ci left: 7.548311e-05	ci right 9.436979e-05	k: 317	n:3750000
Cons ci ratio: 7.338657e-03	ci left: 7.044716e-02	ci right 7.096631e-02	k: 265149	n:3750000
KS ci ratio: 8.475363e-02	ci left: 5.459654e-04	ci right 5.945445e-04	k: 2137	n:3750000
ALS2   3750000 perm   7176 sec   (523 perm/sec)   p_kst 5.698667e-04   p_cons 7.070640e-02   p_joint 8.453333e-05

Joint ci ratio: 2.194685e-01	ci left: 7.553369e-05	ci right 9.439937e-05	k: 318	n:3760000
Cons ci ratio: 7.329041e-03	ci left: 7.044483e-02	ci right 7.096328e-02	k: 265846	n:3760000
KS ci ratio: 8.461521e-02	ci left: 5.463357e-04	ci right 5.948643e-04	k: 2144	n:3760000
ALS2   3760000 perm   7211 sec   (521 perm/sec)   p_kst 5.702128e-04   p_cons 7.070372e-02   p_joint 8.457447e-05

Joint ci ratio: 2.191253e-01	ci left: 7.558401e-05	ci right 9.442878e-05	k: 319	n:3770000
Cons ci ratio: 7.319626e-03	ci left: 7.043960e-02	ci right 7.095734e-02	k: 266532	n:3770000
KS ci ratio: 8.453645e-02	ci left: 5.459251e-04	ci right 5.943699e-04	k: 2148	n:3770000
ALS2   3770000 perm   7246 sec   (520 perm/sec)   p_kst 5.697613e-04   p_cons 7.069814e-02   p_joint 8.461538e-05

Joint ci ratio: 2.187837e-01	ci left: 7.563410e-05	ci right 9.445800e-05	k: 320	n:3780000
Cons ci ratio: 7.309731e-03	ci left: 7.044365e-02	ci right 7.096071e-02	k: 267253	n:3780000
KS ci ratio: 8.439909e-02	ci left: 5.462936e-04	ci right 5.946884e-04	k: 2155	n:3780000
ALS2   3780000 perm   7282 sec   (519 perm/sec)   p_kst 5.701058e-04   p_cons 7.070185e-02   p_joint 8.465608e-05

Joint ci ratio: 2.184438e-01	ci left: 7.568394e-05	ci right 9.448705e-05	k: 321	n:3790000
Cons ci ratio: 7.300199e-03	ci left: 7.044188e-02	ci right 7.095825e-02	k: 267952	n:3790000
KS ci ratio: 8.430140e-02	ci left: 5.461436e-04	ci right 5.944664e-04	k: 2160	n:3790000
ALS2   3790000 perm   7318 sec   (518 perm/sec)   p_kst 5.699208e-04   p_cons 7.069974e-02   p_joint 8.469657e-05

Joint ci ratio: 2.184438e-01	ci left: 7.548477e-05	ci right 9.423840e-05	k: 321	n:3800000
Cons ci ratio: 7.291098e-03	ci left: 7.043302e-02	ci right 7.094869e-02	k: 268624	n:3800000
KS ci ratio: 8.412636e-02	ci left: 5.470249e-04	ci right 5.953203e-04	k: 2169	n:3800000
ALS2   3800000 perm   7353 sec   (517 perm/sec)   p_kst 5.707895e-04   p_cons 7.069053e-02   p_joint 8.447368e-05

Joint ci ratio: 2.184438e-01	ci left: 7.528665e-05	ci right 9.399105e-05	k: 321	n:3810000
Cons ci ratio: 7.281624e-03	ci left: 7.043155e-02	ci right 7.094653e-02	k: 269324	n:3810000
KS ci ratio: 8.404895e-02	ci left: 5.466170e-04	ci right 5.948297e-04	k: 2173	n:3810000
ALS2   3810000 perm   7389 sec   (516 perm/sec)   p_kst 5.703412e-04   p_cons 7.068871e-02   p_joint 8.425197e-05

Joint ci ratio: 2.184438e-01	ci left: 7.508956e-05	ci right 9.374501e-05	k: 321	n:3820000
Cons ci ratio: 7.271389e-03	ci left: 7.044446e-02	ci right 7.095881e-02	k: 270079	n:3820000
KS ci ratio: 8.401036e-02	ci left: 5.456986e-04	ci right 5.938072e-04	k: 2175	n:3820000
ALS2   3820000 perm   7424 sec   (515 perm/sec)   p_kst 5.693717e-04   p_cons 7.070131e-02   p_joint 8.403141e-05

Joint ci ratio: 2.184438e-01	ci left: 7.489351e-05	ci right 9.350024e-05	k: 321	n:3830000
Cons ci ratio: 7.262078e-03	ci left: 7.044140e-02	ci right 7.095507e-02	k: 270773	n:3830000
KS ci ratio: 8.389477e-02	ci left: 5.458075e-04	ci right 5.938562e-04	k: 2181	n:3830000
ALS2   3830000 perm   7460 sec   (513 perm/sec)   p_kst 5.694517e-04   p_cons 7.069791e-02   p_joint 8.381201e-05

Joint ci ratio: 2.174332e-01	ci left: 7.543708e-05	ci right 9.408058e-05	k: 324	n:3840000
Cons ci ratio: 7.252976e-03	ci left: 7.043524e-02	ci right 7.094822e-02	k: 271455	n:3840000
KS ci ratio: 8.379882e-02	ci left: 5.456609e-04	ci right 5.936391e-04	k: 2186	n:3840000
ALS2   3840000 perm   7496 sec   (512 perm/sec)   p_kst 5.692708e-04   p_cons 7.069141e-02   p_joint 8.437500e-05

Joint ci ratio: 2.174333e-01	ci left: 7.524114e-05	ci right 9.383621e-05	k: 324	n:3850000
Cons ci ratio: 7.243062e-03	ci left: 7.044441e-02	ci right 7.095675e-02	k: 272196	n:3850000
KS ci ratio: 8.368410e-02	ci left: 5.457694e-04	ci right 5.936882e-04	k: 2192	n:3850000
ALS2   3850000 perm   7532 sec   (511 perm/sec)   p_kst 5.693506e-04   p_cons 7.070026e-02   p_joint 8.415584e-05

Joint ci ratio: 2.174333e-01	ci left: 7.504621e-05	ci right 9.359311e-05	k: 324	n:3860000
Cons ci ratio: 7.234401e-03	ci left: 7.043155e-02	ci right 7.094318e-02	k: 272852	n:3860000
KS ci ratio: 8.360791e-02	ci left: 5.453701e-04	ci right 5.932081e-04	k: 2196	n:3860000
ALS2   3860000 perm   7569 sec   (510 perm/sec)   p_kst 5.689119e-04   p_cons 7.068705e-02   p_joint 8.393782e-05

Joint ci ratio: 2.174333e-01	ci left: 7.485230e-05	ci right 9.335127e-05	k: 324	n:3870000
Cons ci ratio: 7.225217e-03	ci left: 7.042882e-02	ci right 7.093978e-02	k: 273547	n:3870000
KS ci ratio: 8.356992e-02	ci left: 5.444668e-04	ci right 5.922029e-04	k: 2198	n:3870000
ALS2   3870000 perm   7605 sec   (509 perm/sec)   p_kst 5.679587e-04   p_cons 7.068398e-02   p_joint 8.372093e-05

Joint ci ratio: 2.170996e-01	ci left: 7.490309e-05	ci right 9.338241e-05	k: 325	n:3880000
Cons ci ratio: 7.216464e-03	ci left: 7.041890e-02	ci right 7.092916e-02	k: 274214	n:3880000
KS ci ratio: 8.343721e-02	ci left: 5.448300e-04	ci right 5.925184e-04	k: 2205	n:3880000
ALS2   3880000 perm   7642 sec   (508 perm/sec)   p_kst 5.682990e-04   p_cons 7.067371e-02   p_joint 8.376289e-05

Joint ci ratio: 2.170996e-01	ci left: 7.471053e-05	ci right 9.314235e-05	k: 325	n:3890000
Cons ci ratio: 7.206685e-03	ci left: 7.042828e-02	ci right 7.093791e-02	k: 274956	n:3890000
KS ci ratio: 8.338056e-02	ci left: 5.441845e-04	ci right 5.917825e-04	k: 2208	n:3890000
ALS2   3890000 perm   7678 sec   (507 perm/sec)   p_kst 5.676093e-04   p_cons 7.068278e-02   p_joint 8.354756e-05

Joint ci ratio: 2.170996e-01	ci left: 7.451897e-05	ci right 9.290353e-05	k: 325	n:3900000
Cons ci ratio: 7.197424e-03	ci left: 7.042890e-02	ci right 7.093789e-02	k: 275664	n:3900000
KS ci ratio: 8.334288e-02	ci left: 5.432913e-04	ci right 5.907886e-04	k: 2210	n:3900000
ALS2   3900000 perm   7714 sec   (506 perm/sec)   p_kst 5.666667e-04   p_cons 7.068308e-02   p_joint 8.333333e-05

Joint ci ratio: 2.167674e-01	ci left: 7.457024e-05	ci right 9.293555e-05	k: 326	n:3910000
Cons ci ratio: 7.187834e-03	ci left: 7.043617e-02	ci right 7.094452e-02	k: 276398	n:3910000
KS ci ratio: 8.324881e-02	ci left: 5.431540e-04	ci right 5.905831e-04	k: 2215	n:3910000
ALS2   3910000 perm   7751 sec   (504 perm/sec)   p_kst 5.664962e-04   p_cons 7.069003e-02   p_joint 8.337596e-05

Joint ci ratio: 2.167674e-01	ci left: 7.438001e-05	ci right 9.269847e-05	k: 326	n:3920000
Cons ci ratio: 7.178310e-03	ci left: 7.044288e-02	ci right 7.095061e-02	k: 277130	n:3920000
KS ci ratio: 8.302425e-02	ci left: 5.447660e-04	ci right 5.922013e-04	k: 2227	n:3920000
ALS2   3920000 perm   7787 sec   (503 perm/sec)   p_kst 5.681122e-04   p_cons 7.069643e-02   p_joint 8.316327e-05

Joint ci ratio: 2.164367e-01	ci left: 7.443140e-05	ci right 9.273083e-05	k: 327	n:3930000
Cons ci ratio: 7.168838e-03	ci left: 7.044931e-02	ci right 7.095641e-02	k: 277861	n:3930000
KS ci ratio: 8.293125e-02	ci left: 5.446257e-04	ci right 5.919931e-04	k: 2232	n:3930000
ALS2   3930000 perm   7824 sec   (502 perm/sec)   p_kst 5.679389e-04   p_cons 7.070254e-02   p_joint 8.320611e-05

Joint ci ratio: 2.164368e-01	ci left: 7.424248e-05	ci right 9.249548e-05	k: 327	n:3940000
Cons ci ratio: 7.159348e-03	ci left: 7.045672e-02	ci right 7.096320e-02	k: 278596	n:3940000
KS ci ratio: 8.280156e-02	ci left: 5.449832e-04	ci right 5.923040e-04	k: 2239	n:3940000
ALS2   3940000 perm   7861 sec   (501 perm/sec)   p_kst 5.682741e-04   p_cons 7.070964e-02   p_joint 8.299492e-05

Joint ci ratio: 2.157799e-01	ci left: 7.453345e-05	ci right 9.279500e-05	k: 329	n:3950000
Cons ci ratio: 7.150212e-03	ci left: 7.045828e-02	ci right 7.096412e-02	k: 279308	n:3950000
KS ci ratio: 8.269088e-02	ci left: 5.450910e-04	ci right 5.923549e-04	k: 2245	n:3950000
ALS2   3950000 perm   7899 sec   (500 perm/sec)   p_kst 5.683544e-04   p_cons 7.071089e-02   p_joint 8.329114e-05

Joint ci ratio: 2.154537e-01	ci left: 7.458413e-05	ci right 9.282681e-05	k: 330	n:3960000
Cons ci ratio: 7.141084e-03	ci left: 7.046034e-02	ci right 7.096554e-02	k: 280022	n:3960000
KS ci ratio: 8.259900e-02	ci left: 5.449511e-04	ci right 5.921478e-04	k: 2250	n:3960000
ALS2   3960000 perm   7937 sec   (499 perm/sec)   p_kst 5.681818e-04   p_cons 7.071263e-02   p_joint 8.333333e-05

Joint ci ratio: 2.151289e-01	ci left: 7.463457e-05	ci right 9.285844e-05	k: 331	n:3970000
Cons ci ratio: 7.131881e-03	ci left: 7.046439e-02	ci right 7.096898e-02	k: 280744	n:3970000
KS ci ratio: 8.256237e-02	ci left: 5.440718e-04	ci right 5.911704e-04	k: 2252	n:3970000
ALS2   3970000 perm   7975 sec   (498 perm/sec)   p_kst 5.672544e-04   p_cons 7.071637e-02   p_joint 8.337531e-05

Joint ci ratio: 2.151289e-01	ci left: 7.444704e-05	ci right 9.262513e-05	k: 331	n:3980000
Cons ci ratio: 7.122510e-03	ci left: 7.047219e-02	ci right 7.097617e-02	k: 281481	n:3980000
KS ci ratio: 8.243439e-02	ci left: 5.444273e-04	ci right 5.914801e-04	k: 2259	n:3980000
ALS2   3980000 perm   8012 sec   (497 perm/sec)   p_kst 5.675879e-04   p_cons 7.072387e-02   p_joint 8.316583e-05

Joint ci ratio: 2.151290e-01	ci left: 7.426046e-05	ci right 9.239299e-05	k: 331	n:3990000
Cons ci ratio: 7.113677e-03	ci left: 7.047070e-02	ci right 7.097403e-02	k: 282181	n:3990000
KS ci ratio: 8.234336e-02	ci left: 5.442901e-04	ci right 5.912767e-04	k: 2264	n:3990000
ALS2   3990000 perm   8050 sec   (496 perm/sec)   p_kst 5.674185e-04   p_cons 7.072206e-02   p_joint 8.295739e-05

Joint ci ratio: 2.148057e-01	ci left: 7.431135e-05	ci right 9.242544e-05	k: 332	n:4000000
Cons ci ratio: 7.104485e-03	ci left: 7.047645e-02	ci right 7.097917e-02	k: 282910	n:4000000
KS ci ratio: 8.223451e-02	ci left: 5.443985e-04	ci right 5.913294e-04	k: 2270	n:4000000
ALS2   4000000 perm   8088 sec   (495 perm/sec)   p_kst 5.675000e-04   p_cons 7.072750e-02   p_joint 8.300000e-05

Joint ci ratio: 2.141635e-01	ci left: 7.459800e-05	ci right 9.272046e-05	k: 334	n:4010000
Cons ci ratio: 7.095167e-03	ci left: 7.048516e-02	ci right 7.098728e-02	k: 283651	n:4010000
KS ci ratio: 8.214414e-02	ci left: 5.442622e-04	ci right 5.911272e-04	k: 2275	n:4010000
ALS2   4010000 perm   8126 sec   (493 perm/sec)   p_kst 5.673317e-04   p_cons 7.073591e-02   p_joint 8.329177e-05

Joint ci ratio: 2.141635e-01	ci left: 7.441243e-05	ci right 9.248981e-05	k: 334	n:4020000
Cons ci ratio: 7.086301e-03	ci left: 7.048613e-02	ci right 7.098763e-02	k: 284361	n:4020000
KS ci ratio: 8.209009e-02	ci left: 5.436392e-04	ci right 5.904184e-04	k: 2278	n:4020000
ALS2   4020000 perm   8164 sec   (492 perm/sec)   p_kst 5.666667e-04   p_cons 7.073657e-02   p_joint 8.308458e-05

Joint ci ratio: 2.135271e-01	ci left: 7.469748e-05	ci right 9.278312e-05	k: 336	n:4030000
Cons ci ratio: 7.077455e-03	ci left: 7.048734e-02	ci right 7.098822e-02	k: 285072	n:4030000
KS ci ratio: 8.192844e-02	ci left: 5.444777e-04	ci right 5.912323e-04	k: 2287	n:4030000
ALS2   4030000 perm   8201 sec   (491 perm/sec)   p_kst 5.674938e-04   p_cons 7.073747e-02   p_joint 8.337469e-05

Joint ci ratio: 2.135271e-01	ci left: 7.451259e-05	ci right 9.255346e-05	k: 336	n:4040000
Cons ci ratio: 7.068749e-03	ci left: 7.048657e-02	ci right 7.098682e-02	k: 285775	n:4040000
KS ci ratio: 8.185693e-02	ci left: 5.440998e-04	ci right 5.907793e-04	k: 2291	n:4040000
ALS2   4040000 perm   8240 sec   (490 perm/sec)   p_kst 5.670792e-04   p_cons 7.073639e-02   p_joint 8.316832e-05

Joint ci ratio: 2.132110e-01	ci left: 7.456233e-05	ci right 9.258502e-05	k: 337	n:4050000
Cons ci ratio: 7.059664e-03	ci left: 7.049344e-02	ci right 7.099310e-02	k: 286509	n:4050000
KS ci ratio: 8.182128e-02	ci left: 5.432401e-04	ci right 5.898245e-04	k: 2293	n:4050000
ALS2   4050000 perm   8277 sec   (489 perm/sec)   p_kst 5.661728e-04   p_cons 7.074296e-02   p_joint 8.320988e-05

Joint ci ratio: 2.128963e-01	ci left: 7.461184e-05	ci right 9.261641e-05	k: 338	n:4060000
Cons ci ratio: 7.051445e-03	ci left: 7.048479e-02	ci right 7.098380e-02	k: 287180	n:4060000
KS ci ratio: 8.175006e-02	ci left: 5.428671e-04	ci right 5.893771e-04	k: 2297	n:4060000
ALS2   4060000 perm   8315 sec   (488 perm/sec)   p_kst 5.657635e-04   p_cons 7.073399e-02   p_joint 8.325123e-05

Joint ci ratio: 2.128963e-01	ci left: 7.442852e-05	ci right 9.238885e-05	k: 338	n:4070000
Cons ci ratio: 7.042637e-03	ci left: 7.048771e-02	ci right 7.098612e-02	k: 287898	n:4070000
KS ci ratio: 8.169677e-02	ci left: 5.422553e-04	ci right 5.886812e-04	k: 2300	n:4070000
ALS2   4070000 perm   8354 sec   (487 perm/sec)   p_kst 5.651106e-04   p_cons 7.073661e-02   p_joint 8.304668e-05

Joint ci ratio: 2.128963e-01	ci left: 7.424609e-05	ci right 9.216241e-05	k: 338	n:4080000
Cons ci ratio: 7.034439e-03	ci left: 7.047985e-02	ci right 7.097762e-02	k: 288572	n:4080000
KS ci ratio: 8.155510e-02	ci left: 5.428470e-04	ci right 5.892391e-04	k: 2308	n:4080000
ALS2   4080000 perm   8392 sec   (486 perm/sec)   p_kst 5.656863e-04   p_cons 7.072843e-02   p_joint 8.284314e-05

Joint ci ratio: 2.128963e-01	ci left: 7.406456e-05	ci right 9.193707e-05	k: 338	n:4090000
Cons ci ratio: 7.026256e-03	ci left: 7.047227e-02	ci right 7.096941e-02	k: 289247	n:4090000
KS ci ratio: 8.143174e-02	ci left: 5.431964e-04	ci right 5.895448e-04	k: 2315	n:4090000
ALS2   4090000 perm   8431 sec   (485 perm/sec)   p_kst 5.660147e-04   p_cons 7.072054e-02   p_joint 8.264059e-05

Joint ci ratio: 2.128963e-01	ci left: 7.388392e-05	ci right 9.171284e-05	k: 338	n:4100000
Cons ci ratio: 7.018010e-03	ci left: 7.046644e-02	ci right 7.096295e-02	k: 289929	n:4100000
KS ci ratio: 8.136153e-02	ci left: 5.428273e-04	ci right 5.891023e-04	k: 2319	n:4100000
ALS2   4100000 perm   8469 sec   (484 perm/sec)   p_kst 5.656098e-04   p_cons 7.071439e-02   p_joint 8.243902e-05

Joint ci ratio: 2.128964e-01	ci left: 7.370415e-05	ci right 9.148969e-05	k: 338	n:4110000
Cons ci ratio: 7.009534e-03	ci left: 7.046549e-02	ci right 7.096139e-02	k: 290631	n:4110000
KS ci ratio: 8.125652e-02	ci left: 5.429367e-04	ci right 5.891585e-04	k: 2325	n:4110000
ALS2   4110000 perm   8508 sec   (483 perm/sec)   p_kst 5.656934e-04   p_cons 7.071314e-02   p_joint 8.223844e-05

Joint ci ratio: 2.125831e-01	ci left: 7.375504e-05	ci right 9.152326e-05	k: 339	n:4120000
Cons ci ratio: 7.001425e-03	ci left: 7.045825e-02	ci right 7.095352e-02	k: 291307	n:4120000
KS ci ratio: 8.109974e-02	ci left: 5.437590e-04	ci right 5.899573e-04	k: 2334	n:4120000
ALS2   4120000 perm   8547 sec   (482 perm/sec)   p_kst 5.665049e-04   p_cons 7.070558e-02   p_joint 8.228155e-05

Joint ci ratio: 2.122711e-01	ci left: 7.380571e-05	ci right 9.155665e-05	k: 340	n:4130000
Cons ci ratio: 6.992841e-03	ci left: 7.046047e-02	ci right 7.095515e-02	k: 292022	n:4130000
KS ci ratio: 8.089209e-02	ci left: 5.452891e-04	ci right 5.914932e-04	k: 2346	n:4130000
ALS2   4130000 perm   8586 sec   (481 perm/sec)   p_kst 5.680387e-04   p_cons 7.070751e-02   p_joint 8.232446e-05

Joint ci ratio: 2.119605e-01	ci left: 7.385615e-05	ci right 9.158986e-05	k: 341	n:4140000
Cons ci ratio: 6.984302e-03	ci left: 7.046244e-02	ci right 7.095652e-02	k: 292736	n:4140000
KS ci ratio: 8.082326e-02	ci left: 5.449187e-04	ci right 5.910502e-04	k: 2350	n:4140000
ALS2   4140000 perm   8624 sec   (480 perm/sec)   p_kst 5.676329e-04   p_cons 7.070918e-02   p_joint 8.236715e-05

Joint ci ratio: 2.113435e-01	ci left: 7.413457e-05	ci right 9.187659e-05	k: 343	n:4150000
Cons ci ratio: 6.976024e-03	ci left: 7.046006e-02	ci right 7.095355e-02	k: 293432	n:4150000
KS ci ratio: 8.075461e-02	ci left: 5.445500e-04	ci right 5.906093e-04	k: 2354	n:4150000
ALS2   4150000 perm   8663 sec   (479 perm/sec)   p_kst 5.672289e-04   p_cons 7.070651e-02   p_joint 8.265060e-05

Joint ci ratio: 2.113435e-01	ci left: 7.395636e-05	ci right 9.165573e-05	k: 343	n:4160000
Cons ci ratio: 6.967749e-03	ci left: 7.045818e-02	ci right 7.095107e-02	k: 294130	n:4160000
KS ci ratio: 8.068613e-02	ci left: 5.441831e-04	ci right 5.901705e-04	k: 2358	n:4160000
ALS2   4160000 perm   8702 sec   (478 perm/sec)   p_kst 5.668269e-04   p_cons 7.070433e-02   p_joint 8.245192e-05

Joint ci ratio: 2.113435e-01	ci left: 7.377901e-05	ci right 9.143594e-05	k: 343	n:4170000
Cons ci ratio: 6.959200e-03	ci left: 7.046206e-02	ci right 7.095436e-02	k: 294852	n:4170000
KS ci ratio: 8.056667e-02	ci left: 5.445229e-04	ci right 5.904678e-04	k: 2365	n:4170000
ALS2   4170000 perm   8741 sec   (477 perm/sec)   p_kst 5.671463e-04   p_cons 7.070791e-02   p_joint 8.225420e-05

Joint ci ratio: 2.110370e-01	ci left: 7.382908e-05	ci right 9.146906e-05	k: 344	n:4180000
Cons ci ratio: 6.950821e-03	ci left: 7.046329e-02	ci right 7.095501e-02	k: 295563	n:4180000
KS ci ratio: 8.049867e-02	ci left: 5.441579e-04	ci right 5.900314e-04	k: 2369	n:4180000
ALS2   4180000 perm   8781 sec   (476 perm/sec)   p_kst 5.667464e-04   p_cons 7.070885e-02   p_joint 8.229665e-05

Joint ci ratio: 2.110370e-01	ci left: 7.365288e-05	ci right 9.125076e-05	k: 344	n:4190000
Cons ci ratio: 6.942321e-03	ci left: 7.046738e-02	ci right 7.095852e-02	k: 296286	n:4190000
KS ci ratio: 8.043084e-02	ci left: 5.437946e-04	ci right 5.895970e-04	k: 2373	n:4190000
ALS2   4190000 perm   8820 sec   (475 perm/sec)   p_kst 5.663484e-04   p_cons 7.071265e-02   p_joint 8.210024e-05

Joint ci ratio: 2.107318e-01	ci left: 7.370304e-05	ci right 9.128414e-05	k: 345	n:4200000
Cons ci ratio: 6.934053e-03	ci left: 7.046764e-02	ci right 7.095819e-02	k: 296993	n:4200000
KS ci ratio: 8.034628e-02	ci left: 5.436664e-04	ci right 5.894076e-04	k: 2378	n:4200000
ALS2   4200000 perm   8860 sec   (474 perm/sec)   p_kst 5.661905e-04   p_cons 7.071262e-02   p_joint 8.214286e-05

Joint ci ratio: 2.107318e-01	ci left: 7.352797e-05	ci right 9.106732e-05	k: 345	n:4210000
Cons ci ratio: 6.925589e-03	ci left: 7.047217e-02	ci right 7.096215e-02	k: 297718	n:4210000
KS ci ratio: 8.032944e-02	ci left: 5.426078e-04	ci right 5.882499e-04	k: 2379	n:4210000
ALS2   4210000 perm   8899 sec   (473 perm/sec)   p_kst 5.650831e-04   p_cons 7.071686e-02   p_joint 8.194774e-05

Joint ci ratio: 2.107318e-01	ci left: 7.335373e-05	ci right 9.085152e-05	k: 345	n:4220000
Cons ci ratio: 6.917830e-03	ci left: 7.046390e-02	ci right 7.095328e-02	k: 298389	n:4220000
KS ci ratio: 8.026204e-02	ci left: 5.422508e-04	ci right 5.878229e-04	k: 2383	n:4220000
ALS2   4220000 perm   8939 sec   (472 perm/sec)   p_kst 5.646919e-04   p_cons 7.070829e-02   p_joint 8.175355e-05

Joint ci ratio: 2.101254e-01	ci left: 7.362822e-05	ci right 9.113443e-05	k: 347	n:4230000
Cons ci ratio: 6.909239e-03	ci left: 7.047196e-02	ci right 7.096078e-02	k: 299129	n:4230000
KS ci ratio: 8.016122e-02	ci left: 5.423589e-04	ci right 5.878801e-04	k: 2389	n:4230000
ALS2   4230000 perm   8980 sec   (471 perm/sec)   p_kst 5.647754e-04   p_cons 7.071608e-02   p_joint 8.203310e-05

Joint ci ratio: 2.098241e-01	ci left: 7.367802e-05	ci right 9.116772e-05	k: 348	n:4240000
Cons ci ratio: 6.901150e-03	ci left: 7.047103e-02	ci right 7.095927e-02	k: 299831	n:4240000
KS ci ratio: 8.002738e-02	ci left: 5.429288e-04	ci right 5.884182e-04	k: 2397	n:4240000
ALS2   4240000 perm   9019 sec   (470 perm/sec)   p_kst 5.653302e-04   p_cons 7.071486e-02   p_joint 8.207547e-05

Joint ci ratio: 2.098241e-01	ci left: 7.350466e-05	ci right 9.095321e-05	k: 348	n:4250000
Cons ci ratio: 6.892929e-03	ci left: 7.047316e-02	ci right 7.096083e-02	k: 300546	n:4250000
KS ci ratio: 7.999406e-02	ci left: 5.421124e-04	ci right 5.875137e-04	k: 2399	n:4250000
ALS2   4250000 perm   9059 sec   (469 perm/sec)   p_kst 5.644706e-04   p_cons 7.071671e-02   p_joint 8.188235e-05

Joint ci ratio: 2.092255e-01	ci left: 7.377696e-05	ci right 9.123379e-05	k: 350	n:4260000
Cons ci ratio: 6.884541e-03	ci left: 7.047903e-02	ci right 7.096615e-02	k: 301277	n:4260000
KS ci ratio: 7.977822e-02	ci left: 5.438306e-04	ci right 5.892471e-04	k: 2412	n:4260000
ALS2   4260000 perm   9099 sec   (468 perm/sec)   p_kst 5.661972e-04   p_cons 7.072230e-02   p_joint 8.215962e-05

Joint ci ratio: 2.092255e-01	ci left: 7.360418e-05	ci right 9.102013e-05	k: 350	n:4270000
Cons ci ratio: 6.876490e-03	ci left: 7.047903e-02	ci right 7.096558e-02	k: 301983	n:4270000
KS ci ratio: 7.959695e-02	ci left: 5.450818e-04	ci right 5.904945e-04	k: 2423	n:4270000
ALS2   4270000 perm   9138 sec   (467 perm/sec)   p_kst 5.674473e-04   p_cons 7.072201e-02   p_joint 8.196721e-05

Joint ci ratio: 2.092255e-01	ci left: 7.343221e-05	ci right 9.080746e-05	k: 350	n:4280000
Cons ci ratio: 6.868125e-03	ci left: 7.048556e-02	ci right 7.097156e-02	k: 302717	n:4280000
KS ci ratio: 7.949861e-02	ci left: 5.451822e-04	ci right 5.905446e-04	k: 2429	n:4280000
ALS2   4280000 perm   9178 sec   (466 perm/sec)   p_kst 5.675234e-04   p_cons 7.072827e-02   p_joint 8.177570e-05

Joint ci ratio: 2.092255e-01	ci left: 7.326104e-05	ci right 9.059579e-05	k: 350	n:4290000
Cons ci ratio: 6.860557e-03	ci left: 7.047740e-02	ci right 7.096280e-02	k: 303388	n:4290000
KS ci ratio: 7.938434e-02	ci left: 5.455107e-04	ci right 5.908322e-04	k: 2436	n:4290000
ALS2   4290000 perm   9218 sec   (465 perm/sec)   p_kst 5.678322e-04   p_cons 7.071981e-02   p_joint 8.158508e-05

Joint ci ratio: 2.092256e-01	ci left: 7.309066e-05	ci right 9.038511e-05	k: 350	n:4300000
Cons ci ratio: 6.852347e-03	ci left: 7.048205e-02	ci right 7.096690e-02	k: 304114	n:4300000
KS ci ratio: 7.925434e-02	ci left: 5.460656e-04	ci right 5.913555e-04	k: 2444	n:4300000
ALS2   4300000 perm   9259 sec   (464 perm/sec)   p_kst 5.683721e-04   p_cons 7.072419e-02   p_joint 8.139535e-05

Joint ci ratio: 2.092256e-01	ci left: 7.292108e-05	ci right 9.017540e-05	k: 350	n:4310000
Cons ci ratio: 6.844106e-03	ci left: 7.048783e-02	ci right 7.097214e-02	k: 304845	n:4310000
KS ci ratio: 7.915728e-02	ci left: 5.461632e-04	ci right 5.914031e-04	k: 2450	n:4310000
ALS2   4310000 perm   9299 sec   (464 perm/sec)   p_kst 5.684455e-04   p_cons 7.072970e-02   p_joint 8.120650e-05

Joint ci ratio: 2.089282e-01	ci left: 7.297164e-05	ci right 9.021024e-05	k: 351	n:4320000
Cons ci ratio: 6.836052e-03	ci left: 7.049059e-02	ci right 7.097434e-02	k: 305563	n:4320000
KS ci ratio: 7.902839e-02	ci left: 5.467141e-04	ci right 5.919226e-04	k: 2458	n:4320000
ALS2   4320000 perm   9338 sec   (463 perm/sec)   p_kst 5.689815e-04   p_cons 7.073218e-02   p_joint 8.125000e-05

Joint ci ratio: 2.089282e-01	ci left: 7.280311e-05	ci right 9.000190e-05	k: 351	n:4330000
Cons ci ratio: 6.828205e-03	ci left: 7.048987e-02	ci right 7.097306e-02	k: 306266	n:4330000
KS ci ratio: 7.898025e-02	ci left: 5.461307e-04	ci right 5.912621e-04	k: 2461	n:4330000
ALS2   4330000 perm   9380 sec   (462 perm/sec)   p_kst 5.683603e-04   p_cons 7.073118e-02   p_joint 8.106236e-05

Joint ci ratio: 2.086320e-01	ci left: 7.285373e-05	ci right 9.003697e-05	k: 352	n:4340000
Cons ci ratio: 6.820206e-03	ci left: 7.049261e-02	ci right 7.097525e-02	k: 306984	n:4340000
KS ci ratio: 7.886820e-02	ci left: 5.464534e-04	ci right 5.915445e-04	k: 2468	n:4340000
ALS2   4340000 perm   9419 sec   (461 perm/sec)   p_kst 5.686636e-04   p_cons 7.073364e-02   p_joint 8.110599e-05

Joint ci ratio: 2.086321e-01	ci left: 7.268625e-05	ci right 8.982999e-05	k: 352	n:4350000
Cons ci ratio: 6.812521e-03	ci left: 7.048982e-02	ci right 7.097190e-02	k: 307678	n:4350000
KS ci ratio: 7.880440e-02	ci left: 5.460986e-04	ci right 5.911223e-04	k: 2472	n:4350000
ALS2   4350000 perm   9460 sec   (460 perm/sec)   p_kst 5.682759e-04   p_cons 7.073057e-02   p_joint 8.091954e-05

Joint ci ratio: 2.083372e-01	ci left: 7.273693e-05	ci right 8.986527e-05	k: 353	n:4360000
Cons ci ratio: 6.804838e-03	ci left: 7.048751e-02	ci right 7.096902e-02	k: 308374	n:4360000
KS ci ratio: 7.874076e-02	ci left: 5.457454e-04	ci right 5.907020e-04	k: 2476	n:4360000
ALS2   4360000 perm   9501 sec   (459 perm/sec)   p_kst 5.678899e-04   p_cons 7.072798e-02   p_joint 8.096330e-05

Joint ci ratio: 2.080435e-01	ci left: 7.278738e-05	ci right 8.990038e-05	k: 354	n:4370000
Cons ci ratio: 6.796602e-03	ci left: 7.049640e-02	ci right 7.097739e-02	k: 309119	n:4370000
KS ci ratio: 7.867728e-02	ci left: 5.453939e-04	ci right 5.902836e-04	k: 2480	n:4370000
ALS2   4370000 perm   9541 sec   (458 perm/sec)   p_kst 5.675057e-04   p_cons 7.073661e-02   p_joint 8.100686e-05

Joint ci ratio: 2.080435e-01	ci left: 7.262120e-05	ci right 8.969512e-05	k: 354	n:4380000
Cons ci ratio: 6.788466e-03	ci left: 7.050389e-02	ci right 7.098435e-02	k: 309858	n:4380000
KS ci ratio: 7.858231e-02	ci left: 5.454916e-04	ci right 5.903327e-04	k: 2486	n:4380000
ALS2   4380000 perm   9582 sec   (457 perm/sec)   p_kst 5.675799e-04   p_cons 7.074384e-02   p_joint 8.082192e-05

Joint ci ratio: 2.074599e-01	ci left: 7.288766e-05	ci right 8.997006e-05	k: 356	n:4390000
Cons ci ratio: 6.780876e-03	ci left: 7.050133e-02	ci right 7.098124e-02	k: 310553	n:4390000
KS ci ratio: 7.847194e-02	ci left: 5.458123e-04	ci right 5.906138e-04	k: 2493	n:4390000
ALS2   4390000 perm   9624 sec   (456 perm/sec)   p_kst 5.678815e-04   p_cons 7.074100e-02   p_joint 8.109339e-05

Joint ci ratio: 2.074600e-01	ci left: 7.272200e-05	ci right 8.976558e-05	k: 356	n:4400000
Cons ci ratio: 6.773264e-03	ci left: 7.049970e-02	ci right 7.097905e-02	k: 311252	n:4400000
KS ci ratio: 7.840910e-02	ci left: 5.454630e-04	ci right 5.901985e-04	k: 2497	n:4400000
ALS2   4400000 perm   9665 sec   (455 perm/sec)   p_kst 5.675000e-04   p_cons 7.073909e-02   p_joint 8.090909e-05

Joint ci ratio: 2.074600e-01	ci left: 7.255710e-05	ci right 8.956203e-05	k: 356	n:4410000
Cons ci ratio: 6.765375e-03	ci left: 7.050395e-02	ci right 7.098278e-02	k: 311977	n:4410000
KS ci ratio: 7.836209e-02	ci left: 5.448931e-04	ci right 5.895537e-04	k: 2500	n:4410000
ALS2   4410000 perm   9706 sec   (454 perm/sec)   p_kst 5.668934e-04   p_cons 7.074308e-02   p_joint 8.072562e-05

Joint ci ratio: 2.071700e-01	ci left: 7.260744e-05	ci right 8.959737e-05	k: 357	n:4420000
Cons ci ratio: 6.757711e-03	ci left: 7.050435e-02	ci right 7.098263e-02	k: 312685	n:4420000
KS ci ratio: 7.826826e-02	ci left: 5.449912e-04	ci right 5.896040e-04	k: 2506	n:4420000
ALS2   4420000 perm   9747 sec   (453 perm/sec)   p_kst 5.669683e-04   p_cons 7.074321e-02   p_joint 8.076923e-05

Joint ci ratio: 2.071700e-01	ci left: 7.244354e-05	ci right 8.939512e-05	k: 357	n:4430000
Cons ci ratio: 6.749980e-03	ci left: 7.050655e-02	ci right 7.098430e-02	k: 313401	n:4430000
KS ci ratio: 7.822149e-02	ci left: 5.444249e-04	ci right 5.889635e-04	k: 2509	n:4430000
ALS2   4430000 perm   9788 sec   (453 perm/sec)   p_kst 5.663657e-04   p_cons 7.074515e-02   p_joint 8.058691e-05

Joint ci ratio: 2.068813e-01	ci left: 7.249393e-05	ci right 8.943067e-05	k: 358	n:4440000
Cons ci ratio: 6.741629e-03	ci left: 7.052134e-02	ci right 7.099859e-02	k: 314173	n:4440000
KS ci ratio: 7.806610e-02	ci left: 5.454070e-04	ci right 5.899332e-04	k: 2519	n:4440000
ALS2   4440000 perm   9830 sec   (452 perm/sec)   p_kst 5.673423e-04   p_cons 7.075968e-02   p_joint 8.063063e-05

Joint ci ratio: 2.063074e-01	ci left: 7.275721e-05	ci right 8.970235e-05	k: 360	n:4450000
Cons ci ratio: 6.733885e-03	ci left: 7.052484e-02	ci right 7.100156e-02	k: 314895	n:4450000
KS ci ratio: 7.798877e-02	ci left: 5.452830e-04	ci right 5.897530e-04	k: 2524	n:4450000
ALS2   4450000 perm   9872 sec   (451 perm/sec)   p_kst 5.671910e-04   p_cons 7.076292e-02   p_joint 8.089888e-05

Joint ci ratio: 2.063074e-01	ci left: 7.259408e-05	ci right 8.950123e-05	k: 360	n:4460000
Cons ci ratio: 6.726545e-03	ci left: 7.052093e-02	ci right 7.099711e-02	k: 315584	n:4460000
KS ci ratio: 7.794251e-02	ci left: 5.447199e-04	ci right 5.891165e-04	k: 2527	n:4460000
ALS2   4460000 perm   9914 sec   (450 perm/sec)   p_kst 5.665919e-04   p_cons 7.075874e-02   p_joint 8.071749e-05

Joint ci ratio: 2.057383e-01	ci left: 7.285602e-05	ci right 8.977148e-05	k: 362	n:4470000
Cons ci ratio: 6.718772e-03	ci left: 7.052598e-02	ci right 7.100164e-02	k: 316313	n:4470000
KS ci ratio: 7.789632e-02	ci left: 5.441594e-04	ci right 5.884828e-04	k: 2530	n:4470000
ALS2   4470000 perm   9956 sec   (449 perm/sec)   p_kst 5.659955e-04   p_cons 7.076353e-02   p_joint 8.098434e-05

Joint ci ratio: 2.051738e-01	ci left: 7.311686e-05	ci right 9.004046e-05	k: 364	n:4480000
Cons ci ratio: 6.711424e-03	ci left: 7.052321e-02	ci right 7.099833e-02	k: 317007	n:4480000
KS ci ratio: 7.775817e-02	ci left: 5.449146e-04	ci right 5.892172e-04	k: 2539	n:4480000
ALS2   4480000 perm   9998 sec   (448 perm/sec)   p_kst 5.667411e-04   p_cons 7.076049e-02   p_joint 8.125000e-05

Joint ci ratio: 2.046139e-01	ci left: 7.337660e-05	ci right 9.030818e-05	k: 366	n:4490000
Cons ci ratio: 6.703340e-03	ci left: 7.053535e-02	ci right 7.100997e-02	k: 317768	n:4490000
KS ci ratio: 7.757508e-02	ci left: 5.463217e-04	ci right 5.906294e-04	k: 2551	n:4490000
ALS2   4490000 perm   10040 sec   (447 perm/sec)   p_kst 5.681514e-04   p_cons 7.077238e-02   p_joint 8.151448e-05

Joint ci ratio: 2.046140e-01	ci left: 7.321354e-05	ci right 9.010749e-05	k: 366	n:4500000
Cons ci ratio: 6.696507e-03	ci left: 7.052347e-02	ci right 7.099753e-02	k: 318421	n:4500000
KS ci ratio: 7.749920e-02	ci left: 5.461972e-04	ci right 5.904495e-04	k: 2556	n:4500000
ALS2   4500000 perm   10082 sec   (446 perm/sec)   p_kst 5.680000e-04   p_cons 7.076022e-02   p_joint 8.133333e-05

Joint ci ratio: 2.046140e-01	ci left: 7.305120e-05	ci right 8.990770e-05	k: 366	n:4510000
Cons ci ratio: 6.689503e-03	ci left: 7.051541e-02	ci right 7.098891e-02	k: 319091	n:4510000
KS ci ratio: 7.739333e-02	ci left: 5.465082e-04	ci right 5.907225e-04	k: 2563	n:4510000
ALS2   4510000 perm   10124 sec   (445 perm/sec)   p_kst 5.682927e-04   p_cons 7.075188e-02   p_joint 8.115299e-05

Joint ci ratio: 2.037827e-01	ci left: 7.351937e-05	ci right 9.040639e-05	k: 369	n:4520000
Cons ci ratio: 6.682319e-03	ci left: 7.051136e-02	ci right 7.098433e-02	k: 319779	n:4520000
KS ci ratio: 7.727285e-02	ci left: 5.470348e-04	ci right 5.912197e-04	k: 2571	n:4520000
ALS2   4520000 perm   10167 sec   (445 perm/sec)   p_kst 5.688053e-04   p_cons 7.074757e-02   p_joint 8.163717e-05

Joint ci ratio: 2.037828e-01	ci left: 7.335707e-05	ci right 9.020682e-05	k: 369	n:4530000
Cons ci ratio: 6.674843e-03	ci left: 7.051350e-02	ci right 7.098595e-02	k: 320495	n:4530000
KS ci ratio: 7.722785e-02	ci left: 5.464766e-04	ci right 5.905896e-04	k: 2574	n:4530000
ALS2   4530000 perm   10209 sec   (444 perm/sec)   p_kst 5.682119e-04   p_cons 7.074945e-02   p_joint 8.145695e-05

Joint ci ratio: 2.032342e-01	ci left: 7.361358e-05	ci right 9.047107e-05	k: 371	n:4540000
Cons ci ratio: 6.667628e-03	ci left: 7.051101e-02	ci right 7.098293e-02	k: 321190	n:4540000
KS ci ratio: 7.709321e-02	ci left: 5.472171e-04	ci right 5.913094e-04	k: 2583	n:4540000
ALS2   4540000 perm   10251 sec   (443 perm/sec)   p_kst 5.689427e-04   p_cons 7.074670e-02   p_joint 8.171806e-05

Joint ci ratio: 2.032342e-01	ci left: 7.345179e-05	ci right 9.027224e-05	k: 371	n:4550000
Cons ci ratio: 6.661003e-03	ci left: 7.049734e-02	ci right 7.096870e-02	k: 321834	n:4550000
KS ci ratio: 7.704852e-02	ci left: 5.466610e-04	ci right 5.906819e-04	k: 2586	n:4550000
ALS2   4550000 perm   10295 sec   (442 perm/sec)   p_kst 5.683516e-04   p_cons 7.073275e-02   p_joint 8.153846e-05

Joint ci ratio: 2.032342e-01	ci left: 7.329071e-05	ci right 9.007427e-05	k: 371	n:4560000
Cons ci ratio: 6.653655e-03	ci left: 7.049840e-02	ci right 7.096925e-02	k: 322545	n:4560000
KS ci ratio: 7.694448e-02	ci left: 5.469678e-04	ci right 5.909511e-04	k: 2593	n:4560000
ALS2   4560000 perm   10337 sec   (441 perm/sec)   p_kst 5.686404e-04   p_cons 7.073355e-02   p_joint 8.135965e-05

Joint ci ratio: 2.029616e-01	ci left: 7.333803e-05	ci right 9.010711e-05	k: 372	n:4570000
Cons ci ratio: 6.646486e-03	ci left: 7.049640e-02	ci right 7.096673e-02	k: 323242	n:4570000
KS ci ratio: 7.687044e-02	ci left: 5.468439e-04	ci right 5.907732e-04	k: 2598	n:4570000
ALS2   4570000 perm   10380 sec   (440 perm/sec)   p_kst 5.684902e-04   p_cons 7.073129e-02   p_joint 8.140044e-05

Joint ci ratio: 2.029616e-01	ci left: 7.317790e-05	ci right 8.991037e-05	k: 372	n:4580000
Cons ci ratio: 6.639880e-03	ci left: 7.048373e-02	ci right 7.095350e-02	k: 323890	n:4580000
KS ci ratio: 7.676712e-02	ci left: 5.471490e-04	ci right 5.910410e-04	k: 2605	n:4580000
ALS2   4580000 perm   10423 sec   (439 perm/sec)   p_kst 5.687773e-04   p_cons 7.071834e-02   p_joint 8.122271e-05

Joint ci ratio: 2.024196e-01	ci left: 7.343209e-05	ci right 9.017230e-05	k: 374	n:4590000
Cons ci ratio: 6.632700e-03	ci left: 7.048285e-02	ci right 7.095211e-02	k: 324592	n:4590000
KS ci ratio: 7.666421e-02	ci left: 5.474527e-04	ci right 5.913076e-04	k: 2612	n:4590000
ALS2   4590000 perm   10466 sec   (439 perm/sec)   p_kst 5.690632e-04   p_cons 7.071721e-02   p_joint 8.148148e-05

Joint ci ratio: 2.024197e-01	ci left: 7.327245e-05	ci right 8.997627e-05	k: 374	n:4600000
Cons ci ratio: 6.625401e-03	ci left: 7.048481e-02	ci right 7.095356e-02	k: 325307	n:4600000
KS ci ratio: 7.660561e-02	ci left: 5.471155e-04	ci right 5.909084e-04	k: 2616	n:4600000
ALS2   4600000 perm   10509 sec   (438 perm/sec)   p_kst 5.686957e-04   p_cons 7.071891e-02   p_joint 8.130435e-05

Joint ci ratio: 2.024197e-01	ci left: 7.311351e-05	ci right 8.978109e-05	k: 374	n:4610000
Cons ci ratio: 6.618268e-03	ci left: 7.048394e-02	ci right 7.095218e-02	k: 326009	n:4610000
KS ci ratio: 7.650335e-02	ci left: 5.474181e-04	ci right 5.911741e-04	k: 2623	n:4610000
ALS2   4610000 perm   10552 sec   (437 perm/sec)   p_kst 5.689805e-04   p_cons 7.071779e-02   p_joint 8.112798e-05

Joint ci ratio: 2.021503e-01	ci left: 7.316074e-05	ci right 8.981416e-05	k: 375	n:4620000
Cons ci ratio: 6.611245e-03	ci left: 7.048134e-02	ci right 7.094907e-02	k: 326703	n:4620000
KS ci ratio: 7.634346e-02	ci left: 5.485687e-04	ci right 5.923209e-04	k: 2634	n:4620000
ALS2   4620000 perm   10595 sec   (436 perm/sec)   p_kst 5.701299e-04   p_cons 7.071494e-02   p_joint 8.116883e-05

Joint ci ratio: 2.021503e-01	ci left: 7.300273e-05	ci right 8.962018e-05	k: 375	n:4630000
Cons ci ratio: 6.603691e-03	ci left: 7.048976e-02	ci right 7.095700e-02	k: 327448	n:4630000
KS ci ratio: 7.632901e-02	ci left: 5.475957e-04	ci right 5.912617e-04	k: 2635	n:4630000
ALS2   4630000 perm   10637 sec   (435 perm/sec)   p_kst 5.691145e-04   p_cons 7.072311e-02   p_joint 8.099352e-05

Joint ci ratio: 2.021504e-01	ci left: 7.284539e-05	ci right 8.942703e-05	k: 375	n:4640000
Cons ci ratio: 6.596260e-03	ci left: 7.049620e-02	ci right 7.096296e-02	k: 328184	n:4640000
KS ci ratio: 7.625673e-02	ci left: 5.474726e-04	ci right 5.910856e-04	k: 2640	n:4640000
ALS2   4640000 perm   10681 sec   (434 perm/sec)   p_kst 5.689655e-04   p_cons 7.072931e-02   p_joint 8.081897e-05

Joint ci ratio: 2.021504e-01	ci left: 7.268873e-05	ci right 8.923472e-05	k: 375	n:4650000
Cons ci ratio: 6.589242e-03	ci left: 7.049488e-02	ci right 7.096113e-02	k: 328884	n:4650000
KS ci ratio: 7.621348e-02	ci left: 5.469281e-04	ci right 5.904719e-04	k: 2643	n:4650000
ALS2   4650000 perm   10725 sec   (434 perm/sec)   p_kst 5.683871e-04   p_cons 7.072774e-02   p_joint 8.064516e-05

Joint ci ratio: 2.018821e-01	ci left: 7.273649e-05	ci right 8.926866e-05	k: 376	n:4660000
Cons ci ratio: 6.582074e-03	ci left: 7.049700e-02	ci right 7.096276e-02	k: 329600	n:4660000
KS ci ratio: 7.612715e-02	ci left: 5.470174e-04	ci right 5.905169e-04	k: 2649	n:4660000
ALS2   4660000 perm   10769 sec   (433 perm/sec)   p_kst 5.684549e-04   p_cons 7.072961e-02   p_joint 8.068670e-05

Joint ci ratio: 2.018821e-01	ci left: 7.258073e-05	ci right 8.907751e-05	k: 376	n:4670000
Cons ci ratio: 6.575037e-03	ci left: 7.049698e-02	ci right 7.096223e-02	k: 330306	n:4670000
KS ci ratio: 7.609847e-02	ci left: 5.462662e-04	ci right 5.896888e-04	k: 2651	n:4670000
ALS2   4670000 perm   10813 sec   (432 perm/sec)   p_kst 5.676660e-04   p_cons 7.072934e-02   p_joint 8.051392e-05

Joint ci ratio: 2.016149e-01	ci left: 7.262853e-05	ci right 8.911162e-05	k: 377	n:4680000
Cons ci ratio: 6.567852e-03	ci left: 7.050036e-02	ci right 7.096513e-02	k: 331028	n:4680000
KS ci ratio: 7.605548e-02	ci left: 5.457278e-04	ci right 5.890820e-04	k: 2654	n:4680000
ALS2   4680000 perm   10857 sec   (431 perm/sec)   p_kst 5.670940e-04   p_cons 7.073248e-02   p_joint 8.055556e-05

Joint ci ratio: 2.016149e-01	ci left: 7.247367e-05	ci right 8.892162e-05	k: 377	n:4690000
Cons ci ratio: 6.560679e-03	ci left: 7.050395e-02	ci right 7.096823e-02	k: 331751	n:4690000
KS ci ratio: 7.598398e-02	ci left: 5.456100e-04	ci right 5.889124e-04	k: 2659	n:4690000
ALS2   4690000 perm   10901 sec   (430 perm/sec)   p_kst 5.669510e-04   p_cons 7.073582e-02   p_joint 8.038380e-05

Joint ci ratio: 2.013487e-01	ci left: 7.252150e-05	ci right 8.895591e-05	k: 378	n:4700000
Cons ci ratio: 6.554177e-03	ci left: 7.049456e-02	ci right 7.095831e-02	k: 332413	n:4700000
KS ci ratio: 7.594118e-02	ci left: 5.450753e-04	ci right 5.883098e-04	k: 2662	n:4700000
ALS2   4700000 perm   10945 sec   (429 perm/sec)   p_kst 5.663830e-04   p_cons 7.072617e-02   p_joint 8.042553e-05

Joint ci ratio: 2.008195e-01	ci left: 7.277078e-05	ci right 8.921302e-05	k: 380	n:4710000
Cons ci ratio: 6.547219e-03	ci left: 7.049475e-02	ci right 7.095801e-02	k: 333120	n:4710000
KS ci ratio: 7.584156e-02	ci left: 5.453760e-04	ci right 5.885751e-04	k: 2669	n:4710000
ALS2   4710000 perm   10989 sec   (429 perm/sec)   p_kst 5.666667e-04   p_cons 7.072611e-02   p_joint 8.067941e-05

Joint ci ratio: 2.002945e-01	ci left: 7.301906e-05	ci right 8.946899e-05	k: 382	n:4720000
Cons ci ratio: 6.540282e-03	ci left: 7.049494e-02	ci right 7.095771e-02	k: 333827	n:4720000
KS ci ratio: 7.577065e-02	ci left: 5.452598e-04	ci right 5.884075e-04	k: 2674	n:4720000
ALS2   4720000 perm   11034 sec   (428 perm/sec)   p_kst 5.665254e-04   p_cons 7.072606e-02   p_joint 8.093220e-05

Joint ci ratio: 2.000335e-01	ci left: 7.306550e-05	ci right 8.950184e-05	k: 383	n:4730000
Cons ci ratio: 6.533683e-03	ci left: 7.048879e-02	ci right 7.095106e-02	k: 334504	n:4730000
KS ci ratio: 7.572822e-02	ci left: 5.447293e-04	ci right 5.878098e-04	k: 2677	n:4730000
ALS2   4730000 perm   11078 sec   (427 perm/sec)   p_kst 5.659619e-04   p_cons 7.071966e-02   p_joint 8.097252e-05

Joint ci ratio: 2.000335e-01	ci left: 7.291136e-05	ci right 8.931302e-05	k: 383	n:4740000
Cons ci ratio: 6.526925e-03	ci left: 7.048626e-02	ci right 7.094802e-02	k: 335198	n:4740000
KS ci ratio: 7.564353e-02	ci left: 5.448219e-04	ci right 5.878595e-04	k: 2683	n:4740000
ALS2   4740000 perm   11123 sec   (426 perm/sec)   p_kst 5.660338e-04   p_cons 7.071688e-02   p_joint 8.080169e-05

Joint ci ratio: 1.997736e-01	ci left: 7.295785e-05	ci right 8.934604e-05	k: 384	n:4750000
Cons ci ratio: 6.520492e-03	ci left: 7.047763e-02	ci right 7.093889e-02	k: 335863	n:4750000
KS ci ratio: 7.557317e-02	ci left: 5.447077e-04	ci right 5.876944e-04	k: 2688	n:4750000
ALS2   4750000 perm   11168 sec   (425 perm/sec)   p_kst 5.658947e-04   p_cons 7.070800e-02   p_joint 8.084211e-05

Joint ci ratio: 1.995146e-01	ci left: 7.300416e-05	ci right 8.937891e-05	k: 385	n:4760000
Cons ci ratio: 6.513255e-03	ci left: 7.048562e-02	ci right 7.094641e-02	k: 336607	n:4760000
KS ci ratio: 7.548900e-02	ci left: 5.448000e-04	ci right 5.877441e-04	k: 2694	n:4760000
ALS2   4760000 perm   11212 sec   (425 perm/sec)   p_kst 5.659664e-04   p_cons 7.071576e-02   p_joint 8.088235e-05

Joint ci ratio: 1.992567e-01	ci left: 7.305029e-05	ci right 8.941163e-05	k: 386	n:4770000
Cons ci ratio: 6.506726e-03	ci left: 7.047976e-02	ci right 7.094005e-02	k: 337285	n:4770000
KS ci ratio: 7.539114e-02	ci left: 5.450977e-04	ci right 5.880071e-04	k: 2701	n:4770000
ALS2   4770000 perm   11257 sec   (424 perm/sec)   p_kst 5.662474e-04   p_cons 7.070964e-02   p_joint 8.092243e-05

Joint ci ratio: 1.989998e-01	ci left: 7.309624e-05	ci right 8.944419e-05	k: 387	n:4780000
Cons ci ratio: 6.500176e-03	ci left: 7.047476e-02	ci right 7.093455e-02	k: 337967	n:4780000
KS ci ratio: 7.532149e-02	ci left: 5.449837e-04	ci right 5.878427e-04	k: 2706	n:4780000
ALS2   4780000 perm   11301 sec   (423 perm/sec)   p_kst 5.661088e-04   p_cons 7.070439e-02   p_joint 8.096234e-05

Joint ci ratio: 1.989998e-01	ci left: 7.294364e-05	ci right 8.925746e-05	k: 387	n:4790000
Cons ci ratio: 6.493656e-03	ci left: 7.046957e-02	ci right 7.092886e-02	k: 338648	n:4790000
KS ci ratio: 7.525203e-02	ci left: 5.448701e-04	ci right 5.876789e-04	k: 2711	n:4790000
ALS2   4790000 perm   11345 sec   (422 perm/sec)   p_kst 5.659708e-04   p_cons 7.069896e-02   p_joint 8.079332e-05

Joint ci ratio: 1.987438e-01	ci left: 7.298963e-05	ci right 8.929020e-05	k: 388	n:4800000
Cons ci ratio: 6.486888e-03	ci left: 7.046981e-02	ci right 7.092863e-02	k: 339355	n:4800000
KS ci ratio: 7.518276e-02	ci left: 5.447570e-04	ci right 5.875158e-04	k: 2716	n:4800000
ALS2   4800000 perm   11390 sec   (421 perm/sec)   p_kst 5.658333e-04   p_cons 7.069896e-02   p_joint 8.083333e-05

Joint ci ratio: 1.987438e-01	ci left: 7.283788e-05	ci right 8.910457e-05	k: 388	n:4810000
Cons ci ratio: 6.479998e-03	ci left: 7.047296e-02	ci right 7.093130e-02	k: 340076	n:4810000
KS ci ratio: 7.512749e-02	ci left: 5.444404e-04	ci right 5.871416e-04	k: 2720	n:4810000
ALS2   4810000 perm   11435 sec   (421 perm/sec)   p_kst 5.654886e-04   p_cons 7.070187e-02   p_joint 8.066528e-05

Joint ci ratio: 1.984889e-01	ci left: 7.288392e-05	ci right 8.913748e-05	k: 389	n:4820000
Cons ci ratio: 6.472925e-03	ci left: 7.048023e-02	ci right 7.093813e-02	k: 340817	n:4820000
KS ci ratio: 7.507234e-02	ci left: 5.441252e-04	ci right 5.867690e-04	k: 2724	n:4820000
ALS2   4820000 perm   11479 sec   (420 perm/sec)   p_kst 5.651452e-04   p_cons 7.070892e-02   p_joint 8.070539e-05

Joint ci ratio: 1.982349e-01	ci left: 7.292978e-05	ci right 8.917024e-05	k: 390	n:4830000
Cons ci ratio: 6.466395e-03	ci left: 7.047694e-02	ci right 7.093434e-02	k: 341507	n:4830000
KS ci ratio: 7.497609e-02	ci left: 5.444207e-04	ci right 5.870306e-04	k: 2731	n:4830000
ALS2   4830000 perm   11524 sec   (419 perm/sec)   p_kst 5.654244e-04   p_cons 7.070538e-02   p_joint 8.074534e-05

Joint ci ratio: 1.977298e-01	ci left: 7.317184e-05	ci right 8.941968e-05	k: 392	n:4840000
Cons ci ratio: 6.459804e-03	ci left: 7.047530e-02	ci right 7.093223e-02	k: 342205	n:4840000
KS ci ratio: 7.489390e-02	ci left: 5.445123e-04	ci right 5.870806e-04	k: 2737	n:4840000
ALS2   4840000 perm   11569 sec   (418 perm/sec)   p_kst 5.654959e-04   p_cons 7.070351e-02   p_joint 8.099174e-05

Joint ci ratio: 1.972286e-01	ci left: 7.341295e-05	ci right 8.966804e-05	k: 394	n:4850000
Cons ci ratio: 6.452949e-03	ci left: 7.047944e-02	ci right 7.093591e-02	k: 342931	n:4850000
KS ci ratio: 7.477108e-02	ci left: 5.452106e-04	ci right 5.877605e-04	k: 2746	n:4850000
ALS2   4850000 perm   11615 sec   (418 perm/sec)   p_kst 5.661856e-04   p_cons 7.070742e-02   p_joint 8.123711e-05

Joint ci ratio: 1.967311e-01	ci left: 7.365313e-05	ci right 8.991533e-05	k: 396	n:4860000
Cons ci ratio: 6.446277e-03	ci left: 7.048028e-02	ci right 7.093628e-02	k: 343641	n:4860000
KS ci ratio: 7.467599e-02	ci left: 5.455022e-04	ci right 5.880183e-04	k: 2753	n:4860000
ALS2   4860000 perm   11661 sec   (417 perm/sec)   p_kst 5.664609e-04   p_cons 7.070802e-02   p_joint 8.148148e-05

Joint ci ratio: 1.967311e-01	ci left: 7.350189e-05	ci right 8.973070e-05	k: 396	n:4870000
Cons ci ratio: 6.439545e-03	ci left: 7.048275e-02	ci right 7.093829e-02	k: 344359	n:4870000
KS ci ratio: 7.462183e-02	ci left: 5.451881e-04	ci right 5.876476e-04	k: 2757	n:4870000
ALS2   4870000 perm   11706 sec   (416 perm/sec)   p_kst 5.661191e-04   p_cons 7.071027e-02   p_joint 8.131417e-05

Joint ci ratio: 1.967311e-01	ci left: 7.335127e-05	ci right 8.954683e-05	k: 396	n:4880000
Cons ci ratio: 6.433356e-03	ci left: 7.047458e-02	ci right 7.092962e-02	k: 345025	n:4880000
KS ci ratio: 7.456779e-02	ci left: 5.448752e-04	ci right 5.872784e-04	k: 2761	n:4880000
ALS2   4880000 perm   11751 sec   (415 perm/sec)   p_kst 5.657787e-04   p_cons 7.070184e-02   p_joint 8.114754e-05

Joint ci ratio: 1.964838e-01	ci left: 7.339570e-05	ci right 8.957826e-05	k: 397	n:4890000
Cons ci ratio: 6.426485e-03	ci left: 7.048073e-02	ci right 7.093532e-02	k: 345761	n:4890000
KS ci ratio: 7.444657e-02	ci left: 5.455672e-04	ci right 5.879522e-04	k: 2770	n:4890000
ALS2   4890000 perm   11797 sec   (415 perm/sec)   p_kst 5.664622e-04   p_cons 7.070777e-02   p_joint 8.118609e-05

Joint ci ratio: 1.962375e-01	ci left: 7.343996e-05	ci right 8.960955e-05	k: 398	n:4900000
Cons ci ratio: 6.419875e-03	ci left: 7.048196e-02	ci right 7.093610e-02	k: 346473	n:4900000
KS ci ratio: 7.435270e-02	ci left: 5.458558e-04	ci right 5.882074e-04	k: 2777	n:4900000
ALS2   4900000 perm   11841 sec   (414 perm/sec)   p_kst 5.667347e-04   p_cons 7.070878e-02   p_joint 8.122449e-05

Joint ci ratio: 1.959920e-01	ci left: 7.348405e-05	ci right 8.964070e-05	k: 399	n:4910000
Cons ci ratio: 6.413365e-03	ci left: 7.048156e-02	ci right 7.093524e-02	k: 347177	n:4910000
KS ci ratio: 7.424586e-02	ci left: 5.463431e-04	ci right 5.886690e-04	k: 2785	n:4910000
ALS2   4910000 perm   11887 sec   (413 perm/sec)   p_kst 5.672098e-04   p_cons 7.070815e-02   p_joint 8.126273e-05

Joint ci ratio: 1.957475e-01	ci left: 7.352798e-05	ci right 8.967171e-05	k: 400	n:4920000
Cons ci ratio: 6.406587e-03	ci left: 7.048705e-02	ci right 7.094028e-02	k: 347910	n:4920000
KS ci ratio: 7.423257e-02	ci left: 5.454321e-04	ci right 5.876796e-04	k: 2786	n:4920000
ALS2   4920000 perm   11932 sec   (412 perm/sec)   p_kst 5.662602e-04   p_cons 7.071341e-02   p_joint 8.130081e-05

Joint ci ratio: 1.955038e-01	ci left: 7.357174e-05	ci right 8.970258e-05	k: 401	n:4930000
Cons ci ratio: 6.399752e-03	ci left: 7.049414e-02	ci right 7.094693e-02	k: 348651	n:4930000
KS ci ratio: 7.420598e-02	ci left: 5.447239e-04	ci right 5.869007e-04	k: 2788	n:4930000
ALS2   4930000 perm   11978 sec   (412 perm/sec)   p_kst 5.655172e-04   p_cons 7.072028e-02   p_joint 8.133874e-05

Joint ci ratio: 1.955039e-01	ci left: 7.342281e-05	ci right 8.952100e-05	k: 401	n:4940000
Cons ci ratio: 6.393352e-03	ci left: 7.049271e-02	ci right 7.094504e-02	k: 349350	n:4940000
KS ci ratio: 7.412628e-02	ci left: 5.448133e-04	ci right 5.869498e-04	k: 2794	n:4940000
ALS2   4940000 perm   12024 sec   (411 perm/sec)   p_kst 5.655870e-04   p_cons 7.071862e-02   p_joint 8.117409e-05

Joint ci ratio: 1.952611e-01	ci left: 7.346662e-05	ci right 8.955204e-05	k: 402	n:4950000
Cons ci ratio: 6.386461e-03	ci left: 7.050178e-02	ci right 7.095367e-02	k: 350101	n:4950000
KS ci ratio: 7.404685e-02	ci left: 5.449023e-04	ci right 5.869986e-04	k: 2800	n:4950000
ALS2   4950000 perm   12070 sec   (410 perm/sec)   p_kst 5.656566e-04   p_cons 7.072747e-02   p_joint 8.121212e-05

Joint ci ratio: 1.950193e-01	ci left: 7.351027e-05	ci right 8.958294e-05	k: 403	n:4960000
Cons ci ratio: 6.379777e-03	ci left: 7.050698e-02	ci right 7.095844e-02	k: 350833	n:4960000
KS ci ratio: 7.390183e-02	ci left: 5.459805e-04	ci right 5.880739e-04	k: 2811	n:4960000
ALS2   4960000 perm   12115 sec   (409 perm/sec)   p_kst 5.667339e-04   p_cons 7.073246e-02   p_joint 8.125000e-05

Joint ci ratio: 1.947784e-01	ci left: 7.355375e-05	ci right 8.961370e-05	k: 404	n:4970000
Cons ci ratio: 6.373603e-03	ci left: 7.050212e-02	ci right 7.095311e-02	k: 351515	n:4970000
KS ci ratio: 7.382312e-02	ci left: 5.460669e-04	ci right 5.881201e-04	k: 2817	n:4970000
ALS2   4970000 perm   12163 sec   (409 perm/sec)   p_kst 5.668008e-04   p_cons 7.072736e-02   p_joint 8.128773e-05

Joint ci ratio: 1.947784e-01	ci left: 7.340605e-05	ci right 8.943376e-05	k: 404	n:4980000
Cons ci ratio: 6.367466e-03	ci left: 7.049688e-02	ci right 7.094739e-02	k: 352195	n:4980000
KS ci ratio: 7.378387e-02	ci left: 5.455616e-04	ci right 5.875527e-04	k: 2820	n:4980000
ALS2   4980000 perm   12210 sec   (408 perm/sec)   p_kst 5.662651e-04   p_cons 7.072189e-02   p_joint 8.112450e-05

Joint ci ratio: 1.942992e-01	ci left: 7.364022e-05	ci right 8.967483e-05	k: 406	n:4990000
Cons ci ratio: 6.360871e-03	ci left: 7.050146e-02	ci right 7.095154e-02	k: 352924	n:4990000
KS ci ratio: 7.367946e-02	ci left: 5.460420e-04	ci right 5.880080e-04	k: 2828	n:4990000
ALS2   4990000 perm   12256 sec   (407 perm/sec)   p_kst 5.667335e-04   p_cons 7.072625e-02   p_joint 8.136273e-05

Joint ci ratio: 1.938236e-01	ci left: 7.387351e-05	ci right 8.991489e-05	k: 408	n:5000000
Cons ci ratio: 6.354258e-03	ci left: 7.050683e-02	ci right 7.095647e-02	k: 353657	n:5000000
KS ci ratio: 7.356251e-02	ci left: 5.467168e-04	ci right 5.886651e-04	k: 2837	n:5000000
ALS2   5000000 perm   12302 sec   (406 perm/sec)   p_kst 5.674000e-04   p_cons 7.073140e-02   p_joint 8.160000e-05

Outputting figure to mutsig2_images.part000000000007/ALS2.2_5184_5000000_0.0005674_0.070731_8.16e-05.png
                gene_name: ALS2
               theta_stop: 0.19 
                    nperm: 5000000 
                     p_ks: 0.00057 
        ci_ks_bounds_left: 0.00055 
       ci_ks_bounds_right: 0.00059 
                   p_cons: 0.071 
      ci_cons_bounds_left: 0.071 
     ci_cons_bounds_right: 0.071 
                  p_joint: 8.16e-05 
     ci_joint_bounds_left: 7.39e-05 
    ci_joint_bounds_right: 8.99e-05 

Current progress: 83 percent done.
ANK3
Processing conservation and coverage...
73% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.090088e-01	ci left: 1.082244e-01	ci right 1.208011e-01	k: 1144	n:10000
KS ci ratio: 7.413363e-02	ci left: 2.103351e-01	ci right 2.266292e-01	k: 2184	n:10000
ANK3   10000 perm   4 sec   (2542 perm/sec)   p_kst 2.184000e-01   p_cons 1.144000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 7.814601e-02	ci left: 1.073661e-01	ci right 1.161471e-01	k: 2234	n:20000
KS ci ratio: 5.211589e-02	ci left: 2.147207e-01	ci right 2.262607e-01	k: 4409	n:20000
ANK3   20000 perm   8 sec   (2369 perm/sec)   p_kst 2.204500e-01   p_cons 1.117000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000007/ANK3.2_13639_20000_0.22045_0.1117_1.png
                gene_name: ANK3
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000007
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 7 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1429>
Subject: Job 4397773: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1429>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000008> was used as the working directory.
Started at Wed Oct 24 16:08:17 2012
Results reported at Wed Oct 24 16:10:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000008.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000008.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 8  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000008.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    217.44 sec.
    Max Memory :      1217 MB
    Max Swap   :      3909 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
8
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 8
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 8: processing genes 629 - 718
Calculating significance of each gene.
Using projection method.
629	ANKRD12	4.256935e-01
630	ANKRD13A	1
631	ANKRD13B	1.790347e-01
632	ANKRD13C	1
633	ANKRD13D	1
634	ANKRD16	1
635	ANKRD17	3.307239e-01
636	ANKRD2	1
637	ANKRD20A1	1
638	ANKRD20A4	1
639	ANKRD22	9.604919e-02
640	ANKRD23	1
641	ANKRD24	1
642	ANKRD26	1.751329e-01
643	ANKRD27	1
644	ANKRD28	1
645	ANKRD29	1
646	ANKRD30A	3.385452e-02
647	ANKRD32	1
648	ANKRD33	1
649	ANKRD34A	1
650	ANKRD34B	1
651	ANKRD35	1
652	ANKRD37	1
653	ANKRD39	1
654	ANKRD40	1
655	ANKRD42	1
656	ANKRD44	2.154480e-01
657	ANKRD45	1
658	ANKRD46	1
659	ANKRD49	1
660	ANKRD5	1
661	ANKRD50	1
662	ANKRD52	7.755223e-02
663	ANKRD53	1
664	ANKRD54	1
665	ANKRD55	1
666	ANKRD56	1
667	ANKRD57	1
668	ANKRD58	1
669	ANKRD6	1
670	ANKRD7	1
671	ANKS1A	4.503909e-01
672	ANKS1B	1.996846e-01
673	ANKS3	1
674	ANKS4B	1
675	ANKS6	1.976056e-01
676	ANKZF1	3.502926e-01
677	ANLN	1
678	ANO1	1
679	ANO10	1
680	ANO2	3.357298e-01
681	ANO3	2.914447e-01
682	ANO4	1.251673e-01
683	ANO5	1
684	ANO6	5.576113e-02
685	ANO7	1
686	ANO8	1
687	ANO9	1.574625e-01
688	ANP32A	1
689	ANP32B	1
690	ANP32C	1
691	ANP32D	1
692	ANP32E	1.245851e-01
693	ANPEP	1.772532e-01
694	ANTXR1	1.163620e-01
695	ANTXR2	1
696	ANUBL1	1
697	ANXA1	1
698	ANXA10	1
699	ANXA11	1
700	ANXA13	1
701	ANXA2	1
702	ANXA3	1
703	ANXA4	1
704	ANXA5	1
705	ANXA6	1
706	ANXA7	1
707	ANXA9	1
708	AOAH	2.105198e-01
709	AOC2	1
710	AOC3	1
711	AOX1	1
712	AP1AR	1
713	AP1B1	1
714	AP1G1	1
715	AP1G2	1
716	AP1M1	1
717	AP1M2	1
718	AP1S1	1
Done

Running MutSig 2:
Scatter job 8: processing genes 629 - 718
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ANO6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.654465e-02	ci left: 3.153259e-01	ci right 3.337764e-01	k: 3245	n:10000
Cons ci ratio: 1.039475e-01	ci left: 1.179914e-01	ci right 1.310282e-01	k: 1244	n:10000
KS ci ratio: 7.743137e-02	ci left: 1.960405e-01	ci right 2.119323e-01	k: 2039	n:10000
ANO6   10000 perm   2 sec   (4714 perm/sec)   p_kst 2.039000e-01   p_cons 1.244000e-01   p_joint 3.245000e-01

Joint ci ratio: 4.175332e-02	ci left: 2.994678e-01	ci right 3.122887e-01	k: 6117	n:20000
Cons ci ratio: 7.278719e-02	ci left: 1.220210e-01	ci right 1.312878e-01	k: 2532	n:20000
KS ci ratio: 5.463518e-02	ci left: 1.990769e-01	ci right 2.103091e-01	k: 4093	n:20000
ANO6   20000 perm   8 sec   (2594 perm/sec)   p_kst 2.046500e-01   p_cons 1.266000e-01   p_joint 3.058500e-01

Outputting figure to mutsig2_images.part000000000008/ANO6.3_3101_20000_0.20465_0.1266_0.30585.png
                gene_name: ANO6
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.31 

Current progress: 25 percent done.
ANKRD26
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.367929e-02	ci left: 1.419757e-01	ci right 1.560294e-01	k: 1489	n:10000
Cons ci ratio: 1.033792e-01	ci left: 1.191644e-01	ci right 1.322545e-01	k: 1256	n:10000
KS ci ratio: 4.391342e-03	ci left: 9.853418e-01	ci right 9.897674e-01	k: 9877	n:10000
ANKRD26   10000 perm   2 sec   (4234 perm/sec)   p_kst 9.877000e-01   p_cons 1.256000e-01   p_joint 1.489000e-01

Joint ci ratio: 7.154726e-02	ci left: 1.258113e-01	ci right 1.351964e-01	k: 2609	n:20000
Cons ci ratio: 7.305160e-02	ci left: 1.212336e-01	ci right 1.304754e-01	k: 2516	n:20000
KS ci ratio: 3.143358e-03	ci left: 9.857033e-01	ci right 9.888527e-01	k: 19747	n:20000
ANKRD26   20000 perm   5 sec   (3849 perm/sec)   p_kst 9.873500e-01   p_cons 1.258000e-01   p_joint 1.304500e-01

Outputting figure to mutsig2_images.part000000000008/ANKRD26.2_5269_20000_0.98735_0.1258_0.13045.png
                gene_name: ANKRD26
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 50 percent done.
ANKRD30A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.517934e-02	ci left: 6.988779e-01	ci right 7.168009e-01	k: 7079	n:10000
KS ci ratio: 1.635946e-02	ci left: 8.445820e-01	ci right 8.586125e-01	k: 8517	n:10000
ANKRD30A   10000 perm   2 sec   (4603 perm/sec)   p_kst 8.517000e-01   p_cons 7.079000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000008/ANKRD30A.2_4166_10000_0.8517_0.7079_1.png
                gene_name: ANKRD30A
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
ANKS1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.582440e-02	ci left: 1.651411e-01	ci right 1.800501e-01	k: 1725	n:10000
Cons ci ratio: 6.264161e-02	ci left: 2.725021e-01	ci right 2.902255e-01	k: 2813	n:10000
KS ci ratio: 8.318649e-02	ci left: 1.740876e-01	ci right 1.892983e-01	k: 1816	n:10000
ANKS1A   10000 perm   2 sec   (5144 perm/sec)   p_kst 1.816000e-01   p_cons 2.813000e-01   p_joint 1.725000e-01

Outputting figure to mutsig2_images.part000000000008/ANKS1A.2_3501_10000_0.1816_0.2813_0.1725.png
                gene_name: ANKS1A
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000008
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 8 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4397776: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000009> was used as the working directory.
Started at Wed Oct 24 16:08:19 2012
Results reported at Wed Oct 24 16:11:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000009.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000009.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 9  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000009.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    220.48 sec.
    Max Memory :      1279 MB
    Max Swap   :      4018 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
9
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 9
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 9: processing genes 719 - 807
Calculating significance of each gene.
Using projection method.
719	AP1S2	1
720	AP1S3	1
721	AP2A1	5.745896e-02
722	AP2A2	1
723	AP2B1	1
724	AP2M1	1
725	AP2S1	1
726	AP3B1	1.977297e-01
727	AP3B2	1
728	AP3D1	1
729	AP3M1	1
730	AP3M2	1
731	AP3S1	9.206860e-02
732	AP3S2	1
733	AP4B1	1
734	AP4E1	1
735	AP4M1	1
736	AP4S1	1
737	APAF1	3.759275e-01
738	APBA1	1.375368e-01
739	APBA2	2.054918e-01
740	APBA3	1
741	APBB1	2.224061e-01
742	APBB1IP	9.736509e-02
743	APBB2	2.530997e-02
744	APBB3	1
745	APC	1.365581e-01
746	APC2	1
747	APCDD1	1
748	APCDD1L	1
749	APCS	1
750	APEH	1
751	APEX1	1
752	APEX2	1
753	APH1A	9.746668e-02
754	APH1B	1
755	API5	1
756	APIP	1
757	APITD1	1
758	APLF	1.433711e-01
759	APLNR	1
760	APLP1	1
761	APLP2	3.564584e-01
762	APOA1	1
763	APOA1BP	1
764	APOA2	1
765	APOA4	1.425399e-01
766	APOA5	1
767	APOB	6.431901e-02
768	APOB48R	3.903692e-02
769	APOBEC1	1
770	APOBEC2	1
771	APOBEC3A	1
772	APOBEC3B	1.182210e-01
773	APOBEC3C	1
774	APOBEC3D	1
775	APOBEC3F	1
776	APOBEC3G	1.333969e-01
777	APOBEC3H	1
778	APOBEC4	1
779	APOC1	7.405918e-03
780	APOC2	1
781	APOC3	1
782	APOC4	1
783	APOD	1
784	APOE	1
785	APOF	1
786	APOH	1
787	APOL1	1
788	APOL2	1
789	APOL3	1
790	APOL4	1
791	APOL5	1
792	APOL6	1
793	APOLD1	1
794	APOM	1
795	APOO	1
796	APOOL	1
797	APP	1
798	APPBP2	1
799	APPL1	1
800	APPL2	8.144569e-02
801	APRT	1
802	APTX	1
803	AQP1	1
804	AQP10	1.155984e-01
805	AQP11	1
806	AQP12A	2.346642e-02
807	AQP12B	1
Done

Running MutSig 2:
Scatter job 9: processing genes 719 - 807
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
APOB
Processing conservation and coverage...
72% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.404582e-02	ci left: 4.321347e-01	ci right 4.516992e-01	k: 4419	n:10000
Cons ci ratio: 9.240747e-02	ci left: 1.454077e-01	ci right 1.595954e-01	k: 1524	n:10000
KS ci ratio: 3.700582e-02	ci left: 5.188592e-01	ci right 5.385241e-01	k: 5287	n:10000
APOB   10000 perm   4 sec   (2276 perm/sec)   p_kst 5.287000e-01   p_cons 1.524000e-01   p_joint 4.419000e-01

Outputting figure to mutsig2_images.part000000000009/APOB.7_13808_10000_0.5287_0.1524_0.4419.png
                gene_name: APOB
               theta_stop: 0.092 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 33 percent done.
APC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.352371e-02	ci left: 1.729074e-01	ci right 1.880792e-01	k: 1804	n:10000
Cons ci ratio: 3.965135e-02	ci left: 4.843537e-01	ci right 5.040497e-01	k: 4942	n:10000
KS ci ratio: 1.209147e-01	ci left: 8.932164e-02	ci right 1.009155e-01	k: 950	n:10000
APC   10000 perm   3 sec   (3510 perm/sec)   p_kst 9.500000e-02   p_cons 4.942000e-01   p_joint 1.804000e-01

Joint ci ratio: 6.381919e-02	ci left: 1.536115e-01	ci right 1.637879e-01	k: 3173	n:20000
Cons ci ratio: 2.767774e-02	ci left: 4.937458e-01	ci right 5.076540e-01	k: 10014	n:20000
KS ci ratio: 8.617888e-02	ci left: 8.969559e-02	ci right 9.782296e-02	k: 1874	n:20000
APC   20000 perm   6 sec   (3188 perm/sec)   p_kst 9.370000e-02   p_cons 5.007000e-01   p_joint 1.586500e-01

Outputting figure to mutsig2_images.part000000000009/APC.3_8592_20000_0.0937_0.5007_0.15865.png
                gene_name: APC
               theta_stop: 0.086 
                    nperm: 20000 
                     p_ks: 0.094 
        ci_ks_bounds_left: 0.090 
       ci_ks_bounds_right: 0.098 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.16 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.16 

Current progress: 67 percent done.
APBB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.662153e-02	ci left: 5.240640e-01	ci right 5.437162e-01	k: 5339	n:10000
KS ci ratio: 8.838341e-03	ci left: 9.473144e-01	ci right 9.558201e-01	k: 9517	n:10000
APBB2   10000 perm   2 sec   (5796 perm/sec)   p_kst 9.517000e-01   p_cons 5.339000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000009/APBB2.2_2336_10000_0.9517_0.5339_1.png
                gene_name: APBB2
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000009
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 9 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1555>
Subject: Job 4397779: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1555>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000010> was used as the working directory.
Started at Wed Oct 24 16:08:19 2012
Results reported at Wed Oct 24 16:11:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000010.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000010.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 10  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000010.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    269.37 sec.
    Max Memory :      1721 MB
    Max Swap   :      4064 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
10
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 10
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 10: processing genes 808 - 897
Calculating significance of each gene.
Using projection method.
808	AQP2	6.119775e-05
809	AQP3	1
810	AQP4	1
811	AQP5	1
812	AQP6	1
813	AQP7	1
814	AQP8	1.061294e-01
815	AQP9	1
816	AQPEP	1
817	AQR	4.154921e-01
818	AR	3.047569e-02
819	ARAF	1
820	ARAP1	4.689774e-01
821	ARAP2	1
822	ARAP3	1
823	ARC	1
824	ARCN1	1
825	AREG	1
826	ARF1	1
827	ARF3	1
828	ARF4	1
829	ARF5	1
830	ARF6	1
831	ARFGAP1	1.567803e-01
832	ARFGAP2	1
833	ARFGAP3	1
834	ARFGEF1	1
835	ARFGEF2	1.613551e-01
836	ARFIP1	6.984595e-02
837	ARFIP2	1
838	ARFRP1	1
839	ARG1	1
840	ARG2	1
841	ARGFX	1
842	ARGLU1	1
843	ARHGAP1	1
844	ARHGAP10	1
845	ARHGAP11A	1
846	ARHGAP11B	1
847	ARHGAP12	1
848	ARHGAP15	1
849	ARHGAP17	2.150381e-01
850	ARHGAP18	1
851	ARHGAP19	1
852	ARHGAP20	1
853	ARHGAP21	1.681983e-02
854	ARHGAP22	1
855	ARHGAP24	1
856	ARHGAP25	1
857	ARHGAP26	1
858	ARHGAP27	1
859	ARHGAP28	1
860	ARHGAP29	1
861	ARHGAP30	1.913015e-01
862	ARHGAP31	2.449859e-02
863	ARHGAP32	1
864	ARHGAP33	2.927763e-01
865	ARHGAP36	8.934082e-02
866	ARHGAP39	1
867	ARHGAP4	1.215813e-02
868	ARHGAP5	2.356830e-01
869	ARHGAP6	5.698085e-04
870	ARHGAP8	1
871	ARHGAP9	1
872	ARHGDIA	1
873	ARHGDIB	1
874	ARHGDIG	1
875	ARHGEF1	2.198842e-01
876	ARHGEF10	1
877	ARHGEF10L	1
In gene ARHGEF11 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 4804    n = 1	mu =   4.43e-07
878	ARHGEF11	2.411424e-01
879	ARHGEF12	1
880	ARHGEF15	1
881	ARHGEF16	1
882	ARHGEF17	1
883	ARHGEF18	2.673531e-01
884	ARHGEF19	3.862384e-02
885	ARHGEF2	1
886	ARHGEF3	1.684296e-01
887	ARHGEF35	1
888	ARHGEF37	7.818125e-02
889	ARHGEF38	1
890	ARHGEF4	2.980191e-01
891	ARHGEF5	1
892	ARHGEF6	1.001476e-01
893	ARHGEF7	1
894	ARHGEF9	1
895	ARID1A	7.553128e-04
896	ARID1B	5.440906e-01
897	ARID2	3.303164e-01
Done

Running MutSig 2:
Scatter job 10: processing genes 808 - 897
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ARID1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.533341e-02	ci left: 2.559738e-01	ci right 2.733635e-01	k: 2646	n:10000
Cons ci ratio: 9.982218e-02	ci left: 1.268913e-01	ci right 1.403229e-01	k: 1335	n:10000
KS ci ratio: 3.214337e-02	ci left: 5.882125e-01	ci right 6.075305e-01	k: 5979	n:10000
ARID1A   10000 perm   3 sec   (3521 perm/sec)   p_kst 5.979000e-01   p_cons 1.335000e-01   p_joint 2.646000e-01

Outputting figure to mutsig2_images.part000000000010/ARID1A.5_6938_10000_0.5979_0.1335_0.2646.png
                gene_name: ARID1A
               theta_stop: 0.100 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.27 

Current progress: 9 percent done.
ARFGEF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.375245e-02	ci left: 5.644382e-01	ci right 5.839185e-01	k: 5742	n:10000
KS ci ratio: 1.789910e-02	ci left: 8.199499e-01	ci right 8.348589e-01	k: 8275	n:10000
ARFGEF2   10000 perm   2 sec   (4508 perm/sec)   p_kst 8.275000e-01   p_cons 5.742000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000010/ARFGEF2.4_5514_10000_0.8275_0.5742_1.png
                gene_name: ARFGEF2
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 18 percent done.
ARHGAP30
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.250119e-02	ci left: 2.179321e-01	ci right 2.344277e-01	k: 2261	n:10000
Cons ci ratio: 1.941074e-02	ci left: 7.951683e-01	ci right 8.108548e-01	k: 8031	n:10000
KS ci ratio: 1.588454e-01	ci left: 5.282421e-02	ci right 6.203572e-02	k: 573	n:10000
ARHGAP30   10000 perm   2 sec   (5467 perm/sec)   p_kst 5.730000e-02   p_cons 8.031000e-01   p_joint 2.261000e-01

Joint ci ratio: 6.247896e-02	ci left: 1.592874e-01	ci right 1.696104e-01	k: 3288	n:20000
Cons ci ratio: 1.333997e-02	ci left: 8.064644e-01	ci right 8.173448e-01	k: 16239	n:20000
KS ci ratio: 1.109958e-01	ci left: 5.543290e-02	ci right 6.199612e-02	k: 1173	n:20000
ARHGAP30   20000 perm   4 sec   (4877 perm/sec)   p_kst 5.865000e-02   p_cons 8.119500e-01   p_joint 1.644000e-01

Joint ci ratio: 5.077106e-02	ci left: 1.615415e-01	ci right 1.699900e-01	k: 4972	n:30000
Cons ci ratio: 1.124191e-02	ci left: 7.975458e-01	ci right 8.065957e-01	k: 24063	n:30000
KS ci ratio: 9.087531e-02	ci left: 5.574003e-02	ci right 6.107923e-02	k: 1751	n:30000
ARHGAP30   30000 perm   7 sec   (4613 perm/sec)   p_kst 5.836667e-02   p_cons 8.021000e-01   p_joint 1.657333e-01

Outputting figure to mutsig2_images.part000000000010/ARHGAP30.4_3354_30000_0.058367_0.8021_0.16573.png
                gene_name: ARHGAP30
               theta_stop: 0.091 
                    nperm: 30000 
                     p_ks: 0.058 
        ci_ks_bounds_left: 0.056 
       ci_ks_bounds_right: 0.061 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.16 
    ci_joint_bounds_right: 0.17 

Current progress: 27 percent done.
ARHGAP6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.485289e-02	ci left: 8.678477e-01	ci right 8.809333e-01	k: 8745	n:10000
Cons ci ratio: 5.285046e-02	ci left: 3.454159e-01	ci right 3.642687e-01	k: 3548	n:10000
KS ci ratio: 2.888903e-02	ci left: 6.385473e-01	ci right 6.573664e-01	k: 6480	n:10000
ARHGAP6   10000 perm   2 sec   (5238 perm/sec)   p_kst 6.480000e-01   p_cons 3.548000e-01   p_joint 8.745000e-01

Outputting figure to mutsig2_images.part000000000010/ARHGAP6.4_3099_10000_0.648_0.3548_0.8745.png
                gene_name: ARHGAP6
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.87 
    ci_joint_bounds_right: 0.88 

Current progress: 36 percent done.
AQP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.235680e-02	ci left: 1.770385e-01	ci right 1.923456e-01	k: 1846	n:10000
Cons ci ratio: 1.165621e-01	ci left: 9.564778e-02	ci right 1.075854e-01	k: 1015	n:10000
KS ci ratio: 4.639896e-02	ci left: 4.067137e-01	ci right 4.261351e-01	k: 4164	n:10000
AQP2   10000 perm   2 sec   (6379 perm/sec)   p_kst 4.164000e-01   p_cons 1.015000e-01   p_joint 1.846000e-01

Joint ci ratio: 2.769158e-02	ci left: 4.934958e-01	ci right 5.074040e-01	k: 10009	n:20000
Cons ci ratio: 8.036964e-02	ci left: 1.020117e-01	ci right 1.106031e-01	k: 2125	n:20000
KS ci ratio: 3.132840e-02	ci left: 4.321564e-01	ci right 4.459613e-01	k: 8781	n:20000
AQP2   20000 perm   4 sec   (5624 perm/sec)   p_kst 4.390500e-01   p_cons 1.062500e-01   p_joint 5.004500e-01

Outputting figure to mutsig2_images.part000000000010/AQP2.3_832_20000_0.43905_0.10625_0.50045.png
                gene_name: AQP2
               theta_stop: 0.080 
                    nperm: 20000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 45 percent done.
ARHGAP21
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.259309e-02	ci left: 5.814892e-01	ci right 6.008577e-01	k: 5912	n:10000
Cons ci ratio: 5.497068e-02	ci left: 3.277341e-01	ci right 3.463609e-01	k: 3370	n:10000
KS ci ratio: 2.428697e-02	ci left: 7.137110e-01	ci right 7.313592e-01	k: 7226	n:10000
ARHGAP21   10000 perm   2 sec   (4024 perm/sec)   p_kst 7.226000e-01   p_cons 3.370000e-01   p_joint 5.912000e-01

Outputting figure to mutsig2_images.part000000000010/ARHGAP21.3_5977_10000_0.7226_0.337_0.5912.png
                gene_name: ARHGAP21
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 55 percent done.
ARHGAP31
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.664198e-03	ci left: 9.972795e-01	ci right 9.990094e-01	k: 9983	n:10000
KS ci ratio: 1.577910e-02	ci left: 8.536564e-01	ci right 8.673329e-01	k: 8606	n:10000
ARHGAP31   10000 perm   2 sec   (4780 perm/sec)   p_kst 8.606000e-01   p_cons 9.983000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000010/ARHGAP31.3_4383_10000_0.8606_0.9983_1.png
                gene_name: ARHGAP31
               theta_stop: 0.016 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.87 
                   p_cons: 1.00 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1.00 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 64 percent done.
AR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.380435e-03	ci left: 9.787712e-01	ci right 9.841431e-01	k: 9816	n:10000
Cons ci ratio: 6.587477e-02	ci left: 2.528084e-01	ci right 2.701307e-01	k: 2614	n:10000
KS ci ratio: 2.956342e-02	ci left: 6.278885e-01	ci right 6.468314e-01	k: 6374	n:10000
AR   10000 perm   2 sec   (5703 perm/sec)   p_kst 6.374000e-01   p_cons 2.614000e-01   p_joint 9.816000e-01

Outputting figure to mutsig2_images.part000000000010/AR.2_2819_10000_0.6374_0.2614_0.9816.png
                gene_name: AR
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 73 percent done.
ARHGAP4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.799423e-02	ci left: 3.044128e-01	ci right 3.226959e-01	k: 3135	n:10000
Cons ci ratio: 4.899491e-02	ci left: 3.806225e-01	ci right 3.998415e-01	k: 3902	n:10000
KS ci ratio: 2.131928e-01	ci left: 2.920604e-02	ci right 3.626959e-02	k: 326	n:10000
ARHGAP4   10000 perm   2 sec   (5371 perm/sec)   p_kst 3.260000e-02   p_cons 3.902000e-01   p_joint 3.135000e-01

Joint ci ratio: 4.029061e-02	ci left: 3.147301e-01	ci right 3.277219e-01	k: 6424	n:20000
Cons ci ratio: 3.489683e-02	ci left: 3.800423e-01	ci right 3.935907e-01	k: 7736	n:20000
KS ci ratio: 1.557474e-01	ci left: 2.830458e-02	ci right 3.313313e-02	k: 613	n:20000
ARHGAP4   20000 perm   4 sec   (4821 perm/sec)   p_kst 3.065000e-02   p_cons 3.868000e-01   p_joint 3.212000e-01

Joint ci ratio: 1.719647e-02	ci left: 6.284862e-01	ci right 6.394212e-01	k: 19019	n:30000
Cons ci ratio: 2.851812e-02	ci left: 3.808846e-01	ci right 3.919374e-01	k: 11592	n:30000
KS ci ratio: 1.278863e-01	ci left: 2.842155e-02	ci right 3.233676e-02	k: 910	n:30000
ARHGAP4   30000 perm   7 sec   (4583 perm/sec)   p_kst 3.033333e-02   p_cons 3.864000e-01   p_joint 6.339667e-01

Joint ci ratio: 2.771443e-02	ci left: 3.287549e-01	ci right 3.380193e-01	k: 13335	n:40000
Cons ci ratio: 2.474999e-02	ci left: 3.806265e-01	ci right 3.901902e-01	k: 15416	n:40000
KS ci ratio: 1.106436e-01	ci left: 2.873917e-02	ci right 3.212945e-02	k: 1216	n:40000
ARHGAP4   40000 perm   9 sec   (4440 perm/sec)   p_kst 3.040000e-02   p_cons 3.854000e-01   p_joint 3.333750e-01

Joint ci ratio: 1.908011e-02	ci left: 4.533656e-01	ci right 4.621193e-01	k: 22887	n:50000
Cons ci ratio: 2.208783e-02	ci left: 3.821886e-01	ci right 3.907446e-01	k: 19323	n:50000
KS ci ratio: 9.913947e-02	ci left: 2.881486e-02	ci right 3.184000e-02	k: 1515	n:50000
ARHGAP4   50000 perm   12 sec   (4333 perm/sec)   p_kst 3.030000e-02   p_cons 3.864600e-01   p_joint 4.577400e-01

Outputting figure to mutsig2_images.part000000000010/ARHGAP4.2_3053_50000_0.0303_0.38646_0.45774.png
                gene_name: ARHGAP4
               theta_stop: 0.099 
                    nperm: 50000 
                     p_ks: 0.030 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.46 

Current progress: 82 percent done.
ARHGEF19
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 9.576556e-02	ci left: 1.365853e-01	ci right 1.504231e-01	k: 1434	n:10000
KS ci ratio: 9.997367e-03	ci left: 9.341299e-01	ci right 9.436124e-01	k: 9390	n:10000
ARHGEF19   10000 perm   2 sec   (6064 perm/sec)   p_kst 9.390000e-01   p_cons 1.434000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000010/ARHGEF19.2_2469_10000_0.939_0.1434_1.png
                gene_name: ARHGEF19
               theta_stop: 0.096 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 91 percent done.
ARHGEF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.072269e-03	ci left: 9.553457e-01	ci right 9.631839e-01	k: 9594	n:10000
Cons ci ratio: 1.867131e-02	ci left: 8.073497e-01	ci right 8.226663e-01	k: 8151	n:10000
KS ci ratio: 4.606649e-02	ci left: 4.102013e-01	ci right 4.296454e-01	k: 4199	n:10000
ARHGEF2   10000 perm   2 sec   (5458 perm/sec)   p_kst 4.199000e-01   p_cons 8.151000e-01   p_joint 9.594000e-01

Outputting figure to mutsig2_images.part000000000010/ARHGEF2.2_3049_10000_0.4199_0.8151_0.9594.png
                gene_name: ARHGEF2
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.82 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.96 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000010
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 10 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4397781: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000011> was used as the working directory.
Started at Wed Oct 24 16:08:19 2012
Results reported at Wed Oct 24 16:10:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000011.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000011.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 11  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000011.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    136.21 sec.
    Max Memory :      1153 MB
    Max Swap   :      3913 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
11
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 11
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 11: processing genes 898 - 987
Calculating significance of each gene.
Using projection method.
898	ARID3A	1
899	ARID3B	1
900	ARID3C	1
901	ARID4A	6.737214e-03
902	ARID4B	3.393981e-01
903	ARID5A	1
904	ARID5B	1
905	ARIH1	1
906	ARIH2	2.719298e-03
907	ARL1	1
908	ARL10	1
909	ARL11	1
910	ARL13A	1
911	ARL13B	1
912	ARL14	1
913	ARL15	1
914	ARL16	1
915	ARL2	1
916	ARL2BP	1
917	ARL3	1
918	ARL4A	1
919	ARL4C	1
920	ARL4D	1
921	ARL5A	1
922	ARL5B	1
923	ARL6	1
924	ARL6IP1	1
925	ARL6IP4	1
926	ARL6IP5	1
927	ARL6IP6	1
928	ARL8A	1
929	ARL8B	1
930	ARL9	1
931	ARMC1	8.973122e-02
932	ARMC10	1
933	ARMC2	1
934	ARMC3	1.378139e-01
935	ARMC4	3.008039e-01
936	ARMC5	1
937	ARMC6	1.014414e-01
938	ARMC7	1
939	ARMC8	1
940	ARMC9	1
941	ARMCX1	1
942	ARMCX2	1
943	ARMCX3	1
944	ARMCX5	1
945	ARMCX6	1
946	ARMS2	1
947	ARNT	1
948	ARNT2	1
949	ARNTL	1
950	ARNTL2	1
951	ARPC1A	1
952	ARPC1B	1
953	ARPC2	1
954	ARPC3	1
955	ARPC4	1
956	ARPC5	4.261173e-02
957	ARPC5L	1
958	ARPM1	1
959	ARPP19	1
960	ARPP21	1.026994e-01
961	ARR3	1
962	ARRB1	1
963	ARRB2	1
964	ARRDC1	1
965	ARRDC2	1
966	ARRDC3	1
967	ARRDC4	1
968	ARRDC5	1
969	ARSA	1
970	ARSB	1
971	ARSD	1
972	ARSE	1
973	ARSF	1
974	ARSG	1
975	ARSH	1
976	ARSI	1
977	ARSJ	1
978	ARSK	1
979	ART1	1
980	ART3	1
981	ART4	1
982	ART5	1
983	ARTN	1
984	ARV1	7.313915e-02
985	ARVCF	1.748301e-01
986	AS3MT	1
987	ASAH1	1
Done

Running MutSig 2:
Scatter job 11: processing genes 898 - 987
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ARID4A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.172698e-02	ci left: 3.552563e-01	ci right 3.742225e-01	k: 3647	n:10000
Cons ci ratio: 2.438996e-02	ci left: 7.119950e-01	ci right 7.296762e-01	k: 7209	n:10000
KS ci ratio: 1.140181e-01	ci left: 9.964203e-02	ci right 1.117887e-01	k: 1056	n:10000
ARID4A   10000 perm   2 sec   (4613 perm/sec)   p_kst 1.056000e-01   p_cons 7.209000e-01   p_joint 3.647000e-01

Joint ci ratio: 5.014328e-02	ci left: 2.281465e-01	ci right 2.399310e-01	k: 4680	n:20000
Cons ci ratio: 1.714384e-02	ci left: 7.170428e-01	ci right 7.294923e-01	k: 14466	n:20000
KS ci ratio: 8.098908e-02	ci left: 1.005877e-01	ci right 1.091276e-01	k: 2096	n:20000
ARID4A   20000 perm   7 sec   (2824 perm/sec)   p_kst 1.048000e-01   p_cons 7.233000e-01   p_joint 2.340000e-01

Outputting figure to mutsig2_images.part000000000011/ARID4A.3_3866_20000_0.1048_0.7233_0.234.png
                gene_name: ARID4A
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 50 percent done.
ARIH2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.186508e-02	ci left: 2.209917e-01	ci right 2.375663e-01	k: 2292	n:10000
Cons ci ratio: 2.842204e-02	ci left: 6.459913e-01	ci right 6.647181e-01	k: 6554	n:10000
KS ci ratio: 8.525785e-02	ci left: 1.670085e-01	ci right 1.819816e-01	k: 1744	n:10000
ARIH2   10000 perm   2 sec   (6137 perm/sec)   p_kst 1.744000e-01   p_cons 6.554000e-01   p_joint 2.292000e-01

Outputting figure to mutsig2_images.part000000000011/ARIH2.3_1538_10000_0.1744_0.6554_0.2292.png
                gene_name: ARIH2
               theta_stop: 0.085 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.24 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000011
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 11 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4397784: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000012> was used as the working directory.
Started at Wed Oct 24 16:08:19 2012
Results reported at Wed Oct 24 16:11:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000012.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000012.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 12  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000012.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    195.70 sec.
    Max Memory :      1268 MB
    Max Swap   :      3970 MB

    Max Processes  :         7
    Max Threads    :        72

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
12
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 12
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 12: processing genes 988 - 1077
Calculating significance of each gene.
Using projection method.
988	ASAH2	1
989	ASAM	1
990	ASAP1	2.766505e-01
991	ASAP2	1
992	ASAP3	1
993	ASB1	1
994	ASB10	1
995	ASB11	1
996	ASB12	1
997	ASB13	1
998	ASB14	1
999	ASB15	1
1000/17942 1000	ASB16	1
1001	ASB17	1
1002	ASB18	1
1003	ASB2	1
1004	ASB3	1
1005	ASB4	7.051414e-02
1006	ASB5	1
1007	ASB6	1
1008	ASB7	1
1009	ASB8	1
1010	ASB9	1
1011	ASCC1	1
1012	ASCC2	1
1013	ASCC3	3.296734e-01
1014	ASCL1	1
1015	ASCL3	1
1016	ASCL4	1
1017	ASF1A	1
1018	ASF1B	1
1019	ASGR1	1
1020	ASGR2	1
1021	ASH1L	4.910224e-01
1022	ASH2L	1
1023	ASIP	1
1024	ASL	1
1025	ASMT	1
1026	ASMTL	1
1027	ASNA1	1
1028	ASNS	2.672786e-01
1029	ASNSD1	1
1030	ASPA	1
1031	ASPDH	1
1032	ASPG	1.385661e-01
1033	ASPH	4.161615e-01
1034	ASPHD1	1
1035	ASPHD2	1
1036	ASPM	1.817946e-01
1037	ASPN	1.854316e-01
1038	ASPRV1	1
1039	ASPSCR1	1
1040	ASRGL1	1
1041	ASS1	6.432914e-02
1042	ASTE1	1
1043	ASTL	1.267661e-01
1044	ASTN1	7.963356e-02
1045	ASTN2	1
1046	ASXL1	1
1047	ASXL2	1
1048	ASXL3	5.024620e-01
1049	ASZ1	1
1050	ATAD1	1
1051	ATAD2	1
1052	ATAD2B	1
1053	ATAD3A	1
1054	ATAD3B	1
1055	ATAD5	4.335875e-01
1056	ATCAY	1
1057	ATE1	1
1058	ATF1	1
1059	ATF2	1
1060	ATF3	1
1061	ATF4	1.395841e-01
1062	ATF5	1
1063	ATF6	1
1064	ATF6B	1
1065	ATF7	1
1066	ATF7IP	2.127894e-01
1067	ATF7IP2	1
1068	ATG10	1
1069	ATG12	1
1070	ATG16L1	1
1071	ATG16L2	1
1072	ATG2A	1
1073	ATG2B	6.930542e-01
1074	ATG3	1
1075	ATG4A	1
1076	ATG4B	1
1077	ATG4C	1
Done

Running MutSig 2:
Scatter job 12: processing genes 988 - 1077
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ASH1L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.102203e-01	ci left: 3.005970e-02	ci right 3.721534e-02	k: 335	n:10000
Cons ci ratio: 1.028188e-02	ci left: 9.307143e-01	ci right 9.404301e-01	k: 9357	n:10000
KS ci ratio: 4.884054e-01	ci left: 4.844389e-03	ci right 8.053335e-03	k: 63	n:10000
ASH1L   10000 perm   2 sec   (4424 perm/sec)   p_kst 6.300000e-03   p_cons 9.357000e-01   p_joint 3.350000e-02

Joint ci ratio: 1.752676e-01	ci left: 2.225822e-02	ci right 2.658156e-02	k: 487	n:20000
Cons ci ratio: 7.228988e-03	ci left: 9.328777e-01	ci right 9.396948e-01	k: 18727	n:20000
KS ci ratio: 3.597902e-01	ci left: 4.840441e-03	ci right 7.006997e-03	k: 117	n:20000
ASH1L   20000 perm   7 sec   (3031 perm/sec)   p_kst 5.850000e-03   p_cons 9.363500e-01   p_joint 2.435000e-02

Joint ci ratio: 1.736614e-01	ci left: 1.524830e-02	ci right 1.817970e-02	k: 500	n:30000
Cons ci ratio: 5.839766e-03	ci left: 9.348036e-01	ci right 9.403113e-01	k: 28128	n:30000
KS ci ratio: 2.971666e-01	ci left: 4.910451e-03	ci right 6.654022e-03	k: 172	n:30000
ASH1L   30000 perm   9 sec   (3245 perm/sec)   p_kst 5.733333e-03   p_cons 9.376000e-01   p_joint 1.666667e-02

Joint ci ratio: 1.420780e-01	ci left: 1.734676e-02	ci right 2.002377e-02	k: 746	n:40000
Cons ci ratio: 5.066848e-03	ci left: 9.349562e-01	ci right 9.397301e-01	k: 37495	n:40000
KS ci ratio: 2.629550e-01	ci left: 4.798815e-03	ci right 6.274366e-03	k: 220	n:40000
ASH1L   40000 perm   12 sec   (3343 perm/sec)   p_kst 5.500000e-03   p_cons 9.373750e-01   p_joint 1.865000e-02

Joint ci ratio: 1.297044e-01	ci left: 1.677525e-02	ci right 1.912119e-02	k: 896	n:50000
Cons ci ratio: 4.528511e-03	ci left: 9.353021e-01	ci right 9.395669e-01	k: 46873	n:50000
KS ci ratio: 2.374745e-01	ci left: 4.776484e-03	ci right 6.081948e-03	k: 270	n:50000
ASH1L   50000 perm   15 sec   (3386 perm/sec)   p_kst 5.400000e-03   p_cons 9.374600e-01   p_joint 1.792000e-02

Joint ci ratio: 1.309431e-01	ci left: 1.375222e-02	ci right 1.569514e-02	k: 882	n:60000
Cons ci ratio: 4.138913e-03	ci left: 9.353476e-01	ci right 9.392433e-01	k: 56239	n:60000
KS ci ratio: 2.145401e-01	ci left: 4.939689e-03	ci right 6.142233e-03	k: 331	n:60000
ASH1L   60000 perm   18 sec   (3408 perm/sec)   p_kst 5.516667e-03   p_cons 9.373167e-01   p_joint 1.470000e-02

Joint ci ratio: 1.168820e-01	ci left: 1.488919e-02	ci right 1.675126e-02	k: 1106	n:70000
Cons ci ratio: 3.828651e-03	ci left: 9.355946e-01	ci right 9.391976e-01	k: 65619	n:70000
KS ci ratio: 2.018836e-01	ci left: 4.816266e-03	ci right 5.911065e-03	k: 374	n:70000
ASH1L   70000 perm   21 sec   (3412 perm/sec)   p_kst 5.342857e-03   p_cons 9.374143e-01   p_joint 1.580000e-02

Joint ci ratio: 1.211745e-01	ci left: 1.212950e-02	ci right 1.370611e-02	k: 1032	n:80000
Cons ci ratio: 3.573757e-03	ci left: 9.359650e-01	ci right 9.393282e-01	k: 75013	n:80000
KS ci ratio: 1.896410e-01	ci left: 4.808621e-03	ci right 5.827760e-03	k: 424	n:80000
ASH1L   80000 perm   23 sec   (3407 perm/sec)   p_kst 5.300000e-03   p_cons 9.376625e-01   p_joint 1.290000e-02

Joint ci ratio: 9.624027e-02	ci left: 1.722819e-02	ci right 1.898084e-02	k: 1628	n:90000
Cons ci ratio: 3.367301e-03	ci left: 9.361349e-01	ci right 9.393034e-01	k: 84396	n:90000
KS ci ratio: 1.817076e-01	ci left: 4.676903e-03	ci right 5.622092e-03	k: 462	n:90000
ASH1L   90000 perm   27 sec   (3392 perm/sec)   p_kst 5.133333e-03   p_cons 9.377333e-01   p_joint 1.808889e-02

Joint ci ratio: 1.000460e-01	ci left: 1.436300e-02	ci right 1.588532e-02	k: 1511	n:100000
Cons ci ratio: 3.186633e-03	ci left: 9.365078e-01	ci right 9.395067e-01	k: 93802	n:100000
KS ci ratio: 1.727962e-01	ci left: 4.677482e-03	ci right 5.571592e-03	k: 511	n:100000
ASH1L   100000 perm   30 sec   (3367 perm/sec)   p_kst 5.110000e-03   p_cons 9.380200e-01   p_joint 1.511000e-02

Joint ci ratio: 1.036481e-01	ci left: 1.217060e-02	ci right 1.350981e-02	k: 1411	n:110000
Cons ci ratio: 3.038603e-03	ci left: 9.365679e-01	ci right 9.394271e-01	k: 103181	n:110000
KS ci ratio: 1.640536e-01	ci left: 4.739911e-03	ci right 5.595590e-03	k: 567	n:110000
ASH1L   110000 perm   33 sec   (3343 perm/sec)   p_kst 5.154545e-03   p_cons 9.380091e-01   p_joint 1.282727e-02

Joint ci ratio: 1.047987e-01	ci left: 1.092065e-02	ci right 1.213646e-02	k: 1382	n:120000
Cons ci ratio: 2.911956e-03	ci left: 9.365198e-01	ci right 9.392590e-01	k: 112548	n:120000
KS ci ratio: 1.576634e-01	ci left: 4.720818e-03	ci right 5.536713e-03	k: 614	n:120000
ASH1L   120000 perm   36 sec   (3316 perm/sec)   p_kst 5.116667e-03   p_cons 9.379000e-01   p_joint 1.151667e-02

Joint ci ratio: 1.026909e-01	ci left: 1.051506e-02	ci right 1.166075e-02	k: 1440	n:130000
Cons ci ratio: 2.800291e-03	ci left: 9.364657e-01	ci right 9.390993e-01	k: 121913	n:130000
KS ci ratio: 1.532512e-01	ci left: 4.623811e-03	ci right 5.398522e-03	k: 650	n:130000
ASH1L   130000 perm   40 sec   (3290 perm/sec)   p_kst 5.000000e-03   p_cons 9.377923e-01   p_joint 1.107692e-02

Joint ci ratio: 9.625824e-02	ci left: 1.114328e-02	ci right 1.227708e-02	k: 1638	n:140000
Cons ci ratio: 2.702038e-03	ci left: 9.363564e-01	ci right 9.388969e-01	k: 131269	n:140000
KS ci ratio: 1.476847e-01	ci left: 4.637240e-03	ci right 5.383488e-03	k: 700	n:140000
ASH1L   140000 perm   43 sec   (3264 perm/sec)   p_kst 5.000000e-03   p_cons 9.376357e-01   p_joint 1.170000e-02

Joint ci ratio: 8.558317e-02	ci left: 1.320266e-02	ci right 1.438958e-02	k: 2068	n:150000
Cons ci ratio: 2.612843e-03	ci left: 9.362901e-01	ci right 9.387463e-01	k: 140629	n:150000
KS ci ratio: 1.424933e-01	ci left: 4.662179e-03	ci right 5.383824e-03	k: 752	n:150000
ASH1L   150000 perm   46 sec   (3237 perm/sec)   p_kst 5.013333e-03   p_cons 9.375267e-01   p_joint 1.378667e-02

Joint ci ratio: 7.210434e-02	ci left: 1.748309e-02	ci right 1.879695e-02	k: 2901	n:160000
Cons ci ratio: 2.529499e-03	ci left: 9.363470e-01	ci right 9.387246e-01	k: 150007	n:160000
KS ci ratio: 1.378995e-01	ci left: 4.678366e-03	ci right 5.377255e-03	k: 803	n:160000
ASH1L   160000 perm   50 sec   (3208 perm/sec)   p_kst 5.018750e-03   p_cons 9.375438e-01   p_joint 1.813125e-02

Joint ci ratio: 7.094661e-02	ci left: 1.701491e-02	ci right 1.827221e-02	k: 2998	n:170000
Cons ci ratio: 2.460302e-03	ci left: 9.360779e-01	ci right 9.383895e-01	k: 159331	n:170000
KS ci ratio: 1.336447e-01	ci left: 4.698665e-03	ci right 5.377207e-03	k: 855	n:170000
ASH1L   170000 perm   53 sec   (3178 perm/sec)   p_kst 5.029412e-03   p_cons 9.372412e-01   p_joint 1.763529e-02

Joint ci ratio: 6.940989e-02	ci left: 1.680641e-02	ci right 1.802031e-02	k: 3133	n:180000
Cons ci ratio: 2.390348e-03	ci left: 9.361422e-01	ci right 9.383881e-01	k: 168709	n:180000
KS ci ratio: 1.292610e-01	ci left: 4.754637e-03	ci right 5.417012e-03	k: 914	n:180000
ASH1L   180000 perm   57 sec   (3148 perm/sec)   p_kst 5.077778e-03   p_cons 9.372722e-01   p_joint 1.740556e-02

Joint ci ratio: 6.889664e-02	ci left: 1.617512e-02	ci right 1.733443e-02	k: 3182	n:190000
Cons ci ratio: 2.324270e-03	ci left: 9.362908e-01	ci right 9.384747e-01	k: 178104	n:190000
KS ci ratio: 1.261971e-01	ci left: 4.733664e-03	ci right 5.376316e-03	k: 959	n:190000
ASH1L   190000 perm   61 sec   (3119 perm/sec)   p_kst 5.047368e-03   p_cons 9.373895e-01   p_joint 1.674737e-02

Joint ci ratio: 6.731094e-02	ci left: 1.611340e-02	ci right 1.724067e-02	k: 3334	n:200000
Cons ci ratio: 2.264922e-03	ci left: 9.363446e-01	ci right 9.384727e-01	k: 187483	n:200000
KS ci ratio: 1.234647e-01	ci left: 4.705263e-03	ci right 5.329216e-03	k: 1002	n:200000
ASH1L   200000 perm   65 sec   (3089 perm/sec)   p_kst 5.010000e-03   p_cons 9.374150e-01   p_joint 1.667000e-02

Joint ci ratio: 6.873360e-02	ci left: 1.472785e-02	ci right 1.578083e-02	k: 3202	n:210000
Cons ci ratio: 2.210706e-03	ci left: 9.363507e-01	ci right 9.384277e-01	k: 196853	n:210000
KS ci ratio: 1.202113e-01	ci left: 4.735130e-03	ci right 5.345322e-03	k: 1057	n:210000
ASH1L   210000 perm   69 sec   (3060 perm/sec)   p_kst 5.033333e-03   p_cons 9.373952e-01   p_joint 1.524762e-02

Joint ci ratio: 7.104327e-02	ci left: 1.316481e-02	ci right 1.413897e-02	k: 3002	n:220000
Cons ci ratio: 2.162547e-03	ci left: 9.362286e-01	ci right 9.382599e-01	k: 206195	n:220000
KS ci ratio: 1.174678e-01	ci left: 4.740415e-03	ci right 5.336377e-03	k: 1107	n:220000
ASH1L   220000 perm   73 sec   (3032 perm/sec)   p_kst 5.031818e-03   p_cons 9.372500e-01   p_joint 1.364545e-02

Joint ci ratio: 7.134198e-02	ci left: 1.249406e-02	ci right 1.342262e-02	k: 2979	n:230000
Cons ci ratio: 2.111764e-03	ci left: 9.364330e-01	ci right 9.384169e-01	k: 215609	n:230000
KS ci ratio: 1.150038e-01	ci left: 4.736937e-03	ci right 5.319123e-03	k: 1155	n:230000
ASH1L   230000 perm   77 sec   (3004 perm/sec)   p_kst 5.021739e-03   p_cons 9.374304e-01   p_joint 1.295217e-02

Joint ci ratio: 7.031755e-02	ci left: 1.233361e-02	ci right 1.323655e-02	k: 3067	n:240000
Cons ci ratio: 2.063354e-03	ci left: 9.366795e-01	ci right 9.386183e-01	k: 225037	n:240000
KS ci ratio: 1.123608e-01	ci left: 4.762219e-03	ci right 5.333169e-03	k: 1210	n:240000
ASH1L   240000 perm   81 sec   (2976 perm/sec)   p_kst 5.041667e-03   p_cons 9.376542e-01   p_joint 1.277917e-02

Joint ci ratio: 6.988742e-02	ci left: 1.199346e-02	ci right 1.286590e-02	k: 3106	n:250000
Cons ci ratio: 2.021217e-03	ci left: 9.367253e-01	ci right 9.386245e-01	k: 234420	n:250000
KS ci ratio: 1.101986e-01	ci left: 4.758385e-03	ci right 5.317185e-03	k: 1258	n:250000
ASH1L   250000 perm   85 sec   (2948 perm/sec)   p_kst 5.032000e-03   p_cons 9.376800e-01   p_joint 1.242400e-02

Joint ci ratio: 6.425772e-02	ci left: 1.365787e-02	ci right 1.456839e-02	k: 3668	n:260000
Cons ci ratio: 1.983907e-03	ci left: 9.366286e-01	ci right 9.384924e-01	k: 243767	n:260000
KS ci ratio: 1.084908e-01	ci left: 4.725004e-03	ci right 5.270735e-03	k: 1298	n:260000
ASH1L   260000 perm   89 sec   (2921 perm/sec)   p_kst 4.992308e-03   p_cons 9.375654e-01   p_joint 1.410769e-02

Joint ci ratio: 6.426587e-02	ci left: 1.315556e-02	ci right 1.403270e-02	k: 3669	n:270000
Cons ci ratio: 1.946490e-03	ci left: 9.366662e-01	ci right 9.384948e-01	k: 253148	n:270000
KS ci ratio: 1.064216e-01	ci left: 4.733818e-03	ci right 5.269485e-03	k: 1349	n:270000
ASH1L   270000 perm   93 sec   (2895 perm/sec)   p_kst 4.996296e-03   p_cons 9.375852e-01   p_joint 1.358889e-02

Joint ci ratio: 6.528024e-02	ci left: 1.229905e-02	ci right 1.313251e-02	k: 3559	n:280000
Cons ci ratio: 1.911697e-03	ci left: 9.366654e-01	ci right 9.384612e-01	k: 262519	n:280000
KS ci ratio: 1.045040e-01	ci left: 4.738614e-03	ci right 5.264569e-03	k: 1399	n:280000
ASH1L   280000 perm   98 sec   (2868 perm/sec)   p_kst 4.996429e-03   p_cons 9.375679e-01   p_joint 1.271071e-02

Joint ci ratio: 6.482623e-02	ci left: 1.204789e-02	ci right 1.285845e-02	k: 3610	n:290000
Cons ci ratio: 1.878263e-03	ci left: 9.366927e-01	ci right 9.384571e-01	k: 271898	n:290000
KS ci ratio: 1.027933e-01	ci left: 4.733081e-03	ci right 5.249302e-03	k: 1446	n:290000
ASH1L   290000 perm   102 sec   (2839 perm/sec)   p_kst 4.986207e-03   p_cons 9.375793e-01   p_joint 1.244828e-02

Joint ci ratio: 6.306073e-02	ci left: 1.231548e-02	ci right 1.312064e-02	k: 3814	n:300000
Cons ci ratio: 1.847259e-03	ci left: 9.366715e-01	ci right 9.384067e-01	k: 281263	n:300000
KS ci ratio: 1.011300e-01	ci left: 4.731231e-03	ci right 5.238404e-03	k: 1494	n:300000
ASH1L   300000 perm   107 sec   (2811 perm/sec)   p_kst 4.980000e-03   p_cons 9.375433e-01   p_joint 1.271333e-02

Joint ci ratio: 6.128513e-02	ci left: 1.262644e-02	ci right 1.342787e-02	k: 4037	n:310000
Cons ci ratio: 1.818292e-03	ci left: 9.366162e-01	ci right 9.383240e-01	k: 290617	n:310000
KS ci ratio: 9.957730e-02	ci left: 4.726417e-03	ci right 5.224841e-03	k: 1541	n:310000
ASH1L   310000 perm   111 sec   (2783 perm/sec)   p_kst 4.970968e-03   p_cons 9.374742e-01   p_joint 1.302258e-02

Outputting figure to mutsig2_images.part000000000012/ASH1L.3_9003_310000_0.004971_0.93747_0.013023.png
                gene_name: ASH1L
               theta_stop: 0.100 
                    nperm: 310000 
                     p_ks: 0.0050 
        ci_ks_bounds_left: 0.0047 
       ci_ks_bounds_right: 0.0052 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.013 
     ci_joint_bounds_left: 0.013 
    ci_joint_bounds_right: 0.013 

Current progress: 25 percent done.
ASPM
Processing conservation and coverage...
94% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.221694e-02	ci left: 5.871085e-01	ci right 6.064351e-01	k: 5968	n:10000
Cons ci ratio: 5.394138e-02	ci left: 3.361759e-01	ci right 3.549142e-01	k: 3455	n:10000
KS ci ratio: 7.537082e-02	ci left: 2.048126e-01	ci right 2.209550e-01	k: 2128	n:10000
ASPM   10000 perm   2 sec   (4380 perm/sec)   p_kst 2.128000e-01   p_cons 3.455000e-01   p_joint 5.968000e-01

Outputting figure to mutsig2_images.part000000000012/ASPM.2_10546_10000_0.2128_0.3455_0.5968.png
                gene_name: ASPM
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 50 percent done.
ASTN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.723193e-02	ci left: 2.450955e-01	ci right 2.622482e-01	k: 2536	n:10000
KS ci ratio: 1.260105e-02	ci left: 9.005222e-01	ci right 9.120399e-01	k: 9064	n:10000
ASTN1   10000 perm   2 sec   (6341 perm/sec)   p_kst 9.064000e-01   p_cons 2.536000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000012/ASTN1.2_3981_10000_0.9064_0.2536_1.png
                gene_name: ASTN1
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
ATG2B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.096618e-02	ci left: 4.680674e-01	ci right 4.877455e-01	k: 4779	n:10000
Cons ci ratio: 1.046204e-01	ci left: 1.166232e-01	ci right 1.295972e-01	k: 1230	n:10000
KS ci ratio: 2.545351e-02	ci left: 6.943394e-01	ci right 7.123420e-01	k: 7034	n:10000
ATG2B   10000 perm   2 sec   (5550 perm/sec)   p_kst 7.034000e-01   p_cons 1.230000e-01   p_joint 4.779000e-01

Joint ci ratio: 2.921761e-02	ci left: 4.667094e-01	ci right 4.805983e-01	k: 9473	n:20000
Cons ci ratio: 7.338550e-02	ci left: 1.202495e-01	ci right 1.294599e-01	k: 2496	n:20000
KS ci ratio: 1.802470e-02	ci left: 6.964119e-01	ci right 7.091291e-01	k: 14056	n:20000
ATG2B   20000 perm   4 sec   (5012 perm/sec)   p_kst 7.028000e-01   p_cons 1.248000e-01   p_joint 4.736500e-01

Outputting figure to mutsig2_images.part000000000012/ATG2B.2_6405_20000_0.7028_0.1248_0.47365.png
                gene_name: ATG2B
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.48 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000012
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 12 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4397786: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000013> was used as the working directory.
Started at Wed Oct 24 16:08:22 2012
Results reported at Wed Oct 24 16:10:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000013.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000013.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 13  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000013.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    142.90 sec.
    Max Memory :      1622 MB
    Max Swap   :      3972 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
13
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 13
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 13: processing genes 1078 - 1166
Calculating significance of each gene.
Using projection method.
1078	ATG4D	1
1079	ATG5	1
1080	ATG7	8.000562e-02
1081	ATG9A	1
1082	ATG9B	9.951867e-02
1083	ATHL1	1
1084	ATIC	1
1085	ATL1	2.661647e-01
1086	ATL2	8.371770e-02
1087	ATL3	1
1088	ATM	5.223882e-01
1089	ATMIN	1.877881e-01
1090	ATN1	3.601409e-01
1091	ATOH1	1
1092	ATOH7	1
1093	ATOH8	3.093944e-02
1094	ATOX1	1
1095	ATP10A	2.990359e-01
1096	ATP10B	2.450622e-01
1097	ATP10D	3.674395e-01
1098	ATP11A	5.075890e-01
1099	ATP11B	1.210666e-01
1100	ATP11C	1
1101	ATP12A	1
1102	ATP13A1	3.681554e-01
1103	ATP13A2	1
1104	ATP13A3	1
1105	ATP13A4	8.187634e-02
1106	ATP13A5	1.507585e-01
1107	ATP1A1	3.245093e-01
1108	ATP1A2	1
1109	ATP1A3	1
1110	ATP1A4	1.912014e-01
1111	ATP1B1	1
1112	ATP1B2	1
1113	ATP1B3	1.429394e-01
1114	ATP1B4	6.224682e-02
1115	ATP2A1	1.711762e-01
1116	ATP2A2	1.647436e-01
1117	ATP2A3	1
1118	ATP2B1	8.536921e-02
1119	ATP2B2	5.226673e-01
1120	ATP2B3	1
1121	ATP2B4	7.898926e-02
1122	ATP2C1	1
1123	ATP2C2	1.430524e-01
1124	ATP4A	1
1125	ATP4B	1
1126	ATP5A1	1
1127	ATP5B	1
1128	ATP5C1	1
1129	ATP5E	1
1130	ATP5F1	4.573576e-02
1131	ATP5G1	1
1132	ATP5G2	1
1133	ATP5G3	1
1134	ATP5H	1
1135	ATP5I	1
1136	ATP5J	3.965802e-02
1137	ATP5J2	1
1138	ATP5L	1
1139	ATP5O	1
1140	ATP5S	1
1141	ATP5SL	9.667581e-02
1142	ATP6AP1	1
1143	ATP6AP1L	1
1144	ATP6AP2	1
1145	ATP6V0A1	1
1146	ATP6V0A2	1
1147	ATP6V0A4	1
1148	ATP6V0B	1
1149	ATP6V0C	1
1150	ATP6V0D1	6.788905e-02
1151	ATP6V0D2	1
1152	ATP6V0E1	1
1153	ATP6V0E2	1
1154	ATP6V1A	1
1155	ATP6V1B1	1
1156	ATP6V1B2	1.979891e-01
1157	ATP6V1C1	1
1158	ATP6V1C2	1
1159	ATP6V1D	1
1160	ATP6V1E1	1
1161	ATP6V1E2	9.337856e-02
1162	ATP6V1F	1
1163	ATP6V1G1	1
1164	ATP6V1G2	1
1165	ATP6V1G3	1
1166	ATP6V1H	1
Done

Running MutSig 2:
Scatter job 13: processing genes 1078 - 1166
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ATM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.583094e-02	ci left: 4.126927e-01	ci right 4.321525e-01	k: 4224	n:10000
Cons ci ratio: 5.159332e-02	ci left: 3.564494e-01	ci right 3.754288e-01	k: 3659	n:10000
KS ci ratio: 4.221808e-02	ci left: 4.530892e-01	ci right 4.727324e-01	k: 4629	n:10000
ATM   10000 perm   3 sec   (3970 perm/sec)   p_kst 4.629000e-01   p_cons 3.659000e-01   p_joint 4.224000e-01

Outputting figure to mutsig2_images.part000000000013/ATM.2_9419_10000_0.4629_0.3659_0.4224.png
                gene_name: ATM
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 20 percent done.
ATP11B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.206560e-02	ci left: 4.548861e-01	ci right 4.745345e-01	k: 4647	n:10000
Cons ci ratio: 3.849500e-02	ci left: 4.991503e-01	ci right 5.188444e-01	k: 5090	n:10000
KS ci ratio: 6.149978e-02	ci left: 2.799299e-01	ci right 2.977933e-01	k: 2888	n:10000
ATP11B   10000 perm   2 sec   (5721 perm/sec)   p_kst 2.888000e-01   p_cons 5.090000e-01   p_joint 4.647000e-01

Outputting figure to mutsig2_images.part000000000013/ATP11B.2_3654_10000_0.2888_0.509_0.4647.png
                gene_name: ATP11B
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 40 percent done.
ATP13A4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.852670e-03	ci left: 9.575422e-01	ci right 9.651860e-01	k: 9615	n:10000
Cons ci ratio: 2.681507e-02	ci left: 6.719646e-01	ci right 6.903298e-01	k: 6812	n:10000
KS ci ratio: 5.913147e-02	ci left: 2.961823e-01	ci right 3.143313e-01	k: 3052	n:10000
ATP13A4   10000 perm   2 sec   (5757 perm/sec)   p_kst 3.052000e-01   p_cons 6.812000e-01   p_joint 9.615000e-01

Outputting figure to mutsig2_images.part000000000013/ATP13A4.2_3711_10000_0.3052_0.6812_0.9615.png
                gene_name: ATP13A4
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 60 percent done.
ATP2B1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.386407e-02	ci left: 1.717274e-01	ci right 1.868599e-01	k: 1792	n:10000
KS ci ratio: 2.852906e-02	ci left: 6.442810e-01	ci right 6.630294e-01	k: 6537	n:10000
ATP2B1   10000 perm   2 sec   (5528 perm/sec)   p_kst 6.537000e-01   p_cons 1.792000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000013/ATP2B1.2_3901_10000_0.6537_0.1792_1.png
                gene_name: ATP2B1
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
ATP2B4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.189212e-01	ci left: 9.214310e-02	ci right 1.038923e-01	k: 979	n:10000
KS ci ratio: 1.085878e-02	ci left: 9.235838e-01	ci right 9.337648e-01	k: 9288	n:10000
ATP2B4   10000 perm   2 sec   (5627 perm/sec)   p_kst 9.288000e-01   p_cons 9.790000e-02   p_joint 1

Joint ci ratio: 3.890493e-02	ci left: 3.300998e-01	ci right 3.432477e-01	k: 6733	n:20000
Cons ci ratio: 1.104967e-01	ci left: 5.591985e-02	ci right 6.250903e-02	k: 1183	n:20000
KS ci ratio: 7.656090e-03	ci left: 9.255063e-01	ci right 9.326683e-01	k: 18583	n:20000
ATP2B4   20000 perm   4 sec   (5012 perm/sec)   p_kst 9.291500e-01   p_cons 5.915000e-02   p_joint 3.366500e-01

Joint ci ratio: 2.976802e-02	ci left: 3.608114e-01	ci right 3.717479e-01	k: 10988	n:30000
Cons ci ratio: 8.864005e-02	ci left: 5.848091e-02	ci right 6.393778e-02	k: 1835	n:30000
KS ci ratio: 6.259344e-03	ci left: 9.260014e-01	ci right 9.318485e-01	k: 27869	n:30000
ATP2B4   30000 perm   6 sec   (4790 perm/sec)   p_kst 9.289667e-01   p_cons 6.116667e-02   p_joint 3.662667e-01

Outputting figure to mutsig2_images.part000000000013/ATP2B4.2_3880_30000_0.92897_0.061167_0.36627.png
                gene_name: ATP2B4
               theta_stop: 0.089 
                    nperm: 30000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.061 
      ci_cons_bounds_left: 0.058 
     ci_cons_bounds_right: 0.064 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000013
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 13 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4397788: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000014> was used as the working directory.
Started at Wed Oct 24 16:08:25 2012
Results reported at Wed Oct 24 16:10:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000014.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000014.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 14  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000014.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    102.36 sec.
    Max Memory :      1396 MB
    Max Swap   :      3938 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
14
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 14
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 14: processing genes 1167 - 1256
Calculating significance of each gene.
Using projection method.
1167	ATP7A	1
1168	ATP7B	1
1169	ATP8A1	4.771418e-01
1170	ATP8A2	1
1171	ATP8B1	1
1172	ATP8B2	2.944906e-01
1173	ATP8B3	1
1174	ATP8B4	1
1175	ATP9A	8.020999e-02
1176	ATP9B	1
1177	ATPAF1	1
1178	ATPAF2	1
1179	ATPBD4	1
1180	ATPIF1	1
1181	ATR	3.471381e-01
1182	ATRIP	9.248366e-02
1183	ATRN	3.644806e-01
1184	ATRNL1	1.250397e-01
In gene ATRX the following bins exceed PROBCAP:
    CESC-C5-A0TN-TP	categ 6	N = 7595    n = 1	mu =   6.94e-08
    CESC-DS-A0VL-TP	categ 6	N = 7611    n = 1	mu =   4.43e-07
1185	ATRX	2.383701e-03
1186	ATXN1	2.202283e-01
1187	ATXN10	1
1188	ATXN2	3.263058e-01
1189	ATXN2L	1
1190	ATXN3	1
1191	ATXN3L	1
1192	ATXN7	1
1193	ATXN7L2	1.070480e-01
1194	ATXN7L3	1
1195	AUH	1
1196	AUP1	1
1197	AURKA	2.004607e-01
1198	AURKAIP1	7.485458e-02
1199	AURKB	1
1200	AURKC	1
1201	AUTS2	1
1202	AVEN	2.422985e-02
1203	AVIL	1
1204	AVL9	1
1205	AVP	1
1206	AVPI1	1
1207	AVPR1A	1
1208	AVPR1B	6.431295e-02
1209	AVPR2	1
1210	AWAT1	5.770964e-02
1211	AWAT2	1
1212	AXIN1	1
1213	AXIN2	1.024228e-01
1214	AXL	1
1215	AZGP1	1
1216	AZI1	1
1217	AZI2	2.038182e-01
1218	AZIN1	1
1219	AZU1	1
1220	B2M	1.461552e-03
1221	B3GALNT1	1
1222	B3GALNT2	1
1223	B3GALT1	1.165501e-01
1224	B3GALT2	1
1225	B3GALT4	1.602278e-01
1226	B3GALT5	1
1227	B3GALTL	2.328526e-01
1228	B3GAT1	1
1229	B3GAT2	1
1230	B3GAT3	1
1231	B3GNT1	1
1232	B3GNT2	1
1233	B3GNT3	1.485821e-01
1234	B3GNT4	1
1235	B3GNT5	1
1236	B3GNT6	1
1237	B3GNT7	1
1238	B3GNT8	3.586903e-03
1239	B3GNT9	1
1240	B3GNTL1	1
1241	B4GALNT1	1
1242	B4GALNT2	1
1243	B4GALNT3	1
1244	B4GALNT4	1
1245	B4GALT1	1
1246	B4GALT2	1
1247	B4GALT3	1.951492e-01
1248	B4GALT4	1
1249	B4GALT5	4.344451e-02
1250	B4GALT6	1
1251	B4GALT7	1
1252	B9D1	1
1253	B9D2	1
1254	BAALC	1
1255	BAAT	1
1256	BACE1	1.287184e-01
Done

Running MutSig 2:
Scatter job 14: processing genes 1167 - 1256
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ATRX
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.105821e-02	ci left: 6.046775e-01	ci right 6.238559e-01	k: 6143	n:10000
Cons ci ratio: 7.767058e-02	ci left: 1.950552e-01	ci right 2.109182e-01	k: 2029	n:10000
KS ci ratio: 3.632827e-02	ci left: 5.280685e-01	ci right 5.477094e-01	k: 5379	n:10000
ATRX   10000 perm   2 sec   (4501 perm/sec)   p_kst 5.379000e-01   p_cons 2.029000e-01   p_joint 6.143000e-01

Outputting figure to mutsig2_images.part000000000014/ATRX.4_7619_10000_0.5379_0.2029_0.6143.png
                gene_name: ATRX
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 17 percent done.
ATP9A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.144239e-02	ci left: 7.613202e-01	ci right 7.779225e-01	k: 7697	n:10000
KS ci ratio: 1.355848e-02	ci left: 8.869816e-01	ci right 8.991884e-01	k: 8932	n:10000
ATP9A   10000 perm   2 sec   (6482 perm/sec)   p_kst 8.932000e-01   p_cons 7.697000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000014/ATP9A.2_3256_10000_0.8932_0.7697_1.png
                gene_name: ATP9A
               theta_stop: 0.021 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
ATRIP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.190619e-02	ci left: 9.099797e-01	ci right 9.209768e-01	k: 9156	n:10000
Cons ci ratio: 2.801592e-01	ci left: 1.650803e-02	ci right 2.197711e-02	k: 191	n:10000
KS ci ratio: 5.524235e-02	ci left: 3.255497e-01	ci right 3.441466e-01	k: 3348	n:10000
ATRIP   10000 perm   1 sec   (6973 perm/sec)   p_kst 3.348000e-01   p_cons 1.910000e-02   p_joint 9.156000e-01

Joint ci ratio: 5.526384e-02	ci left: 1.954153e-01	ci right 2.065718e-01	k: 4019	n:20000
Cons ci ratio: 1.612488e-01	ci left: 2.638175e-02	ci right 3.105661e-02	k: 573	n:20000
KS ci ratio: 3.888752e-02	ci left: 3.302989e-01	ci right 3.434486e-01	k: 6737	n:20000
ATRIP   20000 perm   3 sec   (6318 perm/sec)   p_kst 3.368500e-01   p_cons 2.865000e-02   p_joint 2.009500e-01

Joint ci ratio: 4.089823e-02	ci left: 2.296156e-01	ci right 2.392359e-01	k: 7032	n:30000
Cons ci ratio: 1.659150e-01	ci left: 1.674946e-02	ci right 1.981151e-02	k: 547	n:30000
KS ci ratio: 3.179658e-02	ci left: 3.308869e-01	ci right 3.416115e-01	k: 10087	n:30000
ATRIP   30000 perm   5 sec   (6036 perm/sec)   p_kst 3.362333e-01   p_cons 1.823333e-02   p_joint 2.344000e-01

Joint ci ratio: 4.483802e-02	ci left: 1.568159e-01	ci right 1.640334e-01	k: 6416	n:40000
Cons ci ratio: 1.433544e-01	ci left: 1.703317e-02	ci right 1.968741e-02	k: 733	n:40000
KS ci ratio: 2.749147e-02	ci left: 3.323423e-01	ci right 3.416313e-01	k: 13479	n:40000
ATRIP   40000 perm   7 sec   (5844 perm/sec)   p_kst 3.369750e-01   p_cons 1.832500e-02   p_joint 1.604000e-01

Joint ci ratio: 4.014988e-02	ci left: 1.568956e-01	ci right 1.633439e-01	k: 8005	n:50000
Cons ci ratio: 1.294109e-01	ci left: 1.685270e-02	ci right 1.920373e-02	k: 900	n:50000
KS ci ratio: 2.453091e-02	ci left: 3.338932e-01	ci right 3.422056e-01	k: 16902	n:50000
ATRIP   50000 perm   9 sec   (5704 perm/sec)   p_kst 3.380400e-01   p_cons 1.800000e-02   p_joint 1.601000e-01

Joint ci ratio: 2.898681e-02	ci left: 2.302024e-01	ci right 2.369900e-01	k: 14015	n:60000
Cons ci ratio: 1.185382e-01	ci left: 1.683795e-02	ci right 1.897571e-02	k: 1073	n:60000
KS ci ratio: 2.239238e-02	ci left: 3.342811e-01	ci right 3.418679e-01	k: 20284	n:60000
ATRIP   60000 perm   11 sec   (5574 perm/sec)   p_kst 3.380667e-01   p_cons 1.788333e-02   p_joint 2.335833e-01

Joint ci ratio: 2.619224e-02	ci left: 2.392290e-01	ci right 2.455924e-01	k: 16968	n:70000
Cons ci ratio: 1.093019e-01	ci left: 1.705578e-02	ci right 1.904160e-02	k: 1262	n:70000
KS ci ratio: 2.070543e-02	ci left: 3.351224e-01	ci right 3.421481e-01	k: 23704	n:70000
ATRIP   70000 perm   13 sec   (5454 perm/sec)   p_kst 3.386286e-01   p_cons 1.802857e-02   p_joint 2.424000e-01

Joint ci ratio: 2.505435e-02	ci left: 2.313559e-01	ci right 2.372384e-01	k: 18743	n:80000
Cons ci ratio: 1.014379e-01	ci left: 1.739465e-02	ci right 1.926552e-02	k: 1465	n:80000
KS ci ratio: 1.937595e-02	ci left: 3.351707e-01	ci right 3.417410e-01	k: 27076	n:80000
ATRIP   80000 perm   15 sec   (5344 perm/sec)   p_kst 3.384500e-01   p_cons 1.831250e-02   p_joint 2.342875e-01

Joint ci ratio: 2.311638e-02	ci left: 2.393375e-01	ci right 2.449458e-01	k: 21792	n:90000
Cons ci ratio: 9.540855e-02	ci left: 1.753198e-02	ci right 1.929926e-02	k: 1656	n:90000
KS ci ratio: 1.828489e-02	ci left: 3.349426e-01	ci right 3.411345e-01	k: 30423	n:90000
ATRIP   90000 perm   17 sec   (5241 perm/sec)   p_kst 3.380333e-01   p_cons 1.840000e-02   p_joint 2.421333e-01

Outputting figure to mutsig2_images.part000000000014/ATRIP.2_2428_90000_0.33803_0.0184_0.24213.png
                gene_name: ATRIP
               theta_stop: 0.095 
                    nperm: 90000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.018 
      ci_cons_bounds_left: 0.018 
     ci_cons_bounds_right: 0.019 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.24 

Current progress: 50 percent done.
ATRNL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.008330e-02	ci left: 7.840118e-01	ci right 8.000177e-01	k: 7921	n:10000
KS ci ratio: 8.276929e-02	ci left: 1.755630e-01	ci right 1.908220e-01	k: 1831	n:10000
ATRNL1   10000 perm   2 sec   (6367 perm/sec)   p_kst 1.831000e-01   p_cons 7.921000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000014/ATRNL1.2_4256_10000_0.1831_0.7921_1.png
                gene_name: ATRNL1
               theta_stop: 0.083 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
B2M
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.038162e-02	ci left: 7.790450e-01	ci right 7.951874e-01	k: 7872	n:10000
Cons ci ratio: 2.741570e-02	ci left: 6.621957e-01	ci right 6.807043e-01	k: 6715	n:10000
KS ci ratio: 3.378697e-02	ci left: 5.639369e-01	ci right 5.834201e-01	k: 5737	n:10000
B2M   10000 perm   1 sec   (8148 perm/sec)   p_kst 5.737000e-01   p_cons 6.715000e-01   p_joint 7.872000e-01

Outputting figure to mutsig2_images.part000000000014/B2M.2_372_10000_0.5737_0.6715_0.7872.png
                gene_name: B2M
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 83 percent done.
B3GNT8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.318984e-02	ci left: 5.726613e-01	ci right 5.920907e-01	k: 5824	n:10000
Cons ci ratio: 3.839503e-02	ci left: 5.004505e-01	ci right 5.201435e-01	k: 5103	n:10000
KS ci ratio: 4.459463e-02	ci left: 4.260512e-01	ci right 4.455862e-01	k: 4358	n:10000
B3GNT8   10000 perm   1 sec   (7578 perm/sec)   p_kst 4.358000e-01   p_cons 5.103000e-01   p_joint 5.824000e-01

Outputting figure to mutsig2_images.part000000000014/B3GNT8.2_1198_10000_0.4358_0.5103_0.5824.png
                gene_name: B3GNT8
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000014
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 14 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4397791: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000015> was used as the working directory.
Started at Wed Oct 24 16:08:27 2012
Results reported at Wed Oct 24 16:12:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000015.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000015.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 15  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000015.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    277.20 sec.
    Max Memory :      1610 MB
    Max Swap   :      4113 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
15
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 15
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 15: processing genes 1257 - 1346
Calculating significance of each gene.
Using projection method.
1257	BACE2	1
1258	BACH1	1
1259	BACH2	1
1260	BAD	1
1261	BAG1	1
1262	BAG2	1
1263	BAG3	1
1264	BAG4	1
1265	BAG5	1
1266	BAGE	1
1267	BAGE2	1
1268	BAGE3	1
1269	BAGE4	1
1270	BAGE5	1
1271	BAHCC1	8.145177e-03
1272	BAHD1	1
1273	BAI1	7.828194e-04
1274	BAI2	1
1275	BAI3	1
1276	BAIAP2	1
1277	BAIAP2L1	1
1278	BAIAP2L2	1
1279	BAIAP3	2.132176e-02
1280	BAK1	1
1281	BAMBI	1
1282	BANF1	1
1283	BANF2	1
1284	BANK1	1
1285	BANP	1
1286	BAP1	2.713145e-02
1287	BARD1	1.352482e-01
1288	BARHL1	1.446468e-01
1289	BARHL2	4.657675e-02
1290	BARX1	1
1291	BARX2	1
1292	BASP1	1
1293	BAT1	1
1294	BAT2	5.267461e-01
1295	BAT2L1	1.334636e-01
1296	BAT2L2	1
1297	BAT3	1
1298	BAT4	1
1299	BAT5	1
1300	BATF	1
1301	BATF2	1
1302	BATF3	1
1303	BAX	1
1304	BAZ1A	1.036740e-01
1305	BAZ1B	5.736290e-01
1306	BAZ2A	1.995690e-01
1307	BAZ2B	6.974901e-01
1308	BBOX1	1.891304e-02
1309	BBS1	1.294114e-01
1310	BBS10	2.974848e-02
1311	BBS12	1.970654e-02
1312	BBS2	1
1313	BBS4	1
1314	BBS5	1
1315	BBS7	1
1316	BBS9	1
1317	BBX	1
1318	BCAM	1
1319	BCAN	2.159703e-02
1320	BCAP29	1.605784e-01
1321	BCAP31	1.107374e-01
1322	BCAR1	1
1323	BCAR3	1
1324	BCAS1	1
1325	BCAS2	1
1326	BCAS3	1.609793e-01
1327	BCAS4	1
1328	BCAT1	1
1329	BCAT2	1
1330	BCCIP	1
1331	BCDIN3D	1
1332	BCHE	1
1333	BCKDHA	1
1334	BCKDHB	1
1335	BCKDK	7.086203e-02
1336	BCL10	1
1337	BCL11A	1
1338	BCL11B	1
1339	BCL2	1
1340	BCL2A1	1
1341	BCL2L1	1
1342	BCL2L10	1
1343	BCL2L11	1
1344	BCL2L12	1
1345	BCL2L13	1
1346	BCL2L14	1
Done

Running MutSig 2:
Scatter job 15: processing genes 1257 - 1346
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BAI1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.238882e-01	ci left: 8.533549e-02	ci right 9.670407e-02	k: 909	n:10000
Cons ci ratio: 3.005121e-02	ci left: 6.202494e-01	ci right 6.392749e-01	k: 6298	n:10000
KS ci ratio: 2.043162e-01	ci left: 3.186407e-02	ci right 3.920972e-02	k: 354	n:10000
BAI1   10000 perm   2 sec   (4810 perm/sec)   p_kst 3.540000e-02   p_cons 6.298000e-01   p_joint 9.090000e-02

Joint ci ratio: 5.043875e-02	ci left: 2.260652e-01	ci right 2.378129e-01	k: 4638	n:20000
Cons ci ratio: 2.144679e-02	ci left: 6.187495e-01	ci right 6.322140e-01	k: 12510	n:20000
KS ci ratio: 1.415071e-01	ci left: 3.432986e-02	ci right 3.960586e-02	k: 738	n:20000
BAI1   20000 perm   7 sec   (2713 perm/sec)   p_kst 3.690000e-02   p_cons 6.255000e-01   p_joint 2.319000e-01

Joint ci ratio: 5.635030e-02	ci left: 1.349720e-01	ci right 1.428314e-01	k: 4166	n:30000
Cons ci ratio: 1.745301e-02	ci left: 6.215657e-01	ci right 6.325430e-01	k: 18812	n:30000
KS ci ratio: 1.137159e-01	ci left: 3.592946e-02	ci right 4.029391e-02	k: 1142	n:30000
BAI1   30000 perm   10 sec   (2992 perm/sec)   p_kst 3.806667e-02   p_cons 6.270667e-01   p_joint 1.388667e-01

Joint ci ratio: 5.535573e-02	ci left: 1.083078e-01	ci right 1.144987e-01	k: 4455	n:40000
Cons ci ratio: 1.511056e-02	ci left: 6.224397e-01	ci right 6.319418e-01	k: 25088	n:40000
KS ci ratio: 9.875102e-02	ci left: 3.602539e-02	ci right 3.979208e-02	k: 1515	n:40000
BAI1   40000 perm   13 sec   (3192 perm/sec)   p_kst 3.787500e-02   p_cons 6.272000e-01   p_joint 1.113750e-01

Outputting figure to mutsig2_images.part000000000015/BAI1.3_4875_40000_0.037875_0.6272_0.11138.png
                gene_name: BAI1
               theta_stop: 0.099 
                    nperm: 40000 
                     p_ks: 0.038 
        ci_ks_bounds_left: 0.036 
       ci_ks_bounds_right: 0.040 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.11 

Current progress: 9 percent done.
BBOX1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.777013e-01	ci left: 4.226411e-02	ci right 5.060268e-02	k: 463	n:10000
Cons ci ratio: 4.827181e-02	ci left: 3.876902e-01	ci right 4.069696e-01	k: 3973	n:10000
KS ci ratio: 3.634162e-01	ci left: 9.412543e-03	ci right 1.367914e-02	k: 114	n:10000
BBOX1   10000 perm   1 sec   (6759 perm/sec)   p_kst 1.140000e-02   p_cons 3.973000e-01   p_joint 4.630000e-02

Joint ci ratio: 2.005164e-01	ci left: 1.686783e-02	ci right 2.067391e-02	k: 374	n:20000
Cons ci ratio: 3.454633e-02	ci left: 3.848265e-01	ci right 3.984051e-01	k: 7832	n:20000
KS ci ratio: 2.723712e-01	ci left: 8.854025e-03	ci right 1.169107e-02	k: 204	n:20000
BBOX1   20000 perm   3 sec   (5959 perm/sec)   p_kst 1.020000e-02   p_cons 3.916000e-01   p_joint 1.870000e-02

Joint ci ratio: 1.202071e-01	ci left: 3.217197e-02	ci right 3.631887e-02	k: 1026	n:30000
Cons ci ratio: 2.823552e-02	ci left: 3.856052e-01	ci right 3.966825e-01	k: 11734	n:30000
KS ci ratio: 2.302770e-01	ci left: 8.464779e-03	ci right 1.069841e-02	k: 286	n:30000
BBOX1   30000 perm   5 sec   (5657 perm/sec)   p_kst 9.533333e-03   p_cons 3.911333e-01   p_joint 3.420000e-02

Joint ci ratio: 1.382602e-01	ci left: 1.833645e-02	ci right 2.108390e-02	k: 787	n:40000
Cons ci ratio: 2.382229e-02	ci left: 3.988366e-01	ci right 4.084774e-01	k: 16146	n:40000
KS ci ratio: 2.014743e-01	ci left: 8.430095e-03	ci right 1.034215e-02	k: 374	n:40000
BBOX1   40000 perm   7 sec   (5467 perm/sec)   p_kst 9.350000e-03   p_cons 4.036500e-01   p_joint 1.967500e-02

Joint ci ratio: 1.337870e-01	ci left: 1.574962e-02	ci right 1.802697e-02	k: 843	n:50000
Cons ci ratio: 2.127700e-02	ci left: 4.000340e-01	ci right 4.086571e-01	k: 20217	n:50000
KS ci ratio: 1.819265e-01	ci left: 8.362639e-03	ci right 1.005508e-02	k: 459	n:50000
BBOX1   50000 perm   10 sec   (5186 perm/sec)   p_kst 9.180000e-03   p_cons 4.043400e-01   p_joint 1.686000e-02

Joint ci ratio: 1.153528e-01	ci left: 1.779301e-02	ci right 1.998721e-02	k: 1132	n:60000
Cons ci ratio: 1.943363e-02	ci left: 4.001533e-01	ci right 4.080227e-01	k: 24245	n:60000
KS ci ratio: 1.538789e-01	ci left: 9.876125e-03	ci right 1.153838e-02	k: 641	n:60000
BBOX1   60000 perm   12 sec   (5071 perm/sec)   p_kst 1.068333e-02   p_cons 4.040833e-01   p_joint 1.886667e-02

Joint ci ratio: 1.065021e-01	ci left: 1.797364e-02	ci right 2.000937e-02	k: 1328	n:70000
Cons ci ratio: 1.797924e-02	ci left: 4.007898e-01	ci right 4.080753e-01	k: 28310	n:70000
KS ci ratio: 1.426570e-01	ci left: 9.909673e-03	ci right 1.144558e-02	k: 746	n:70000
BBOX1   70000 perm   14 sec   (4968 perm/sec)   p_kst 1.065714e-02   p_cons 4.044286e-01   p_joint 1.897143e-02

Joint ci ratio: 7.514088e-02	ci left: 3.166239e-02	ci right 3.414664e-02	k: 2631	n:80000
Cons ci ratio: 1.681560e-02	ci left: 4.010963e-01	ci right 4.079106e-01	k: 32360	n:80000
KS ci ratio: 1.336584e-01	ci left: 9.926066e-03	ci right 1.135975e-02	k: 850	n:80000
BBOX1   80000 perm   16 sec   (4873 perm/sec)   p_kst 1.062500e-02   p_cons 4.045000e-01   p_joint 3.288750e-02

Joint ci ratio: 7.475777e-02	ci left: 2.853510e-02	ci right 3.076202e-02	k: 2667	n:90000
Cons ci ratio: 1.585979e-02	ci left: 4.011136e-01	ci right 4.075371e-01	k: 36389	n:90000
KS ci ratio: 1.249227e-01	ci left: 1.014574e-02	ci right 1.150829e-02	k: 973	n:90000
BBOX1   90000 perm   19 sec   (4784 perm/sec)   p_kst 1.081111e-02   p_cons 4.043222e-01   p_joint 2.963333e-02

Joint ci ratio: 7.160194e-02	ci left: 2.805706e-02	ci right 3.015038e-02	k: 2909	n:100000
Cons ci ratio: 1.505509e-02	ci left: 4.009865e-01	ci right 4.070791e-01	k: 40403	n:100000
KS ci ratio: 1.180839e-01	ci left: 1.025596e-02	ci right 1.155264e-02	k: 1089	n:100000
BBOX1   100000 perm   21 sec   (4698 perm/sec)   p_kst 1.089000e-02   p_cons 4.040300e-01   p_joint 2.909000e-02

Joint ci ratio: 5.552566e-02	ci left: 4.214062e-02	ci right 4.455626e-02	k: 4767	n:110000
Cons ci ratio: 1.437111e-02	ci left: 4.005716e-01	ci right 4.063790e-01	k: 44382	n:110000
KS ci ratio: 1.136475e-01	ci left: 1.009154e-02	ci right 1.131628e-02	k: 1176	n:110000
BBOX1   110000 perm   24 sec   (4613 perm/sec)   p_kst 1.069091e-02   p_cons 4.034727e-01   p_joint 4.333636e-02

Joint ci ratio: 5.348209e-02	ci left: 4.170283e-02	ci right 4.400266e-02	k: 5141	n:120000
Cons ci ratio: 1.376520e-02	ci left: 4.004893e-01	ci right 4.060487e-01	k: 48392	n:120000
KS ci ratio: 1.091535e-01	ci left: 1.005258e-02	ci right 1.122125e-02	k: 1275	n:120000
BBOX1   120000 perm   26 sec   (4529 perm/sec)   p_kst 1.062500e-02   p_cons 4.032667e-01   p_joint 4.284167e-02

Joint ci ratio: 5.824507e-02	ci left: 3.268769e-02	ci right 3.465626e-02	k: 4376	n:130000
Cons ci ratio: 1.321752e-02	ci left: 4.008776e-01	ci right 4.062191e-01	k: 52461	n:130000
KS ci ratio: 1.049609e-01	ci left: 1.005789e-02	ci right 1.117948e-02	k: 1379	n:130000
BBOX1   130000 perm   29 sec   (4449 perm/sec)   p_kst 1.060769e-02   p_cons 4.035462e-01   p_joint 3.366154e-02

Joint ci ratio: 7.053404e-02	ci left: 2.082379e-02	ci right 2.235326e-02	k: 3021	n:140000
Cons ci ratio: 1.273871e-02	ci left: 4.009000e-01	ci right 4.060468e-01	k: 56486	n:140000
KS ci ratio: 1.009082e-01	ci left: 1.012585e-02	ci right 1.120884e-02	k: 1492	n:140000
BBOX1   140000 perm   32 sec   (4371 perm/sec)   p_kst 1.065714e-02   p_cons 4.034714e-01   p_joint 2.157857e-02

Joint ci ratio: 6.778862e-02	ci left: 2.106692e-02	ci right 2.255164e-02	k: 3270	n:150000
Cons ci ratio: 1.231474e-02	ci left: 4.006762e-01	ci right 4.056476e-01	k: 60474	n:150000
KS ci ratio: 9.723021e-02	ci left: 1.019849e-02	ci right 1.124722e-02	k: 1607	n:150000
BBOX1   150000 perm   35 sec   (4300 perm/sec)   p_kst 1.071333e-02   p_cons 4.031600e-01   p_joint 2.180000e-02

Outputting figure to mutsig2_images.part000000000015/BBOX1.3_1192_150000_0.010713_0.40316_0.0218.png
                gene_name: BBOX1
               theta_stop: 0.097 
                    nperm: 150000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.022 
     ci_joint_bounds_left: 0.021 
    ci_joint_bounds_right: 0.023 

Current progress: 18 percent done.
BAHCC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.345683e-02	ci left: 2.673539e-01	ci right 2.849767e-01	k: 2761	n:10000
KS ci ratio: 5.584290e-02	ci left: 3.207846e-01	ci right 3.393145e-01	k: 3300	n:10000
BAHCC1   10000 perm   2 sec   (4386 perm/sec)   p_kst 3.300000e-01   p_cons 2.761000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000015/BAHCC1.2_7770_10000_0.33_0.2761_1.png
                gene_name: BAHCC1
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.28 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 27 percent done.
BAIAP3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.142700e-02	ci left: 3.579408e-01	ci right 3.769365e-01	k: 3674	n:10000
Cons ci ratio: 8.902215e-02	ci left: 1.551222e-01	ci right 1.696750e-01	k: 1623	n:10000
KS ci ratio: 2.269812e-02	ci left: 7.402790e-01	ci right 7.573759e-01	k: 7489	n:10000
BAIAP3   10000 perm   2 sec   (5738 perm/sec)   p_kst 7.489000e-01   p_cons 1.623000e-01   p_joint 3.674000e-01

Outputting figure to mutsig2_images.part000000000015/BAIAP3.2_3700_10000_0.7489_0.1623_0.3674.png
                gene_name: BAIAP3
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.38 

Current progress: 36 percent done.
BAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.702786e-01	ci left: 1.781300e-02	ci right 2.347108e-02	k: 205	n:10000
Cons ci ratio: 1.572648e-02	ci left: 8.544725e-01	ci right 8.681163e-01	k: 8614	n:10000
KS ci ratio: 4.208622e-01	ci left: 6.794980e-03	ci right 1.049980e-02	k: 85	n:10000
BAP1   10000 perm   2 sec   (6129 perm/sec)   p_kst 8.500000e-03   p_cons 8.614000e-01   p_joint 2.050000e-02

Joint ci ratio: 1.908840e-01	ci left: 1.867638e-02	ci right 2.266469e-02	k: 412	n:20000
Cons ci ratio: 1.102150e-02	ci left: 8.586641e-01	ci right 8.682300e-01	k: 17270	n:20000
KS ci ratio: 2.876468e-01	ci left: 7.877125e-03	ci right 1.056846e-02	k: 183	n:20000
BAP1   20000 perm   4 sec   (5468 perm/sec)   p_kst 9.150000e-03   p_cons 8.635000e-01   p_joint 2.060000e-02

Joint ci ratio: 1.573553e-01	ci left: 1.867001e-02	ci right 2.189050e-02	k: 607	n:30000
Cons ci ratio: 8.909523e-03	ci left: 8.619244e-01	ci right 8.696712e-01	k: 25975	n:30000
KS ci ratio: 2.388263e-01	ci left: 7.836974e-03	ci right 9.993079e-03	k: 266	n:30000
BAP1   30000 perm   6 sec   (5213 perm/sec)   p_kst 8.866667e-03   p_cons 8.658333e-01   p_joint 2.023333e-02

Joint ci ratio: 1.334185e-01	ci left: 1.971394e-02	ci right 2.255618e-02	k: 844	n:40000
Cons ci ratio: 7.704419e-03	ci left: 8.627994e-01	ci right 8.694973e-01	k: 34647	n:40000
KS ci ratio: 1.990767e-01	ci left: 8.643905e-03	ci right 1.057829e-02	k: 383	n:40000
BAP1   40000 perm   8 sec   (5048 perm/sec)   p_kst 9.575000e-03   p_cons 8.661750e-01   p_joint 2.110000e-02

Joint ci ratio: 1.180413e-01	ci left: 2.030476e-02	ci right 2.287121e-02	k: 1078	n:50000
Cons ci ratio: 6.867636e-03	ci left: 8.639519e-01	ci right 8.699255e-01	k: 43348	n:50000
KS ci ratio: 1.744273e-01	ci left: 9.127276e-03	ci right 1.089031e-02	k: 499	n:50000
BAP1   50000 perm   10 sec   (4925 perm/sec)   p_kst 9.980000e-03   p_cons 8.669600e-01   p_joint 2.156000e-02

Joint ci ratio: 1.063301e-01	ci left: 2.097100e-02	ci right 2.334220e-02	k: 1328	n:60000
Cons ci ratio: 6.275841e-03	ci left: 8.639710e-01	ci right 8.694268e-01	k: 52003	n:60000
KS ci ratio: 1.569985e-01	ci left: 9.475512e-03	ci right 1.110571e-02	k: 616	n:60000
BAP1   60000 perm   12 sec   (4817 perm/sec)   p_kst 1.026667e-02   p_cons 8.667167e-01   p_joint 2.213333e-02

Joint ci ratio: 9.842643e-02	ci left: 2.106549e-02	ci right 2.326008e-02	k: 1550	n:70000
Cons ci ratio: 5.816801e-03	ci left: 8.639149e-01	ci right 8.689690e-01	k: 60652	n:70000
KS ci ratio: 1.469947e-01	ci left: 9.317433e-03	ci right 1.080931e-02	k: 703	n:70000
BAP1   70000 perm   15 sec   (4715 perm/sec)   p_kst 1.004286e-02   p_cons 8.664571e-01   p_joint 2.214286e-02

Joint ci ratio: 9.208476e-02	ci left: 2.112906e-02	ci right 2.318079e-02	k: 1771	n:80000
Cons ci ratio: 5.454487e-03	ci left: 8.635066e-01	ci right 8.682418e-01	k: 69271	n:80000
KS ci ratio: 1.374641e-01	ci left: 9.370380e-03	ci right 1.076549e-02	k: 804	n:80000
BAP1   80000 perm   17 sec   (4618 perm/sec)   p_kst 1.005000e-02   p_cons 8.658875e-01   p_joint 2.213750e-02

Joint ci ratio: 8.612508e-02	ci left: 2.153009e-02	ci right 2.347864e-02	k: 2024	n:90000
Cons ci ratio: 5.132407e-03	ci left: 8.641039e-01	ci right 8.685613e-01	k: 77971	n:90000
KS ci ratio: 1.285051e-01	ci left: 9.575334e-03	ci right 1.090096e-02	k: 920	n:90000
BAP1   90000 perm   20 sec   (4459 perm/sec)   p_kst 1.022222e-02   p_cons 8.663444e-01   p_joint 2.248889e-02

Joint ci ratio: 8.194798e-02	ci left: 2.145250e-02	ci right 2.329535e-02	k: 2236	n:100000
Cons ci ratio: 4.870374e-03	ci left: 8.641549e-01	ci right 8.683838e-01	k: 86628	n:100000
KS ci ratio: 1.224762e-01	ci left: 9.518597e-03	ci right 1.077006e-02	k: 1013	n:100000
BAP1   100000 perm   23 sec   (4388 perm/sec)   p_kst 1.013000e-02   p_cons 8.662800e-01   p_joint 2.236000e-02

Joint ci ratio: 7.793536e-02	ci left: 2.160491e-02	ci right 2.336585e-02	k: 2472	n:110000
Cons ci ratio: 4.651326e-03	ci left: 8.638721e-01	ci right 8.679086e-01	k: 95249	n:110000
KS ci ratio: 1.163767e-01	ci left: 9.614616e-03	ci right 1.081142e-02	k: 1122	n:110000
BAP1   110000 perm   25 sec   (4316 perm/sec)   p_kst 1.020000e-02   p_cons 8.659000e-01   p_joint 2.247273e-02

Joint ci ratio: 7.465735e-02	ci left: 2.161921e-02	ci right 2.330397e-02	k: 2694	n:120000
Cons ci ratio: 4.452181e-03	ci left: 8.640177e-01	ci right 8.678813e-01	k: 103915	n:120000
KS ci ratio: 1.114264e-01	ci left: 9.639193e-03	ci right 1.078466e-02	k: 1224	n:120000
BAP1   120000 perm   28 sec   (4244 perm/sec)   p_kst 1.020000e-02   p_cons 8.659583e-01   p_joint 2.245000e-02

Joint ci ratio: 7.116429e-02	ci left: 2.199541e-02	ci right 2.362597e-02	k: 2964	n:130000
Cons ci ratio: 4.282130e-03	ci left: 8.638422e-01	ci right 8.675568e-01	k: 112542	n:130000
KS ci ratio: 1.060537e-01	ci left: 9.848134e-03	ci right 1.095848e-02	k: 1351	n:130000
BAP1   130000 perm   31 sec   (4174 perm/sec)   p_kst 1.039231e-02   p_cons 8.657077e-01   p_joint 2.280000e-02

Joint ci ratio: 6.824910e-02	ci left: 2.223514e-02	ci right 2.381327e-02	k: 3222	n:140000
Cons ci ratio: 4.127003e-03	ci left: 8.638740e-01	ci right 8.674537e-01	k: 121194	n:140000
KS ci ratio: 1.013898e-01	ci left: 1.002836e-02	ci right 1.110634e-02	k: 1478	n:140000
BAP1   140000 perm   34 sec   (4107 perm/sec)   p_kst 1.055714e-02   p_cons 8.656714e-01   p_joint 2.301429e-02

Joint ci ratio: 6.622220e-02	ci left: 2.207020e-02	ci right 2.358832e-02	k: 3423	n:150000
Cons ci ratio: 3.985657e-03	ci left: 8.640177e-01	ci right 8.674748e-01	k: 129863	n:150000
KS ci ratio: 9.828600e-02	ci left: 9.977308e-03	ci right 1.101508e-02	k: 1573	n:150000
BAP1   150000 perm   37 sec   (4042 perm/sec)   p_kst 1.048667e-02   p_cons 8.657533e-01   p_joint 2.282000e-02

Outputting figure to mutsig2_images.part000000000015/BAP1.2_2258_150000_0.010487_0.86575_0.02282.png
                gene_name: BAP1
               theta_stop: 0.098 
                    nperm: 150000 
                     p_ks: 0.010 
        ci_ks_bounds_left: 0.0100 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.023 
     ci_joint_bounds_left: 0.022 
    ci_joint_bounds_right: 0.024 

Current progress: 45 percent done.
BAT2L1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.915738e-03	ci left: 9.663613e-01	ci right 9.731614e-01	k: 9699	n:10000
Cons ci ratio: 4.841319e-02	ci left: 3.862964e-01	ci right 4.055643e-01	k: 3959	n:10000
KS ci ratio: 2.879412e-02	ci left: 6.400560e-01	ci right 6.588569e-01	k: 6495	n:10000
BAT2L1   10000 perm   2 sec   (4619 perm/sec)   p_kst 6.495000e-01   p_cons 3.959000e-01   p_joint 9.699000e-01

Outputting figure to mutsig2_images.part000000000015/BAT2L1.2_6814_10000_0.6495_0.3959_0.9699.png
                gene_name: BAT2L1
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.97 

Current progress: 55 percent done.
BAZ1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.025877e-02	ci left: 4.767588e-01	ci right 4.964490e-01	k: 4866	n:10000
Cons ci ratio: 9.427484e-02	ci left: 1.404072e-01	ci right 1.543988e-01	k: 1473	n:10000
KS ci ratio: 3.749121e-02	ci left: 5.123546e-01	ci right 5.320325e-01	k: 5222	n:10000
BAZ1A   10000 perm   2 sec   (5002 perm/sec)   p_kst 5.222000e-01   p_cons 1.473000e-01   p_joint 4.866000e-01

Outputting figure to mutsig2_images.part000000000015/BAZ1A.2_4775_10000_0.5222_0.1473_0.4866.png
                gene_name: BAZ1A
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 64 percent done.
BAZ2A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.424278e-02	ci left: 4.299405e-01	ci right 4.494947e-01	k: 4397	n:10000
Cons ci ratio: 2.164788e-02	ci left: 7.578789e-01	ci right 7.745658e-01	k: 7663	n:10000
KS ci ratio: 7.743137e-02	ci left: 1.960405e-01	ci right 2.119323e-01	k: 2039	n:10000
BAZ2A   10000 perm   2 sec   (4781 perm/sec)   p_kst 2.039000e-01   p_cons 7.663000e-01   p_joint 4.397000e-01

Outputting figure to mutsig2_images.part000000000015/BAZ2A.2_5834_10000_0.2039_0.7663_0.4397.png
                gene_name: BAZ2A
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 73 percent done.
BBS10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.745367e-02	ci left: 5.128549e-01	ci right 5.325319e-01	k: 5227	n:10000
Cons ci ratio: 1.918346e-02	ci left: 7.989230e-01	ci right 8.144979e-01	k: 8068	n:10000
KS ci ratio: 1.077377e-01	ci left: 1.105672e-01	ci right 1.232569e-01	k: 1168	n:10000
BBS10   10000 perm   2 sec   (6402 perm/sec)   p_kst 1.168000e-01   p_cons 8.068000e-01   p_joint 5.227000e-01

Joint ci ratio: 2.972938e-02	ci left: 4.580680e-01	ci right 4.719422e-01	k: 9300	n:20000
Cons ci ratio: 1.288370e-02	ci left: 8.169811e-01	ci right 8.276250e-01	k: 16447	n:20000
KS ci ratio: 7.498993e-02	ci left: 1.156744e-01	ci right 1.247364e-01	k: 2403	n:20000
BBS10   20000 perm   4 sec   (5698 perm/sec)   p_kst 1.201500e-01   p_cons 8.223500e-01   p_joint 4.650000e-01

Outputting figure to mutsig2_images.part000000000015/BBS10.2_2180_20000_0.12015_0.82235_0.465.png
                gene_name: BBS10
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.47 

Current progress: 82 percent done.
BBS12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.098618e-02	ci left: 6.057823e-01	ci right 6.249505e-01	k: 6154	n:10000
Cons ci ratio: 7.389568e-02	ci left: 2.114201e-01	ci right 2.277435e-01	k: 2195	n:10000
KS ci ratio: 3.563461e-03	ci left: 9.899424e-01	ci right 9.935624e-01	k: 9919	n:10000
BBS12   10000 perm   2 sec   (6048 perm/sec)   p_kst 9.919000e-01   p_cons 2.195000e-01   p_joint 6.154000e-01

Outputting figure to mutsig2_images.part000000000015/BBS12.2_2137_10000_0.9919_0.2195_0.6154.png
                gene_name: BBS12
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.62 

Current progress: 91 percent done.
BCAN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.556943e-02	ci left: 6.924235e-01	ci right 7.104591e-01	k: 7015	n:10000
KS ci ratio: 2.392992e-02	ci left: 7.196677e-01	ci right 7.371991e-01	k: 7285	n:10000
BCAN   10000 perm   2 sec   (5782 perm/sec)   p_kst 7.285000e-01   p_cons 7.015000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000015/BCAN.2_2862_10000_0.7285_0.7015_1.png
                gene_name: BCAN
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000015
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 15 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1424>
Subject: Job 4397793: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1424>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000016> was used as the working directory.
Started at Wed Oct 24 16:08:27 2012
Results reported at Wed Oct 24 16:11:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000016.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000016.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 16  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000016.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    226.26 sec.
    Max Memory :      1627 MB
    Max Swap   :      4090 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
16
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 16
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 16: processing genes 1347 - 1435
Calculating significance of each gene.
Using projection method.
1347	BCL2L15	1
1348	BCL2L2	1
1349	BCL3	1.699326e-02
1350	BCL6	1
1351	BCL6B	1
1352	BCL7A	1
1353	BCL7B	1
1354	BCL7C	1
1355	BCL9	1.430434e-01
1356	BCL9L	4.860838e-01
1357	BCLAF1	1
1358	BCMO1	2.225526e-01
1359	BCO2	1
1360	BCOR	4.392269e-01
1361	BCORL1	3.172352e-01
1362	BCR	3.425413e-01
1363	BCS1L	1
1364	BDH1	1
1365	BDH2	1
1366	BDKRB1	1
1367	BDKRB2	1
1368	BDNF	1
1369	BDP1	6.909462e-02
1370	BECN1	1
1371	BEGAIN	1.294214e-01
1372	BEND2	1.377699e-01
1373	BEND3	7.776521e-02
1374	BEND4	1.575777e-01
1375	BEND5	1
1376	BEND6	1
1377	BEND7	1
1378	BEST1	1
1379	BEST2	1
1380	BEST3	4.708366e-02
1381	BEST4	1
1382	BET1	1
1383	BET1L	1
1384	BEX1	1
1385	BEX2	1
1386	BEX4	1
1387	BEX5	1
1388	BFAR	6.284890e-02
1389	BFSP1	1
1390	BFSP2	1
1391	BGLAP	1
1392	BGN	5.153386e-02
1393	BHLHB9	2.437448e-01
1394	BHLHE23	1
1395	BHLHE40	2.036064e-01
1396	BHLHE41	1
1397	BHMT	1
1398	BHMT2	1
1399	BICC1	1.469458e-01
1400	BICD1	1
1401	BICD2	2.496171e-01
1402	BID	1
1403	BIK	7.647601e-02
1404	BIN1	6.133971e-02
1405	BIN2	1
1406	BIN3	1
1407	BIRC2	1
1408	BIRC3	1
1409	BIRC5	1
1410	BIRC6	6.651185e-01
1411	BIRC7	1
1412	BIRC8	3.326809e-02
1413	BIVM	1
1414	BLCAP	1
1415	BLID	1
1416	BLK	1
1417	BLM	5.447601e-01
1418	BLMH	1
1419	BLNK	1
1420	BLOC1S1	1
1421	BLOC1S2	1
1422	BLOC1S3	1
1423	BLVRA	1
1424	BLVRB	1
1425	BLZF1	1
1426	BMF	1
1427	BMI1	1.721639e-01
1428	BMP1	1
1429	BMP10	1
1430	BMP15	1.389183e-01
1431	BMP2	1
1432	BMP2K	1
1433	BMP3	1
1434	BMP4	1
1435	BMP5	1
Done

Running MutSig 2:
Scatter job 16: processing genes 1347 - 1435
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BDP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.385608e-02	ci left: 5.629343e-01	ci right 5.824233e-01	k: 5727	n:10000
Cons ci ratio: 2.941013e-02	ci left: 6.303014e-01	ci right 6.492171e-01	k: 6398	n:10000
KS ci ratio: 5.047820e-02	ci left: 3.665931e-01	ci right 3.856792e-01	k: 3761	n:10000
BDP1   10000 perm   3 sec   (3372 perm/sec)   p_kst 3.761000e-01   p_cons 6.398000e-01   p_joint 5.727000e-01

Outputting figure to mutsig2_images.part000000000016/BDP1.4_8031_10000_0.3761_0.6398_0.5727.png
                gene_name: BDP1
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 20 percent done.
BEST3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.244799e-02	ci left: 4.503941e-01	ci right 4.700291e-01	k: 4602	n:10000
Cons ci ratio: 2.777680e-02	ci left: 6.563567e-01	ci right 6.749467e-01	k: 6657	n:10000
KS ci ratio: 5.748628e-02	ci left: 3.081821e-01	ci right 3.265244e-01	k: 3173	n:10000
BEST3   10000 perm   2 sec   (6263 perm/sec)   p_kst 3.173000e-01   p_cons 6.657000e-01   p_joint 4.602000e-01

Outputting figure to mutsig2_images.part000000000016/BEST3.3_2043_10000_0.3173_0.6657_0.4602.png
                gene_name: BEST3
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.67 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 40 percent done.
BCL9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.089155e-02	ci left: 9.231709e-01	ci right 9.333780e-01	k: 9284	n:10000
Cons ci ratio: 1.282976e-02	ci left: 8.973393e-01	ci right 9.090246e-01	k: 9033	n:10000
KS ci ratio: 4.066371e-02	ci left: 4.717634e-01	ci right 4.914473e-01	k: 4816	n:10000
BCL9   10000 perm   2 sec   (5098 perm/sec)   p_kst 4.816000e-01   p_cons 9.033000e-01   p_joint 9.284000e-01

Outputting figure to mutsig2_images.part000000000016/BCL9.2_4309_10000_0.4816_0.9033_0.9284.png
                gene_name: BCL9
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 60 percent done.
BEND3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.457464e-03	ci left: 9.513780e-01	ci right 9.595540e-01	k: 9556	n:10000
Cons ci ratio: 2.586887e-02	ci left: 6.874832e-01	ci right 7.056022e-01	k: 6966	n:10000
KS ci ratio: 1.492718e-02	ci left: 8.667238e-01	ci right 8.798579e-01	k: 8734	n:10000
BEND3   10000 perm   2 sec   (6007 perm/sec)   p_kst 8.734000e-01   p_cons 6.966000e-01   p_joint 9.556000e-01

Outputting figure to mutsig2_images.part000000000016/BEND3.2_2499_10000_0.8734_0.6966_0.9556.png
                gene_name: BEND3
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.87 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 80 percent done.
BICD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.160355e-02	ci left: 4.603775e-01	ci right 4.800399e-01	k: 4702	n:10000
KS ci ratio: 3.740117e-02	ci left: 5.135553e-01	ci right 5.332311e-01	k: 5234	n:10000
BICD2   10000 perm   2 sec   (5677 perm/sec)   p_kst 5.234000e-01   p_cons 4.702000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000016/BICD2.2_2606_10000_0.5234_0.4702_1.png
                gene_name: BICD2
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000016
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 16 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4397795: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000017> was used as the working directory.
Started at Wed Oct 24 16:08:27 2012
Results reported at Wed Oct 24 16:11:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000017.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000017.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 17  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000017.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    197.07 sec.
    Max Memory :      1701 MB
    Max Swap   :      4044 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
17
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 17
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 17: processing genes 1436 - 1525
Calculating significance of each gene.
Using projection method.
1436	BMP6	1
1437	BMP7	1
1438	BMP8A	1
1439	BMP8B	1
1440	BMPER	1
1441	BMPR1A	1
1442	BMPR1B	1.569230e-01
1443	BMPR2	2.956160e-01
1444	BMS1	1
1445	BMX	1
1446	BNC1	1
1447	BNC2	1
1448	BNIP1	1
1449	BNIP2	1
1450	BNIP3	1
1451	BNIP3L	1
1452	BNIPL	1
1453	BOC	1
1454	BOD1	1
1455	BOD1L	1.384793e-01
1456	BOK	1
1457	BOLA1	1
1458	BOLA3	1
1459	BOLL	1
1460	BPGM	1
1461	BPHL	1
1462	BPI	1
1463	BPIL1	1
1464	BPIL2	1
1465	BPIL3	1
1466	BPNT1	1
1467	BPTF	1.812676e-01
1468	BRAF	1.156498e-01
1469	BRAP	1.899597e-01
1470	BRCA1	2.757097e-01
1471	BRCA2	5.088603e-01
1472	BRCC3	1.363842e-01
1473	BRD1	3.343944e-02
1474	BRD2	2.993168e-01
1475	BRD3	1
1476	BRD4	2.405746e-02
1477	BRD7	1
1478	BRD8	1
1479	BRD9	1
1480	BRDT	1
1481	BRE	1.440312e-01
1482	BRF1	1
1483	BRF2	1
1484	BRI3	1
1485	BRI3BP	1
1486	BRIP1	1
1487	BRIX1	1
1488	BRMS1	1.006508e-01
1489	BRMS1L	1.134448e-01
1490	BRP44	1
1491	BRP44L	1
1492	BRPF1	5.247852e-02
1493	BRPF3	3.532248e-01
1494	BRS3	1.060556e-02
1495	BRSK1	1
1496	BRSK2	1
1497	BRWD1	1.793351e-02
1498	BRWD3	1.753965e-01
1499	BSCL2	1
1500	BSDC1	1
1501	BSG	3.762868e-02
1502	BSN	5.029509e-01
1503	BSND	1
1504	BSPRY	1.326990e-01
1505	BST1	1
1506	BST2	1
1507	BSX	1
1508	BTAF1	6.077307e-01
1509	BTBD1	1
1510	BTBD10	3.212375e-02
1511	BTBD11	2.389127e-01
1512	BTBD12	1
1513	BTBD16	1
1514	BTBD17	1
1515	BTBD2	1
1516	BTBD3	1
1517	BTBD6	1
1518	BTBD7	3.367694e-01
1519	BTBD8	1
1520	BTBD9	1
1521	BTC	6.015965e-02
1522	BTD	1
1523	BTF3	1
1524	BTF3L4	1
1525	BTG1	1
Done

Running MutSig 2:
Scatter job 17: processing genes 1436 - 1525
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BRWD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 9.839580e-03	ci left: 9.359947e-01	ci right 9.453466e-01	k: 9408	n:10000
KS ci ratio: 1.359396e-02	ci left: 8.864693e-01	ci right 8.987010e-01	k: 8927	n:10000
BRWD1   10000 perm   2 sec   (4156 perm/sec)   p_kst 8.927000e-01   p_cons 9.408000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000017/BRWD1.5_7384_10000_0.8927_0.9408_1.png
                gene_name: BRWD1
               theta_stop: 0.014 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 9 percent done.
BOD1L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.110410e-02	ci left: 6.039745e-01	ci right 6.231593e-01	k: 6136	n:10000
Cons ci ratio: 6.784775e-03	ci left: 9.675208e-01	ci right 9.742012e-01	k: 9710	n:10000
KS ci ratio: 3.717692e-02	ci left: 5.165574e-01	ci right 5.362273e-01	k: 5264	n:10000
BOD1L   10000 perm   3 sec   (3881 perm/sec)   p_kst 5.264000e-01   p_cons 9.710000e-01   p_joint 6.136000e-01

Outputting figure to mutsig2_images.part000000000017/BOD1L.4_9260_10000_0.5264_0.971_0.6136.png
                gene_name: BOD1L
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 18 percent done.
BRPF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.208438e-02	ci left: 1.780224e-01	ci right 1.933612e-01	k: 1856	n:10000
Cons ci ratio: 3.536014e-02	ci left: 5.414881e-01	ci right 5.610820e-01	k: 5513	n:10000
KS ci ratio: 1.264263e-01	ci left: 8.212963e-02	ci right 9.331191e-02	k: 876	n:10000
BRPF1   10000 perm   2 sec   (5175 perm/sec)   p_kst 8.760000e-02   p_cons 5.513000e-01   p_joint 1.856000e-01

Joint ci ratio: 8.231076e-02	ci left: 9.764233e-02	ci right 1.060738e-01	k: 2036	n:20000
Cons ci ratio: 2.470824e-02	ci left: 5.502831e-01	ci right 5.641003e-01	k: 11144	n:20000
KS ci ratio: 8.832658e-02	ci left: 8.567661e-02	ci right 9.364316e-02	k: 1792	n:20000
BRPF1   20000 perm   4 sec   (4679 perm/sec)   p_kst 8.960000e-02   p_cons 5.572000e-01   p_joint 1.018000e-01

Outputting figure to mutsig2_images.part000000000017/BRPF1.3_3715_20000_0.0896_0.5572_0.1018.png
                gene_name: BRPF1
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.090 
        ci_ks_bounds_left: 0.086 
       ci_ks_bounds_right: 0.094 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.098 
    ci_joint_bounds_right: 0.11 

Current progress: 27 percent done.
BPTF
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.540566e-03	ci left: 9.605805e-01	ci right 9.679458e-01	k: 9644	n:10000
Cons ci ratio: 2.364582e-02	ci left: 7.244142e-01	ci right 7.418498e-01	k: 7332	n:10000
KS ci ratio: 6.458655e-02	ci left: 2.604260e-01	ci right 2.779087e-01	k: 2691	n:10000
BPTF   10000 perm   2 sec   (4026 perm/sec)   p_kst 2.691000e-01   p_cons 7.332000e-01   p_joint 9.644000e-01

Outputting figure to mutsig2_images.part000000000017/BPTF.2_9261_10000_0.2691_0.7332_0.9644.png
                gene_name: BPTF
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 36 percent done.
BRCA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.573434e-02	ci left: 6.897011e-01	ci right 7.077830e-01	k: 6988	n:10000
Cons ci ratio: 5.278129e-02	ci left: 3.460122e-01	ci right 3.648721e-01	k: 3554	n:10000
KS ci ratio: 8.000136e-02	ci left: 1.857974e-01	ci right 2.013815e-01	k: 1935	n:10000
BRCA1   10000 perm   2 sec   (4797 perm/sec)   p_kst 1.935000e-01   p_cons 3.554000e-01   p_joint 6.988000e-01

Outputting figure to mutsig2_images.part000000000017/BRCA1.2_5750_10000_0.1935_0.3554_0.6988.png
                gene_name: BRCA1
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.69 
    ci_joint_bounds_right: 0.71 

Current progress: 45 percent done.
BRD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.384917e-02	ci left: 5.630346e-01	ci right 5.825230e-01	k: 5728	n:10000
Cons ci ratio: 5.740679e-02	ci left: 3.087773e-01	ci right 3.271288e-01	k: 3179	n:10000
KS ci ratio: 3.533871e-02	ci left: 5.417887e-01	ci right 5.613813e-01	k: 5516	n:10000
BRD1   10000 perm   2 sec   (5704 perm/sec)   p_kst 5.516000e-01   p_cons 3.179000e-01   p_joint 5.728000e-01

Outputting figure to mutsig2_images.part000000000017/BRD1.2_3225_10000_0.5516_0.3179_0.5728.png
                gene_name: BRD1
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 55 percent done.
BRD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 9.009714e-03	ci left: 9.454415e-01	ci right 9.540941e-01	k: 9499	n:10000
KS ci ratio: 2.574045e-02	ci left: 6.896003e-01	ci right 7.076838e-01	k: 6987	n:10000
BRD4   10000 perm   2 sec   (5037 perm/sec)   p_kst 6.987000e-01   p_cons 9.499000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000017/BRD4.2_4180_10000_0.6987_0.9499_1.png
                gene_name: BRD4
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.95 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 64 percent done.
BRS3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.878868e-02	ci left: 4.953504e-01	ci right 5.150466e-01	k: 5052	n:10000
Cons ci ratio: 3.668779e-02	ci left: 5.231631e-01	ci right 5.428176e-01	k: 5330	n:10000
KS ci ratio: 1.204951e-01	ci left: 8.990526e-02	ci right 1.015315e-01	k: 956	n:10000
BRS3   10000 perm   1 sec   (6857 perm/sec)   p_kst 9.560000e-02   p_cons 5.330000e-01   p_joint 5.052000e-01

Joint ci ratio: 1.302675e-02	ci left: 8.136939e-01	ci right 8.244132e-01	k: 16382	n:20000
Cons ci ratio: 2.556337e-02	ci left: 5.334126e-01	ci right 5.472756e-01	k: 10807	n:20000
KS ci ratio: 8.728774e-02	ci left: 8.758778e-02	ci right 9.563141e-02	k: 1831	n:20000
BRS3   20000 perm   3 sec   (5852 perm/sec)   p_kst 9.155000e-02   p_cons 5.403500e-01   p_joint 8.191000e-01

Outputting figure to mutsig2_images.part000000000017/BRS3.2_1212_20000_0.09155_0.54035_0.8191.png
                gene_name: BRS3
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.092 
        ci_ks_bounds_left: 0.088 
       ci_ks_bounds_right: 0.096 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.82 

Current progress: 73 percent done.
BRWD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.841039e-02	ci left: 5.002504e-01	ci right 5.199437e-01	k: 5101	n:10000
Cons ci ratio: 7.550600e-02	ci left: 2.042211e-01	ci right 2.203469e-01	k: 2122	n:10000
KS ci ratio: 3.023188e-02	ci left: 6.174357e-01	ci right 6.364903e-01	k: 6270	n:10000
BRWD3   10000 perm   2 sec   (4856 perm/sec)   p_kst 6.270000e-01   p_cons 2.122000e-01   p_joint 5.101000e-01

Outputting figure to mutsig2_images.part000000000017/BRWD3.2_5573_10000_0.627_0.2122_0.5101.png
                gene_name: BRWD3
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.51 
     ci_joint_bounds_left: 0.50 
    ci_joint_bounds_right: 0.52 

Current progress: 82 percent done.
BSN
Processing conservation and coverage...
84% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.928435e-02	ci left: 3.778359e-01	ci right 3.970298e-01	k: 3874	n:10000
Cons ci ratio: 5.163782e-02	ci left: 3.560517e-01	ci right 3.750267e-01	k: 3655	n:10000
KS ci ratio: 2.089368e-01	ci left: 3.043932e-02	ci right 3.763545e-02	k: 339	n:10000
BSN   10000 perm   3 sec   (3615 perm/sec)   p_kst 3.390000e-02   p_cons 3.655000e-01   p_joint 3.874000e-01

Joint ci ratio: 7.947324e-02	ci left: 1.041236e-01	ci right 1.127906e-01	k: 2168	n:20000
Cons ci ratio: 3.645828e-02	ci left: 3.595678e-01	ci right 3.729711e-01	k: 7325	n:20000
KS ci ratio: 1.517155e-01	ci left: 2.984481e-02	ci right 3.479239e-02	k: 645	n:20000
BSN   20000 perm   6 sec   (3296 perm/sec)   p_kst 3.225000e-02   p_cons 3.662500e-01   p_joint 1.084000e-01

Joint ci ratio: 6.123904e-02	ci left: 1.164746e-01	ci right 1.238658e-01	k: 3604	n:30000
Cons ci ratio: 2.977871e-02	ci left: 3.606452e-01	ci right 3.715807e-01	k: 10983	n:30000
KS ci ratio: 1.254227e-01	ci left: 2.955233e-02	ci right 3.353907e-02	k: 945	n:30000
BSN   30000 perm   10 sec   (3130 perm/sec)   p_kst 3.150000e-02   p_cons 3.661000e-01   p_joint 1.201333e-01

Joint ci ratio: 1.654865e-02	ci left: 5.789510e-01	ci right 5.886369e-01	k: 23352	n:40000
Cons ci ratio: 2.581181e-02	ci left: 3.609775e-01	ci right 3.704420e-01	k: 14628	n:40000
KS ci ratio: 1.075386e-01	ci left: 3.041851e-02	ci right 3.389984e-02	k: 1285	n:40000
BSN   40000 perm   13 sec   (3076 perm/sec)   p_kst 3.212500e-02   p_cons 3.657000e-01   p_joint 5.838000e-01

Joint ci ratio: 9.757979e-03	ci left: 7.597099e-01	ci right 7.671795e-01	k: 38173	n:50000
Cons ci ratio: 2.307409e-02	ci left: 3.617357e-01	ci right 3.701999e-01	k: 18298	n:50000
KS ci ratio: 9.673107e-02	ci left: 3.025969e-02	ci right 3.335498e-02	k: 1589	n:50000
BSN   50000 perm   17 sec   (3027 perm/sec)   p_kst 3.178000e-02   p_cons 3.659600e-01   p_joint 7.634600e-01

Outputting figure to mutsig2_images.part000000000017/BSN.2_11821_50000_0.03178_0.36596_0.76346.png
                gene_name: BSN
               theta_stop: 0.097 
                    nperm: 50000 
                     p_ks: 0.032 
        ci_ks_bounds_left: 0.030 
       ci_ks_bounds_right: 0.033 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.76 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.77 

Current progress: 91 percent done.
BTBD10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.117314e-02	ci left: 1.813680e-01	ci right 1.968136e-01	k: 1890	n:10000
KS ci ratio: 2.480849e-02	ci left: 7.050317e-01	ci right 7.228435e-01	k: 7140	n:10000
BTBD10   10000 perm   2 sec   (6587 perm/sec)   p_kst 7.140000e-01   p_cons 1.890000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000017/BTBD10.2_1460_10000_0.714_0.189_1.png
                gene_name: BTBD10
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000017
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 17 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 4397799: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000018> was used as the working directory.
Started at Wed Oct 24 16:08:27 2012
Results reported at Wed Oct 24 16:10:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000018.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000018.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 18  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000018.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    180.68 sec.
    Max Memory :      1224 MB
    Max Swap   :      4069 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
18
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 18
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 18: processing genes 1526 - 1615
Calculating significance of each gene.
Using projection method.
1526	BTG2	1
1527	BTG3	1
1528	BTG4	1
1529	BTK	1.324349e-01
1530	BTLA	1
1531	BTN1A1	1
1532	BTN2A1	1.476846e-01
1533	BTN2A2	5.551340e-02
1534	BTN3A1	1
1535	BTN3A2	1
1536	BTN3A3	1
1537	BTNL2	5.863170e-02
1538	BTNL3	7.039799e-02
1539	BTNL8	1
1540	BTNL9	1
1541	BTRC	1
1542	BUB1	1
1543	BUB1B	1
1544	BUB3	1
1545	BUD13	1
1546	BUD31	1
1547	BVES	1
1548	BYSL	1
1549	BZRAP1	1.915641e-01
1550	BZW1	1
1551	BZW2	2.056039e-01
1552	C10orf10	1
1553	C10orf107	1
1554	C10orf11	1
1555	C10orf111	1
1556	C10orf113	1
1557	C10orf114	1
1558	C10orf116	1
1559	C10orf118	1
1560	C10orf119	1
1561	C10orf12	1
1562	C10orf120	3.820962e-02
1563	C10orf125	1
1564	C10orf128	1
1565	C10orf129	1
1566	C10orf137	1
1567	C10orf140	1
1568	C10orf18	1
1569	C10orf2	1
1570	C10orf25	1
1571	C10orf26	1
1572	C10orf27	3.761990e-02
1573	C10orf28	1
1574	C10orf32	1
1575	C10orf35	1
1576	C10orf46	1
1577	C10orf47	1
1578	C10orf53	1
1579	C10orf54	1
1580	C10orf57	1.808153e-02
1581	C10orf58	1
1582	C10orf62	1
1583	C10orf67	1
1584	C10orf68	2.860769e-01
1585	C10orf71	8.139432e-02
1586	C10orf72	1
1587	C10orf76	1
1588	C10orf78	1
1589	C10orf79	2.254522e-01
1590	C10orf81	1
1591	C10orf82	1
1592	C10orf84	1
1593	C10orf88	1
1594	C10orf90	1.776168e-01
1595	C10orf91	1
1596	C10orf93	1
1597	C10orf95	1
1598	C10orf96	1
1599	C10orf99	1
1600	C11orf1	1
1601	C11orf10	1
1602	C11orf16	1
1603	C11orf17	1
1604	C11orf2	2.453413e-01
1605	C11orf24	1
1606	C11orf30	1
1607	C11orf31	1
1608	C11orf35	1
1609	C11orf40	1
1610	C11orf41	1
1611	C11orf42	1
1612	C11orf45	1
1613	C11orf46	8.952455e-02
1614	C11orf48	1
1615	C11orf49	1
Done

Running MutSig 2:
Scatter job 18: processing genes 1526 - 1615
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BZRAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.717362e-02	ci left: 8.316480e-01	ci right 8.461540e-01	k: 8390	n:10000
KS ci ratio: 1.001478e-02	ci left: 9.339228e-01	ci right 9.434196e-01	k: 9388	n:10000
BZRAP1   10000 perm   2 sec   (4154 perm/sec)   p_kst 9.388000e-01   p_cons 8.390000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000018/BZRAP1.2_5698_10000_0.9388_0.839_1.png
                gene_name: BZRAP1
               theta_stop: 0.017 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.85 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000018
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 18 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1431>
Subject: Job 4397802: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1431>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000019> was used as the working directory.
Started at Wed Oct 24 16:08:27 2012
Results reported at Wed Oct 24 16:10:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000019.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000019.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 19  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000019.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    180.35 sec.
    Max Memory :      1272 MB
    Max Swap   :      4006 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
19
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 19
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 19: processing genes 1616 - 1704
Calculating significance of each gene.
Using projection method.
1616	C11orf51	1
1617	C11orf52	9.713075e-03
1618	C11orf53	1
1619	C11orf54	1
1620	C11orf57	2.086444e-02
1621	C11orf58	1
1622	C11orf59	6.101550e-02
1623	C11orf61	1
1624	C11orf63	1
1625	C11orf65	6.486097e-02
1626	C11orf66	1
1627	C11orf67	1
1628	C11orf68	1
1629	C11orf70	1
1630	C11orf71	1
1631	C11orf73	1
1632	C11orf74	1
1633	C11orf75	1
1634	C11orf80	1.556153e-01
1635	C11orf82	1
1636	C11orf83	1
1637	C11orf84	1
1638	C11orf85	1
1639	C11orf87	1
1640	C11orf88	1
1641	C11orf9	1
1642	C11orf92	1
1643	C11orf94	1
1644	C12orf10	1.105982e-01
1645	C12orf11	1
1646	C12orf12	1
1647	C12orf23	1
1648	C12orf24	1
1649	C12orf26	1
1650	C12orf29	1
1651	C12orf34	1
1652	C12orf35	5.122674e-01
1653	C12orf36	1
1654	C12orf39	1
1655	C12orf4	1
1656	C12orf40	1
1657	C12orf41	1
1658	C12orf42	1
1659	C12orf43	1.198982e-01
1660	C12orf44	1
1661	C12orf45	1
1662	C12orf48	1
1663	C12orf49	1
1664	C12orf5	1
1665	C12orf50	1
1666	C12orf51	1
1667	C12orf52	1
1668	C12orf53	1
1669	C12orf54	1
1670	C12orf56	1
1671	C12orf57	1
1672	C12orf59	1
1673	C12orf60	1
1674	C12orf61	2.334473e-02
1675	C12orf62	1
1676	C12orf63	9.111313e-02
1677	C12orf64	1
1678	C12orf65	1
1679	C12orf66	1
1680	C12orf68	1
1681	C12orf69	1
1682	C12orf71	1
1683	C12orf72	1
1684	C12orf74	1
1685	C12orf76	1
1686	C12orf77	1
1687	C13orf1	1
1688	C13orf15	1
1689	C13orf16	1
1690	C13orf18	1.791806e-01
1691	C13orf23	1
1692	C13orf26	1
1693	C13orf27	1
1694	C13orf28	1
1695	C13orf30	1
1696	C13orf31	1.561912e-01
1697	C13orf33	1
1698	C13orf34	2.724625e-01
1699	C13orf35	1
1700	C13orf36	3.466179e-02
1701	C13orf37	1
1702	C13orf39	1
1703	C14orf1	1
1704	C14orf101	1
Done

Running MutSig 2:
Scatter job 19: processing genes 1616 - 1704
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C12orf63
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.112967e-02	ci left: 3.606257e-01	ci right 3.796501e-01	k: 3701	n:10000
KS ci ratio: 2.593619e-02	ci left: 6.863743e-01	ci right 7.045117e-01	k: 6955	n:10000
C12orf63   10000 perm   2 sec   (4812 perm/sec)   p_kst 6.955000e-01   p_cons 3.701000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000019/C12orf63.2_3698_10000_0.6955_0.3701_1.png
                gene_name: C12orf63
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000019
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 19 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4397805: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000020> was used as the working directory.
Started at Wed Oct 24 16:08:46 2012
Results reported at Wed Oct 24 16:10:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000020.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000020.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 20  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000020.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    126.00 sec.
    Max Memory :      1205 MB
    Max Swap   :      3996 MB

    Max Processes  :         7
    Max Threads    :        60

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
20
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 20
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 20: processing genes 1705 - 1794
Calculating significance of each gene.
Using projection method.
1705	C14orf102	1
1706	C14orf104	5.831434e-02
1707	C14orf105	1
1708	C14orf106	2.525675e-01
1709	C14orf109	1
1710	C14orf115	1
1711	C14orf118	1
1712	C14orf119	1
1713	C14orf126	1
1714	C14orf129	1
1715	C14orf135	1
1716	C14orf138	1
1717	C14orf142	1
1718	C14orf143	1
1719	C14orf145	5.934715e-02
1720	C14orf147	1
1721	C14orf148	1
1722	C14orf149	1
1723	C14orf153	1
1724	C14orf156	1
1725	C14orf159	3.038483e-01
1726	C14orf166	3.546650e-02
1727	C14orf166B	1
1728	C14orf169	1
1729	C14orf174	1
1730	C14orf177	1
1731	C14orf178	1
1732	C14orf179	1
1733	C14orf181	1
1734	C14orf182	1
1735	C14orf183	1
1736	C14orf2	1
1737	C14orf21	1
1738	C14orf28	1
1739	C14orf37	1
1740	C14orf39	1.456843e-02
1741	C14orf4	1
1742	C14orf43	1
1743	C14orf45	1
1744	C14orf49	1
1745	C14orf50	1
1746	C14orf68	1
1747	C14orf73	9.583814e-02
1748	C14orf79	1
1749	C14orf93	1
1750	C15orf17	1
1751	C15orf2	1.591702e-01
1752	C15orf23	1
1753	C15orf24	1
1754	C15orf26	1
1755	C15orf27	1
1756	C15orf29	1
1757	C15orf32	1
1758	C15orf33	1
1759	C15orf38	1
1760	C15orf39	1
1761	C15orf40	1
1762	C15orf41	7.218249e-02
1763	C15orf42	3.418423e-01
1764	C15orf43	1
1765	C15orf44	1
1766	C15orf48	1
1767	C15orf52	1
1768	C15orf53	1
1769	C15orf54	1
1770	C15orf55	1
1771	C15orf57	1
1772	C15orf58	1
1773	C15orf59	1
1774	C15orf60	1
1775	C15orf63	1
1776	C16orf11	1
1777	C16orf13	1
1778	C16orf3	1
1779	C16orf42	1
1780	C16orf45	1
1781	C16orf46	1
1782	C16orf48	1
1783	C16orf5	1
1784	C16orf53	1
1785	C16orf54	1
1786	C16orf55	1
1787	C16orf57	1
1788	C16orf58	1
1789	C16orf59	1
1790	C16orf61	1
1791	C16orf62	1
1792	C16orf63	1
1793	C16orf68	1
1794	C16orf7	1
Done

Running MutSig 2:
Scatter job 20: processing genes 1705 - 1794
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C14orf145
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.238060e-02	ci left: 3.494907e-01	ci right 3.683915e-01	k: 3589	n:10000
Cons ci ratio: 5.851007e-02	ci left: 3.006442e-01	ci right 3.188667e-01	k: 3097	n:10000
KS ci ratio: 2.391178e-02	ci left: 7.199706e-01	ci right 7.374960e-01	k: 7288	n:10000
C14orf145   10000 perm   2 sec   (4786 perm/sec)   p_kst 7.288000e-01   p_cons 3.097000e-01   p_joint 3.589000e-01

Outputting figure to mutsig2_images.part000000000020/C14orf145.2_3377_10000_0.7288_0.3097_0.3589.png
                gene_name: C14orf145
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 50 percent done.
C14orf39
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.432516e-02	ci left: 3.329974e-01	ci right 3.516945e-01	k: 3423	n:10000
Cons ci ratio: 1.053537e-01	ci left: 1.151575e-01	ci right 1.280638e-01	k: 1215	n:10000
KS ci ratio: 3.920980e-02	ci left: 4.899514e-01	ci right 5.096487e-01	k: 4998	n:10000
C14orf39   10000 perm   2 sec   (6185 perm/sec)   p_kst 4.998000e-01   p_cons 1.215000e-01   p_joint 3.423000e-01

Joint ci ratio: 6.353391e-02	ci left: 1.547958e-01	ci right 1.650033e-01	k: 3197	n:20000
Cons ci ratio: 6.937729e-02	ci left: 1.328538e-01	ci right 1.424518e-01	k: 2752	n:20000
KS ci ratio: 2.778032e-02	ci left: 4.918961e-01	ci right 5.058042e-01	k: 9977	n:20000
C14orf39   20000 perm   4 sec   (5534 perm/sec)   p_kst 4.988500e-01   p_cons 1.376000e-01   p_joint 1.598500e-01

Outputting figure to mutsig2_images.part000000000020/C14orf39.2_1832_20000_0.49885_0.1376_0.15985.png
                gene_name: C14orf39
               theta_stop: 0.069 
                    nperm: 20000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.16 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.17 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000020
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 20 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4397820: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000021> was used as the working directory.
Started at Wed Oct 24 16:08:46 2012
Results reported at Wed Oct 24 16:10:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000021.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000021.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 21  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000021.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     82.05 sec.
    Max Memory :      1186 MB
    Max Swap   :      3976 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
21
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 21
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 21: processing genes 1795 - 1884
Calculating significance of each gene.
Using projection method.
1795	C16orf70	1
1796	C16orf71	1
1797	C16orf72	1
1798	C16orf73	1
1799	C16orf75	1
1800	C16orf78	1
1801	C16orf79	1
1802	C16orf80	1
1803	C16orf82	1
1804	C16orf86	1
1805	C16orf87	1
1806	C16orf88	1
1807	C16orf89	1
1808	C16orf90	1
1809	C16orf91	1
1810	C16orf92	1
1811	C16orf93	1
1812	C17orf101	1
1813	C17orf102	1
1814	C17orf103	1
1815	C17orf104	1
1816	C17orf108	1
1817	C17orf28	1
1818	C17orf37	1
1819	C17orf39	1
1820	C17orf42	1
1821	C17orf46	1
1822	C17orf47	1
1823	C17orf48	1
1824	C17orf49	1
1825	C17orf53	5.540704e-02
1826	C17orf56	1
1827	C17orf57	1
1828	C17orf58	1
1829	C17orf59	1
1830	C17orf60	1
1831	C17orf61	1
1832	C17orf62	2.461871e-02
1833	C17orf63	1
1834	C17orf64	1
1835	C17orf65	1
1836	C17orf66	3.023212e-02
1837	C17orf67	1
1838	C17orf68	1
1839	C17orf70	1
1840	C17orf71	1.152573e-02
1841	C17orf74	1
1842	C17orf75	1
1843	C17orf76	1
1844	C17orf77	1
1845	C17orf78	1
1846	C17orf79	1
1847	C17orf80	1
1848	C17orf81	4.000161e-02
1849	C17orf82	1
1850	C17orf85	1
1851	C17orf87	1
1852	C17orf90	9.632701e-03
1853	C17orf95	1
1854	C17orf98	1
1855	C18orf1	1
1856	C18orf10	1
1857	C18orf19	1
1858	C18orf21	1.132843e-02
1859	C18orf22	1
1860	C18orf25	1
1861	C18orf26	1
1862	C18orf32	1
1863	C18orf34	1
1864	C18orf45	1
1865	C18orf54	1
1866	C18orf55	1
1867	C18orf62	1
1868	C18orf8	1
1869	C19orf10	1
1870	C19orf12	1
1871	C19orf18	2.389184e-02
1872	C19orf2	1
1873	C19orf21	1
1874	C19orf22	1
1875	C19orf26	1
1876	C19orf28	1.759059e-01
1877	C19orf29	1
1878	C19orf33	1
1879	C19orf35	1
1880	C19orf36	1
1881	C19orf39	1.170579e-01
1882	C19orf40	1
1883	C19orf41	1
1884	C19orf42	1
Done

Running MutSig 2:
Scatter job 21: processing genes 1795 - 1884
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C17orf71
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 9.243504e-03	ci left: 9.428427e-01	ci right 9.516945e-01	k: 9474	n:10000
KS ci ratio: 6.688109e-03	ci left: 9.683648e-01	ci right 9.749566e-01	k: 9718	n:10000
C17orf71   10000 perm   2 sec   (5477 perm/sec)   p_kst 9.718000e-01   p_cons 9.474000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000021/C17orf71.3_2992_10000_0.9718_0.9474_1.png
                gene_name: C17orf71
               theta_stop: 0.0092 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
C17orf66
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.856436e-02	ci left: 4.982503e-01	ci right 5.179450e-01	k: 5081	n:10000
Cons ci ratio: 3.332647e-02	ci left: 5.706554e-01	ci right 5.900977e-01	k: 5804	n:10000
KS ci ratio: 9.603921e-02	ci left: 1.358995e-01	ci right 1.497093e-01	k: 1427	n:10000
C17orf66   10000 perm   2 sec   (6393 perm/sec)   p_kst 1.427000e-01   p_cons 5.804000e-01   p_joint 5.081000e-01

Outputting figure to mutsig2_images.part000000000021/C17orf66.2_1773_10000_0.1427_0.5804_0.5081.png
                gene_name: C17orf66
               theta_stop: 0.096 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.51 
     ci_joint_bounds_left: 0.50 
    ci_joint_bounds_right: 0.52 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000021
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 21 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1430>
Subject: Job 4397822: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1430>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000022> was used as the working directory.
Started at Wed Oct 24 16:08:46 2012
Results reported at Wed Oct 24 16:11:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000022.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000022.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 22  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000022.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    183.80 sec.
    Max Memory :      1022 MB
    Max Swap   :      3849 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
22
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 22
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 22: processing genes 1885 - 1974
Calculating significance of each gene.
Using projection method.
1885	C19orf43	1
1886	C19orf44	1
1887	C19orf45	1
1888	C19orf46	2.748789e-02
1889	C19orf47	1
1890	C19orf48	1
1891	C19orf50	1
1892	C19orf51	1.886672e-01
1893	C19orf52	1
1894	C19orf53	1
1895	C19orf54	1
1896	C19orf55	1
1897	C19orf56	1
1898	C19orf57	1
1899	C19orf59	1
1900	C19orf6	5.643412e-02
1901	C19orf61	1
1902	C19orf62	1
1903	C19orf63	1
1904	C19orf66	1
1905	C19orf70	1
1906	C19orf73	1
1907	C19orf75	1
1908	C1D	1
1909	C1GALT1	1
1910	C1GALT1C1	1
1911	C1QA	1
1912	C1QB	1
1913	C1QBP	1
1914	C1QC	1
1915	C1QL1	4.068471e-02
1916	C1QL2	1
1917	C1QL3	1
1918	C1QL4	1.276950e-02
1919	C1QTNF1	1
1920	C1QTNF2	1
1921	C1QTNF3	1
1922	C1QTNF4	1
1923	C1QTNF5	1
1924	C1QTNF6	1
1925	C1QTNF7	1
1926	C1QTNF8	1
1927	C1QTNF9	1
1928	C1QTNF9B	1
1929	C1R	1
1930	C1RL	1
1931	C1S	1.322403e-01
1932	C1orf100	1
1933	C1orf101	1
1934	C1orf103	1
1935	C1orf104	1
1936	C1orf105	1
1937	C1orf106	1
1938	C1orf107	2.518303e-01
1939	C1orf109	1
1940	C1orf110	1.280589e-01
1941	C1orf111	1
1942	C1orf112	7.171420e-02
1943	C1orf113	1
1944	C1orf114	1
1945	C1orf115	1
1946	C1orf116	1
1947	C1orf122	1.579091e-02
1948	C1orf123	1
1949	C1orf124	1
1950	C1orf125	1.455284e-01
1951	C1orf127	1
1952	C1orf128	2.672278e-02
1953	C1orf129	1
1954	C1orf130	1
1955	C1orf131	5.509163e-02
1956	C1orf135	1
1957	C1orf14	1.706991e-01
1958	C1orf141	1
1959	C1orf144	1
1960	C1orf146	1
1961	C1orf150	1
1962	C1orf151	1
1963	C1orf156	1
1964	C1orf158	1
1965	C1orf159	1
1966	C1orf161	1
1967	C1orf162	1
1968	C1orf163	1
1969	C1orf168	2.798901e-01
1970	C1orf172	1
1971	C1orf173	4.814510e-01
1972	C1orf174	1
1973	C1orf175	1
1974	C1orf177	1
Done

Running MutSig 2:
Scatter job 22: processing genes 1885 - 1974
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C1orf112
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.204321e-02	ci left: 5.897180e-01	ci right 6.090241e-01	k: 5994	n:10000
Cons ci ratio: 2.456575e-02	ci left: 7.090681e-01	ci right 7.268048e-01	k: 7180	n:10000
KS ci ratio: 3.941418e-02	ci left: 4.873523e-01	ci right 5.070493e-01	k: 4972	n:10000
C1orf112   10000 perm   2 sec   (5465 perm/sec)   p_kst 4.972000e-01   p_cons 7.180000e-01   p_joint 5.994000e-01

Outputting figure to mutsig2_images.part000000000022/C1orf112.2_2650_10000_0.4972_0.718_0.5994.png
                gene_name: C1orf112
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000022
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 22 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4397827: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000023> was used as the working directory.
Started at Wed Oct 24 16:08:46 2012
Results reported at Wed Oct 24 16:10:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000023.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000023.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 23  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000023.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    127.72 sec.
    Max Memory :      1225 MB
    Max Swap   :      3954 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
23
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 23
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 23: processing genes 1975 - 2063
Calculating significance of each gene.
Using projection method.
1975	C1orf182	1
1976	C1orf183	1
1977	C1orf186	1
1978	C1orf187	1
1979	C1orf189	1
1980	C1orf190	1.060520e-01
1981	C1orf192	1
1982	C1orf194	1
1983	C1orf198	1
1984	C1orf201	1
1985	C1orf21	1
1986	C1orf210	1
1987	C1orf213	1
1988	C1orf216	1
1989	C1orf226	2.479062e-02
1990	C1orf227	1
1991	C1orf25	1
1992	C1orf26	1.082277e-01
1993	C1orf27	1
1994	C1orf31	1
1995	C1orf35	1
1996	C1orf38	1
1997	C1orf43	1
1998	C1orf49	1
1999	C1orf50	1
2000/17942 2000	C1orf51	1
2001	C1orf52	1
2002	C1orf53	1
2003	C1orf54	1
2004	C1orf55	1
2005	C1orf56	1
2006	C1orf57	1
2007	C1orf58	1.947523e-01
2008	C1orf59	1
2009	C1orf61	1
2010	C1orf63	1
2011	C1orf64	1
2012	C1orf65	1
2013	C1orf66	1
2014	C1orf69	1
2015	C1orf74	1
2016	C1orf77	1
2017	C1orf83	1
2018	C1orf84	1
2019	C1orf85	1
2020	C1orf86	1
2021	C1orf87	1
2022	C1orf88	1
2023	C1orf89	1
2024	C1orf9	2.811753e-01
2025	C1orf91	1
2026	C1orf92	1
2027	C1orf93	1
2028	C1orf94	1
2029	C1orf95	1
2030	C1orf96	1
2031	C2	1
2032	C20orf103	1
2033	C20orf106	4.251545e-02
2034	C20orf107	5.226185e-02
2035	C20orf108	1
2036	C20orf11	4.332520e-02
2037	C20orf111	1
2038	C20orf112	1
2039	C20orf114	1
2040	C20orf117	1
2041	C20orf118	1.026822e-01
2042	C20orf12	1.132881e-01
2043	C20orf132	2.790870e-01
2044	C20orf134	1.444703e-03
2045	C20orf135	1
2046	C20orf141	1
2047	C20orf151	1
2048	C20orf152	2.875286e-01
2049	C20orf160	1
2050	C20orf165	1
2051	C20orf166	1
2052	C20orf177	1.463153e-01
2053	C20orf185	1
2054	C20orf186	1.459527e-01
2055	C20orf194	1
2056	C20orf195	1
2057	C20orf196	1
2058	C20orf197	1
2059	C20orf20	1
2060	C20orf24	1
2061	C20orf26	1
2062	C20orf27	1
2063	C20orf29	1
Done

Running MutSig 2:
Scatter job 23: processing genes 1975 - 2063
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C20orf134
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.043957e-02	ci left: 1.841239e-01	ci right 1.996560e-01	k: 1918	n:10000
Cons ci ratio: 1.148566e-02	ci left: 9.155397e-01	ci right 9.262136e-01	k: 9210	n:10000
KS ci ratio: 2.244374e-01	ci left: 2.627129e-02	ci right 3.300643e-02	k: 295	n:10000
C20orf134   10000 perm   2 sec   (6629 perm/sec)   p_kst 2.950000e-02   p_cons 9.210000e-01   p_joint 1.918000e-01

Joint ci ratio: 6.292600e-02	ci left: 1.573622e-01	ci right 1.676361e-01	k: 3249	n:20000
Cons ci ratio: 8.055540e-03	ci left: 9.183500e-01	ci right 9.258268e-01	k: 18443	n:20000
KS ci ratio: 1.602456e-01	ci left: 2.671804e-02	ci right 3.142021e-02	k: 580	n:20000
C20orf134   20000 perm   5 sec   (3846 perm/sec)   p_kst 2.900000e-02   p_cons 9.221500e-01   p_joint 1.624500e-01

Joint ci ratio: 5.881648e-02	ci left: 1.251605e-01	ci right 1.327782e-01	k: 3868	n:30000
Cons ci ratio: 6.519433e-03	ci left: 9.203326e-01	ci right 9.263851e-01	k: 27702	n:30000
KS ci ratio: 1.314246e-01	ci left: 2.690430e-02	ci right 3.072102e-02	k: 863	n:30000
C20orf134   30000 perm   7 sec   (4228 perm/sec)   p_kst 2.876667e-02   p_cons 9.234000e-01   p_joint 1.289333e-01

Joint ci ratio: 2.942014e-02	ci left: 3.028549e-01	ci right 3.119231e-01	k: 12295	n:40000
Cons ci ratio: 5.620809e-03	ci left: 9.213851e-01	ci right 9.266032e-01	k: 36961	n:40000
KS ci ratio: 1.124185e-01	ci left: 2.783925e-02	ci right 3.117952e-02	k: 1179	n:40000
C20orf134   40000 perm   9 sec   (4423 perm/sec)   p_kst 2.947500e-02   p_cons 9.240250e-01   p_joint 3.073750e-01

Joint ci ratio: 1.620385e-02	ci left: 5.348787e-01	ci right 5.436367e-01	k: 26963	n:50000
Cons ci ratio: 5.037485e-03	ci left: 9.213789e-01	ci right 9.260518e-01	k: 46187	n:50000
KS ci ratio: 1.014396e-01	ci left: 2.752703e-02	ci right 3.048799e-02	k: 1449	n:50000
C20orf134   50000 perm   11 sec   (4514 perm/sec)   p_kst 2.898000e-02   p_cons 9.237400e-01   p_joint 5.392600e-01

Joint ci ratio: 1.416213e-02	ci left: 5.568177e-01	ci right 5.647764e-01	k: 33648	n:60000
Cons ci ratio: 4.624235e-03	ci left: 9.207874e-01	ci right 9.250716e-01	k: 55377	n:60000
KS ci ratio: 9.227424e-02	ci left: 2.785099e-02	ci right 3.056147e-02	k: 1751	n:60000
C20orf134   60000 perm   13 sec   (4553 perm/sec)   p_kst 2.918333e-02   p_cons 9.229500e-01   p_joint 5.608000e-01

Outputting figure to mutsig2_images.part000000000023/C20orf134.2_742_60000_0.029183_0.92295_0.5608.png
                gene_name: C20orf134
               theta_stop: 0.092 
                    nperm: 60000 
                     p_ks: 0.029 
        ci_ks_bounds_left: 0.028 
       ci_ks_bounds_right: 0.031 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.56 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000023
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 23 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1530>
Subject: Job 4397830: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1530>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000024> was used as the working directory.
Started at Wed Oct 24 16:08:52 2012
Results reported at Wed Oct 24 19:31:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000024.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000024.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 24  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000024.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :  12980.80 sec.
    Max Memory :      1492 MB
    Max Swap   :      4126 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
24
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 24
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 24: processing genes 2064 - 2153
Calculating significance of each gene.
Using projection method.
2064	C20orf3	1
2065	C20orf30	1
2066	C20orf4	1
2067	C20orf43	1
2068	C20orf46	1
2069	C20orf54	1
2070	C20orf7	1
2071	C20orf70	1
2072	C20orf71	1
2073	C20orf72	1
2074	C20orf79	1
2075	C20orf85	1
2076	C20orf94	1
2077	C20orf96	1
2078	C21orf2	1
2079	C21orf29	3.030584e-01
2080	C21orf33	1
2081	C21orf45	1
2082	C21orf56	1
2083	C21orf57	1
2084	C21orf58	1
2085	C21orf59	1
2086	C21orf63	1
2087	C21orf7	1
2088	C21orf70	1
2089	C21orf91	1
2090	C22orf13	1
2091	C22orf15	1
2092	C22orf23	1
2093	C22orf24	1
2094	C22orf25	1
2095	C22orf28	1.008088e-01
2096	C22orf29	4.219008e-02
2097	C22orf31	1
2098	C22orf32	1
2099	C22orf33	6.850514e-02
2100	C22orf36	1
2101	C22orf39	1
2102	C22orf40	1
2103	C22orf42	1
2104	C22orf43	1
2105	C22orf9	1
2106	C2CD2	1
2107	C2CD2L	1
2108	C2CD3	2.407817e-01
2109	C2orf15	1
2110	C2orf16	1.909006e-01
2111	C2orf18	1
2112	C2orf24	1
2113	C2orf28	1
2114	C2orf29	1
2115	C2orf3	1
2116	C2orf34	1
2117	C2orf39	3.674826e-01
2118	C2orf40	1.973647e-02
2119	C2orf42	1
2120	C2orf43	1
2121	C2orf44	1
2122	C2orf47	1
2123	C2orf48	1
2124	C2orf49	1
2125	C2orf50	1
2126	C2orf51	1
2127	C2orf53	2.085237e-01
2128	C2orf54	1
2129	C2orf55	1.611003e-01
2130	C2orf56	1
2131	C2orf57	1
2132	C2orf60	1
2133	C2orf61	1
2134	C2orf62	1
2135	C2orf63	1
2136	C2orf64	1
2137	C2orf65	1
2138	C2orf66	1
2139	C2orf67	2.563972e-01
2140	C2orf68	1
2141	C2orf69	1
2142	C2orf7	1
2143	C2orf70	1
2144	C2orf71	4.384208e-01
2145	C2orf73	1
2146	C2orf76	1
2147	C2orf77	1
2148	C2orf78	4.338229e-02
2149	C2orf79	1
2150	C2orf80	1
2151	C2orf83	1
2152	C2orf84	5.503534e-03
2153	C2orf85	1
Done

Running MutSig 2:
Scatter job 24: processing genes 2064 - 2153
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C2CD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.238931e+00	ci left: 4.116173e-04	ci right 1.707790e-03	k: 9	n:10000
Cons ci ratio: 5.806165e-02	ci left: 3.039169e-01	ci right 3.221921e-01	k: 3130	n:10000
KS ci ratio: 1.599773e+00	ci left: 1.623679e-04	ci right 1.166444e-03	k: 5	n:10000
C2CD3   10000 perm   3 sec   (3839 perm/sec)   p_kst 5.000000e-04   p_cons 3.130000e-01   p_joint 9.000000e-04

Joint ci ratio: 1.959755e+00	ci left: 3.093467e-05	ci right 4.383005e-04	k: 3	n:20000
Cons ci ratio: 3.939780e-02	ci left: 3.245280e-01	ci right 3.376211e-01	k: 6621	n:20000
KS ci ratio: 1.959755e+00	ci left: 3.093467e-05	ci right 4.383005e-04	k: 3	n:20000
C2CD3   20000 perm   8 sec   (2387 perm/sec)   p_kst 1.500000e-04   p_cons 3.310500e-01   p_joint 1.500000e-04

Joint ci ratio: 1.481423e+00	ci left: 7.339990e-05	ci right 4.352646e-04	k: 6	n:30000
Cons ci ratio: 3.210292e-02	ci left: 3.266376e-01	ci right 3.373283e-01	k: 9959	n:30000
KS ci ratio: 1.481423e+00	ci left: 7.339990e-05	ci right 4.352646e-04	k: 6	n:30000
C2CD3   30000 perm   11 sec   (2625 perm/sec)   p_kst 2.000000e-04   p_cons 3.319667e-01   p_joint 2.000000e-04

Joint ci ratio: 1.306503e+00	ci left: 8.634963e-05	ci right 3.940415e-04	k: 8	n:40000
Cons ci ratio: 2.785688e-02	ci left: 3.264880e-01	ci right 3.357365e-01	k: 13244	n:40000
KS ci ratio: 1.306503e+00	ci left: 8.634963e-05	ci right 3.940415e-04	k: 8	n:40000
C2CD3   40000 perm   15 sec   (2718 perm/sec)   p_kst 2.000000e-04   p_cons 3.311000e-01   p_joint 2.000000e-04

Joint ci ratio: 1.385805e+00	ci left: 5.628905e-05	ci right 2.884321e-04	k: 7	n:50000
Cons ci ratio: 2.500424e-02	ci left: 3.254199e-01	ci right 3.336799e-01	k: 16477	n:50000
KS ci ratio: 1.181783e+00	ci left: 9.591181e-05	ci right 3.677763e-04	k: 10	n:50000
C2CD3   50000 perm   18 sec   (2787 perm/sec)   p_kst 2.000000e-04   p_cons 3.295400e-01   p_joint 1.400000e-04

Joint ci ratio: 1.181806e+00	ci left: 7.992595e-05	ci right 3.064845e-04	k: 10	n:60000
Cons ci ratio: 2.284339e-02	ci left: 3.254399e-01	ci right 3.329766e-01	k: 19752	n:60000
KS ci ratio: 1.181806e+00	ci left: 7.992595e-05	ci right 3.064845e-04	k: 10	n:60000
C2CD3   60000 perm   21 sec   (2825 perm/sec)   p_kst 1.666667e-04   p_cons 3.292000e-01   p_joint 1.666667e-04

Joint ci ratio: 1.181823e+00	ci left: 6.850761e-05	ci right 2.627036e-04	k: 10	n:70000
Cons ci ratio: 2.119834e-02	ci left: 3.246931e-01	ci right 3.316640e-01	k: 22972	n:70000
KS ci ratio: 1.181823e+00	ci left: 6.850761e-05	ci right 2.627036e-04	k: 10	n:70000
C2CD3   70000 perm   25 sec   (2835 perm/sec)   p_kst 1.428571e-04   p_cons 3.281714e-01   p_joint 1.428571e-04

Joint ci ratio: 1.181836e+00	ci left: 5.994393e-05	ci right 2.298674e-04	k: 10	n:80000
Cons ci ratio: 1.983083e-02	ci left: 3.248839e-01	ci right 3.314036e-01	k: 26251	n:80000
KS ci ratio: 1.181836e+00	ci left: 5.994393e-05	ci right 2.298674e-04	k: 10	n:80000
C2CD3   80000 perm   28 sec   (2839 perm/sec)   p_kst 1.250000e-04   p_cons 3.281375e-01   p_joint 1.250000e-04

Joint ci ratio: 1.181846e+00	ci left: 5.328334e-05	ci right 2.043278e-04	k: 10	n:90000
Cons ci ratio: 1.871437e-02	ci left: 3.246557e-01	ci right 3.307999e-01	k: 29495	n:90000
KS ci ratio: 1.181846e+00	ci left: 5.328334e-05	ci right 2.043278e-04	k: 10	n:90000
C2CD3   90000 perm   32 sec   (2833 perm/sec)   p_kst 1.111111e-04   p_cons 3.277222e-01   p_joint 1.111111e-04

Joint ci ratio: 1.087136e+00	ci left: 6.200724e-05	ci right 2.096065e-04	k: 12	n:100000
Cons ci ratio: 1.776947e-02	ci left: 3.244317e-01	ci right 3.302583e-01	k: 32734	n:100000
KS ci ratio: 1.087136e+00	ci left: 6.200724e-05	ci right 2.096065e-04	k: 12	n:100000
C2CD3   100000 perm   35 sec   (2822 perm/sec)   p_kst 1.200000e-04   p_cons 3.273400e-01   p_joint 1.200000e-04

Joint ci ratio: 1.087143e+00	ci left: 5.637009e-05	ci right 1.905521e-04	k: 12	n:110000
Cons ci ratio: 1.753819e-02	ci left: 3.095708e-01	ci right 3.150572e-01	k: 34354	n:110000
KS ci ratio: 1.087143e+00	ci left: 5.637009e-05	ci right 1.905521e-04	k: 12	n:110000
C2CD3   110000 perm   39 sec   (2803 perm/sec)   p_kst 1.090909e-04   p_cons 3.123091e-01   p_joint 1.090909e-04

Joint ci ratio: 1.087149e+00	ci left: 5.167249e-05	ci right 1.746734e-04	k: 12	n:120000
Cons ci ratio: 1.678769e-02	ci left: 3.097864e-01	ci right 3.150393e-01	k: 37489	n:120000
KS ci ratio: 1.087149e+00	ci left: 5.167249e-05	ci right 1.746734e-04	k: 12	n:120000
C2CD3   120000 perm   43 sec   (2782 perm/sec)   p_kst 1.000000e-04   p_cons 3.124083e-01   p_joint 1.000000e-04

Joint ci ratio: 1.047604e+00	ci left: 5.324683e-05	ci right 1.709970e-04	k: 13	n:130000
Cons ci ratio: 1.612048e-02	ci left: 3.101189e-01	ci right 3.151664e-01	k: 40643	n:130000
KS ci ratio: 1.047604e+00	ci left: 5.324683e-05	ci right 1.709970e-04	k: 13	n:130000
C2CD3   130000 perm   47 sec   (2765 perm/sec)   p_kst 1.000000e-04   p_cons 3.126385e-01   p_joint 1.000000e-04

Joint ci ratio: 8.992454e-01	ci left: 7.620130e-05	ci right 2.031907e-04	k: 18	n:140000
Cons ci ratio: 1.553936e-02	ci left: 3.100652e-01	ci right 3.149283e-01	k: 43749	n:140000
KS ci ratio: 8.992454e-01	ci left: 7.620130e-05	ci right 2.031907e-04	k: 18	n:140000
C2CD3   140000 perm   51 sec   (2747 perm/sec)   p_kst 1.285714e-04   p_cons 3.124929e-01   p_joint 1.285714e-04

Joint ci ratio: 8.553514e-01	ci left: 8.144531e-05	ci right 2.059150e-04	k: 20	n:150000
Cons ci ratio: 1.500337e-02	ci left: 3.104075e-01	ci right 3.151064e-01	k: 46913	n:150000
KS ci ratio: 8.553514e-01	ci left: 8.144531e-05	ci right 2.059150e-04	k: 20	n:150000
C2CD3   150000 perm   55 sec   (2727 perm/sec)   p_kst 1.333333e-04   p_cons 3.127533e-01   p_joint 1.333333e-04

Joint ci ratio: 8.356867e-01	ci left: 8.124760e-05	ci right 2.006226e-04	k: 21	n:160000
Cons ci ratio: 1.453405e-02	ci left: 3.102728e-01	ci right 3.148215e-01	k: 50007	n:160000
KS ci ratio: 8.356867e-01	ci left: 8.124760e-05	ci right 2.006226e-04	k: 21	n:160000
C2CD3   160000 perm   59 sec   (2706 perm/sec)   p_kst 1.312500e-04   p_cons 3.125438e-01   p_joint 1.312500e-04

Joint ci ratio: 8.001078e-01	ci left: 8.576674e-05	ci right 2.030007e-04	k: 23	n:170000
Cons ci ratio: 1.409403e-02	ci left: 3.105259e-01	ci right 3.149393e-01	k: 53164	n:170000
KS ci ratio: 8.001078e-01	ci left: 8.576674e-05	ci right 2.030007e-04	k: 23	n:170000
C2CD3   170000 perm   63 sec   (2683 perm/sec)   p_kst 1.352941e-04   p_cons 3.127294e-01   p_joint 1.352941e-04

Joint ci ratio: 8.001111e-01	ci left: 8.100182e-05	ci right 1.917233e-04	k: 23	n:180000
Cons ci ratio: 1.370195e-02	ci left: 3.104311e-01	ci right 3.147194e-01	k: 56263	n:180000
KS ci ratio: 8.001111e-01	ci left: 8.100182e-05	ci right 1.917233e-04	k: 23	n:180000
C2CD3   180000 perm   68 sec   (2660 perm/sec)   p_kst 1.277778e-04   p_cons 3.125722e-01   p_joint 1.277778e-04

Joint ci ratio: 7.839464e-01	ci left: 8.093453e-05	ci right 1.879421e-04	k: 24	n:190000
Cons ci ratio: 1.334267e-02	ci left: 3.102900e-01	ci right 3.144631e-01	k: 59351	n:190000
KS ci ratio: 7.839464e-01	ci left: 8.093453e-05	ci right 1.879421e-04	k: 24	n:190000
C2CD3   190000 perm   72 sec   (2638 perm/sec)   p_kst 1.263158e-04   p_cons 3.123737e-01   p_joint 1.263158e-04

Joint ci ratio: 7.839490e-01	ci left: 7.688773e-05	ci right 1.785453e-04	k: 24	n:200000
Cons ci ratio: 1.301358e-02	ci left: 3.100546e-01	ci right 3.141209e-01	k: 62417	n:200000
KS ci ratio: 7.839490e-01	ci left: 7.688773e-05	ci right 1.785453e-04	k: 24	n:200000
C2CD3   200000 perm   76 sec   (2615 perm/sec)   p_kst 1.200000e-04   p_cons 3.120850e-01   p_joint 1.200000e-04

Joint ci ratio: 7.839515e-01	ci left: 7.322634e-05	ci right 1.700433e-04	k: 24	n:210000
Cons ci ratio: 1.270501e-02	ci left: 3.099331e-01	ci right 3.139007e-01	k: 65502	n:210000
KS ci ratio: 7.839515e-01	ci left: 7.322634e-05	ci right 1.700433e-04	k: 24	n:210000
C2CD3   210000 perm   81 sec   (2591 perm/sec)   p_kst 1.142857e-04   p_cons 3.119143e-01   p_joint 1.142857e-04

Joint ci ratio: 7.543563e-01	ci left: 7.720169e-05	ci right 1.731590e-04	k: 26	n:220000
Cons ci ratio: 1.240807e-02	ci left: 3.101459e-01	ci right 3.140227e-01	k: 68658	n:220000
KS ci ratio: 7.543563e-01	ci left: 7.720169e-05	ci right 1.731590e-04	k: 26	n:220000
C2CD3   220000 perm   86 sec   (2567 perm/sec)   p_kst 1.181818e-04   p_cons 3.120818e-01   p_joint 1.181818e-04

Joint ci ratio: 7.407637e-01	ci left: 7.736299e-05	ci right 1.707936e-04	k: 27	n:230000
Cons ci ratio: 1.214171e-02	ci left: 3.099635e-01	ci right 3.137543e-01	k: 71727	n:230000
KS ci ratio: 7.407637e-01	ci left: 7.736299e-05	ci right 1.707936e-04	k: 27	n:230000
C2CD3   230000 perm   90 sec   (2546 perm/sec)   p_kst 1.173913e-04   p_cons 3.118565e-01   p_joint 1.173913e-04

Joint ci ratio: 6.929170e-01	ci left: 8.776412e-05	ci right 1.833368e-04	k: 31	n:240000
Cons ci ratio: 1.188636e-02	ci left: 3.099927e-01	ci right 3.137035e-01	k: 74843	n:240000
KS ci ratio: 6.929170e-01	ci left: 8.776412e-05	ci right 1.833368e-04	k: 31	n:240000
C2CD3   240000 perm   95 sec   (2523 perm/sec)   p_kst 1.291667e-04   p_cons 3.118458e-01   p_joint 1.291667e-04

Joint ci ratio: 6.823380e-01	ci left: 8.755350e-05	ci right 1.806930e-04	k: 32	n:250000
Cons ci ratio: 1.164561e-02	ci left: 3.100523e-01	ci right 3.136881e-01	k: 77967	n:250000
KS ci ratio: 6.823380e-01	ci left: 8.755350e-05	ci right 1.806930e-04	k: 32	n:250000
C2CD3   250000 perm   100 sec   (2498 perm/sec)   p_kst 1.280000e-04   p_cons 3.118680e-01   p_joint 1.280000e-04

Joint ci ratio: 6.625551e-01	ci left: 9.056314e-05	ci right 1.827321e-04	k: 34	n:260000
Cons ci ratio: 1.141800e-02	ci left: 3.101425e-01	ci right 3.137078e-01	k: 81100	n:260000
KS ci ratio: 6.625551e-01	ci left: 9.056314e-05	ci right 1.827321e-04	k: 34	n:260000
C2CD3   260000 perm   105 sec   (2475 perm/sec)   p_kst 1.307692e-04   p_cons 3.119231e-01   p_joint 1.307692e-04

Joint ci ratio: 6.532886e-01	ci left: 9.029340e-05	ci right 1.802789e-04	k: 35	n:270000
Cons ci ratio: 1.120043e-02	ci left: 3.103339e-01	ci right 3.138331e-01	k: 84262	n:270000
KS ci ratio: 6.532886e-01	ci left: 9.029340e-05	ci right 1.802789e-04	k: 35	n:270000
C2CD3   270000 perm   110 sec   (2453 perm/sec)   p_kst 1.296296e-04   p_cons 3.120815e-01   p_joint 1.296296e-04

Joint ci ratio: 6.532902e-01	ci left: 8.706858e-05	ci right 1.738405e-04	k: 35	n:280000
Cons ci ratio: 1.100418e-02	ci left: 3.101486e-01	ci right 3.135839e-01	k: 87322	n:280000
KS ci ratio: 6.532902e-01	ci left: 8.706858e-05	ci right 1.738405e-04	k: 35	n:280000
C2CD3   280000 perm   115 sec   (2429 perm/sec)   p_kst 1.250000e-04   p_cons 3.118643e-01   p_joint 1.250000e-04

Joint ci ratio: 6.358652e-01	ci left: 8.983400e-05	ci right 1.758565e-04	k: 37	n:290000
Cons ci ratio: 1.081311e-02	ci left: 3.101659e-01	ci right 3.135413e-01	k: 90437	n:290000
KS ci ratio: 6.358652e-01	ci left: 8.983400e-05	ci right 1.758565e-04	k: 37	n:290000
C2CD3   290000 perm   121 sec   (2405 perm/sec)   p_kst 1.275862e-04   p_cons 3.118517e-01   p_joint 1.275862e-04

Joint ci ratio: 6.358666e-01	ci left: 8.683949e-05	ci right 1.699948e-04	k: 37	n:300000
Cons ci ratio: 1.063256e-02	ci left: 3.101459e-01	ci right 3.134644e-01	k: 93541	n:300000
KS ci ratio: 6.358666e-01	ci left: 8.683949e-05	ci right 1.699948e-04	k: 37	n:300000
C2CD3   300000 perm   126 sec   (2376 perm/sec)   p_kst 1.233333e-04   p_cons 3.118033e-01   p_joint 1.233333e-04

Joint ci ratio: 6.276619e-01	ci left: 8.674677e-05	ci right 1.682477e-04	k: 38	n:310000
Cons ci ratio: 1.046163e-02	ci left: 3.100922e-01	ci right 3.133565e-01	k: 96634	n:310000
KS ci ratio: 6.276619e-01	ci left: 8.674677e-05	ci right 1.682477e-04	k: 38	n:310000
C2CD3   310000 perm   132 sec   (2353 perm/sec)   p_kst 1.225806e-04   p_cons 3.117226e-01   p_joint 1.225806e-04

Joint ci ratio: 6.197667e-01	ci left: 8.666643e-05	ci right 1.666034e-04	k: 39	n:320000
Cons ci ratio: 1.029922e-02	ci left: 3.100204e-01	ci right 3.132330e-01	k: 99720	n:320000
KS ci ratio: 6.197667e-01	ci left: 8.666643e-05	ci right 1.666034e-04	k: 39	n:320000
C2CD3   320000 perm   137 sec   (2332 perm/sec)   p_kst 1.218750e-04   p_cons 3.116250e-01   p_joint 1.218750e-04

Joint ci ratio: 6.121622e-01	ci left: 8.659708e-05	ci right 1.650529e-04	k: 40	n:330000
Cons ci ratio: 1.013504e-02	ci left: 3.103377e-01	ci right 3.135020e-01	k: 102933	n:330000
KS ci ratio: 6.121622e-01	ci left: 8.659708e-05	ci right 1.650529e-04	k: 40	n:330000
C2CD3   330000 perm   143 sec   (2311 perm/sec)   p_kst 1.212121e-04   p_cons 3.119182e-01   p_joint 1.212121e-04

Joint ci ratio: 5.909231e-01	ci left: 9.152886e-05	ci right 1.703513e-04	k: 43	n:340000
Cons ci ratio: 9.990309e-03	ci left: 3.101285e-01	ci right 3.132453e-01	k: 105973	n:340000
KS ci ratio: 5.909231e-01	ci left: 9.152886e-05	ci right 1.703513e-04	k: 43	n:340000
C2CD3   340000 perm   149 sec   (2285 perm/sec)   p_kst 1.264706e-04   p_cons 3.116853e-01   p_joint 1.264706e-04

Joint ci ratio: 5.779337e-01	ci left: 9.378238e-05	ci right 1.720349e-04	k: 45	n:350000
Cons ci ratio: 9.848910e-03	ci left: 3.100486e-01	ci right 3.131202e-01	k: 109054	n:350000
KS ci ratio: 5.779337e-01	ci left: 9.378238e-05	ci right 1.720349e-04	k: 45	n:350000
C2CD3   350000 perm   155 sec   (2263 perm/sec)   p_kst 1.285714e-04   p_cons 3.115829e-01   p_joint 1.285714e-04

Joint ci ratio: 5.599611e-01	ci left: 9.831106e-05	ci right 1.767768e-04	k: 48	n:360000
Cons ci ratio: 9.712027e-03	ci left: 3.100317e-01	ci right 3.130602e-01	k: 112156	n:360000
KS ci ratio: 5.599611e-01	ci left: 9.831106e-05	ci right 1.767768e-04	k: 48	n:360000
C2CD3   360000 perm   161 sec   (2243 perm/sec)   p_kst 1.333333e-04   p_cons 3.115444e-01   p_joint 1.333333e-04

Joint ci ratio: 5.599622e-01	ci left: 9.565396e-05	ci right 1.719992e-04	k: 48	n:370000
Cons ci ratio: 9.578344e-03	ci left: 3.101213e-01	ci right 3.131087e-01	k: 115297	n:370000
KS ci ratio: 5.599622e-01	ci left: 9.565396e-05	ci right 1.719992e-04	k: 48	n:370000
C2CD3   370000 perm   166 sec   (2223 perm/sec)   p_kst 1.297297e-04   p_cons 3.116135e-01   p_joint 1.297297e-04

Joint ci ratio: 5.543345e-01	ci left: 9.539745e-05	ci right 1.704717e-04	k: 49	n:380000
Cons ci ratio: 9.451656e-03	ci left: 3.101328e-01	ci right 3.130806e-01	k: 118410	n:380000
KS ci ratio: 5.543345e-01	ci left: 9.539745e-05	ci right 1.704717e-04	k: 49	n:380000
C2CD3   380000 perm   172 sec   (2204 perm/sec)   p_kst 1.289474e-04   p_cons 3.116053e-01   p_joint 1.289474e-04

Joint ci ratio: 5.488732e-01	ci left: 9.515777e-05	ci right 1.690190e-04	k: 50	n:390000
Cons ci ratio: 9.327413e-03	ci left: 3.102567e-01	ci right 3.131666e-01	k: 121567	n:390000
KS ci ratio: 5.488732e-01	ci left: 9.515777e-05	ci right 1.690190e-04	k: 50	n:390000
C2CD3   390000 perm   179 sec   (2184 perm/sec)   p_kst 1.282051e-04   p_cons 3.117103e-01   p_joint 1.282051e-04

Joint ci ratio: 5.435702e-01	ci left: 9.493355e-05	ci right 1.676356e-04	k: 51	n:400000
Cons ci ratio: 9.212558e-03	ci left: 3.101598e-01	ci right 3.130329e-01	k: 124638	n:400000
KS ci ratio: 5.435702e-01	ci left: 9.493355e-05	ci right 1.676356e-04	k: 51	n:400000
C2CD3   400000 perm   185 sec   (2164 perm/sec)   p_kst 1.275000e-04   p_cons 3.115950e-01   p_joint 1.275000e-04

Joint ci ratio: 5.384180e-01	ci left: 9.472357e-05	ci right 1.663164e-04	k: 52	n:410000
Cons ci ratio: 9.097912e-03	ci left: 3.102531e-01	ci right 3.130910e-01	k: 127785	n:410000
KS ci ratio: 5.384180e-01	ci left: 9.472357e-05	ci right 1.663164e-04	k: 52	n:410000
C2CD3   410000 perm   191 sec   (2147 perm/sec)   p_kst 1.268293e-04   p_cons 3.116707e-01   p_joint 1.268293e-04

Joint ci ratio: 5.285375e-01	ci left: 9.658824e-05	ci right 1.677545e-04	k: 54	n:420000
Cons ci ratio: 8.989436e-03	ci left: 3.102470e-01	ci right 3.130509e-01	k: 130892	n:420000
KS ci ratio: 5.285375e-01	ci left: 9.658824e-05	ci right 1.677545e-04	k: 54	n:420000
C2CD3   420000 perm   197 sec   (2128 perm/sec)   p_kst 1.285714e-04   p_cons 3.116476e-01   p_joint 1.285714e-04

Joint ci ratio: 5.191817e-01	ci left: 9.837773e-05	ci right 1.691145e-04	k: 56	n:430000
Cons ci ratio: 8.887111e-03	ci left: 3.101275e-01	ci right 3.128983e-01	k: 133950	n:430000
KS ci ratio: 5.191817e-01	ci left: 9.837773e-05	ci right 1.691145e-04	k: 56	n:430000
C2CD3   430000 perm   204 sec   (2110 perm/sec)   p_kst 1.302326e-04   p_cons 3.115116e-01   p_joint 1.302326e-04

Joint ci ratio: 5.103057e-01	ci left: 1.000965e-04	ci right 1.704023e-04	k: 58	n:440000
Cons ci ratio: 8.786199e-03	ci left: 3.101113e-01	ci right 3.128503e-01	k: 137051	n:440000
KS ci ratio: 5.103057e-01	ci left: 1.000965e-04	ci right 1.704023e-04	k: 58	n:440000
C2CD3   440000 perm   210 sec   (2091 perm/sec)   p_kst 1.318182e-04   p_cons 3.114795e-01   p_joint 1.318182e-04

Joint ci ratio: 4.938385e-01	ci left: 1.056350e-04	ci right 1.766215e-04	k: 62	n:450000
Cons ci ratio: 8.686263e-03	ci left: 3.102136e-01	ci right 3.129221e-01	k: 140205	n:450000
KS ci ratio: 4.938385e-01	ci left: 1.056350e-04	ci right 1.766215e-04	k: 62	n:450000
C2CD3   450000 perm   217 sec   (2074 perm/sec)   p_kst 1.377778e-04   p_cons 3.115667e-01   p_joint 1.377778e-04

Joint ci ratio: 4.938392e-01	ci left: 1.033386e-04	ci right 1.727819e-04	k: 62	n:460000
Cons ci ratio: 8.589791e-03	ci left: 3.103051e-01	ci right 3.129842e-01	k: 143356	n:460000
KS ci ratio: 4.938392e-01	ci left: 1.033386e-04	ci right 1.727819e-04	k: 62	n:460000
C2CD3   460000 perm   224 sec   (2057 perm/sec)   p_kst 1.347826e-04   p_cons 3.116435e-01   p_joint 1.347826e-04

Joint ci ratio: 4.938400e-01	ci left: 1.011398e-04	ci right 1.691058e-04	k: 62	n:470000
Cons ci ratio: 8.498318e-03	ci left: 3.102994e-01	ci right 3.129497e-01	k: 146463	n:470000
KS ci ratio: 4.938400e-01	ci left: 1.011398e-04	ci right 1.691058e-04	k: 62	n:470000
C2CD3   470000 perm   230 sec   (2041 perm/sec)   p_kst 1.319149e-04   p_cons 3.116234e-01   p_joint 1.319149e-04

Joint ci ratio: 4.938407e-01	ci left: 9.903273e-05	ci right 1.655828e-04	k: 62	n:480000
Cons ci ratio: 8.409542e-03	ci left: 3.103024e-01	ci right 3.129249e-01	k: 149574	n:480000
KS ci ratio: 4.938407e-01	ci left: 9.903273e-05	ci right 1.655828e-04	k: 62	n:480000
C2CD3   480000 perm   237 sec   (2025 perm/sec)   p_kst 1.291667e-04   p_cons 3.116125e-01   p_joint 1.291667e-04

Joint ci ratio: 4.861834e-01	ci left: 1.005888e-04	ci right 1.667859e-04	k: 64	n:490000
Cons ci ratio: 8.319415e-03	ci left: 3.105153e-01	ci right 3.131114e-01	k: 152788	n:490000
KS ci ratio: 4.861834e-01	ci left: 1.005888e-04	ci right 1.667859e-04	k: 64	n:490000
C2CD3   490000 perm   246 sec   (1994 perm/sec)   p_kst 1.306122e-04   p_cons 3.118122e-01   p_joint 1.306122e-04

Joint ci ratio: 4.861841e-01	ci left: 9.857695e-05	ci right 1.634502e-04	k: 64	n:500000
Cons ci ratio: 8.236996e-03	ci left: 3.104662e-01	ci right 3.130360e-01	k: 155875	n:500000
KS ci ratio: 4.861841e-01	ci left: 9.857695e-05	ci right 1.634502e-04	k: 64	n:500000
C2CD3   500000 perm   253 sec   (1978 perm/sec)   p_kst 1.280000e-04   p_cons 3.117500e-01   p_joint 1.280000e-04

Joint ci ratio: 4.824869e-01	ci left: 9.836531e-05	ci right 1.624439e-04	k: 65	n:510000
Cons ci ratio: 8.155712e-03	ci left: 3.104857e-01	ci right 3.130302e-01	k: 158996	n:510000
KS ci ratio: 4.824869e-01	ci left: 9.836531e-05	ci right 1.624439e-04	k: 65	n:510000
C2CD3   510000 perm   260 sec   (1963 perm/sec)   p_kst 1.274510e-04   p_cons 3.117569e-01   p_joint 1.274510e-04

Joint ci ratio: 4.753383e-01	ci left: 9.985535e-05	ci right 1.636272e-04	k: 67	n:520000
Cons ci ratio: 8.079141e-03	ci left: 3.103797e-01	ci right 3.128993e-01	k: 162052	n:520000
KS ci ratio: 4.753383e-01	ci left: 9.985535e-05	ci right 1.636272e-04	k: 67	n:520000
C2CD3   520000 perm   267 sec   (1948 perm/sec)   p_kst 1.288462e-04   p_cons 3.116385e-01   p_joint 1.288462e-04

Joint ci ratio: 4.718814e-01	ci left: 9.963277e-05	ci right 1.626504e-04	k: 68	n:530000
Cons ci ratio: 8.004263e-03	ci left: 3.103004e-01	ci right 3.127960e-01	k: 165120	n:530000
KS ci ratio: 4.718814e-01	ci left: 9.963277e-05	ci right 1.626504e-04	k: 68	n:530000
C2CD3   530000 perm   274 sec   (1933 perm/sec)   p_kst 1.283019e-04   p_cons 3.115472e-01   p_joint 1.283019e-04

Joint ci ratio: 4.718820e-01	ci left: 9.778769e-05	ci right 1.596384e-04	k: 68	n:540000
Cons ci ratio: 7.930916e-03	ci left: 3.102520e-01	ci right 3.127241e-01	k: 168203	n:540000
KS ci ratio: 4.718820e-01	ci left: 9.778769e-05	ci right 1.596384e-04	k: 68	n:540000
C2CD3   540000 perm   282 sec   (1918 perm/sec)   p_kst 1.259259e-04   p_cons 3.114870e-01   p_joint 1.259259e-04

Joint ci ratio: 4.587704e-01	ci left: 1.024297e-04	ci right 1.648555e-04	k: 72	n:550000
Cons ci ratio: 7.858116e-03	ci left: 3.102834e-01	ci right 3.127331e-01	k: 171329	n:550000
KS ci ratio: 4.587704e-01	ci left: 1.024297e-04	ci right 1.648555e-04	k: 72	n:550000
C2CD3   550000 perm   289 sec   (1903 perm/sec)   p_kst 1.309091e-04   p_cons 3.115073e-01   p_joint 1.309091e-04

Joint ci ratio: 4.496239e-01	ci left: 1.053447e-04	ci right 1.678778e-04	k: 75	n:560000
Cons ci ratio: 7.785016e-03	ci left: 3.104388e-01	ci right 3.128667e-01	k: 174525	n:560000
KS ci ratio: 4.496239e-01	ci left: 1.053447e-04	ci right 1.678778e-04	k: 75	n:560000
C2CD3   560000 perm   296 sec   (1889 perm/sec)   p_kst 1.339286e-04   p_cons 3.116518e-01   p_joint 1.339286e-04

Joint ci ratio: 4.496245e-01	ci left: 1.034966e-04	ci right 1.649326e-04	k: 75	n:570000
Cons ci ratio: 7.716946e-03	ci left: 3.104205e-01	ci right 3.128270e-01	k: 177625	n:570000
KS ci ratio: 4.496245e-01	ci left: 1.034966e-04	ci right 1.649326e-04	k: 75	n:570000
C2CD3   570000 perm   304 sec   (1875 perm/sec)   p_kst 1.315789e-04   p_cons 3.116228e-01   p_joint 1.315789e-04

Joint ci ratio: 4.466954e-01	ci left: 1.032416e-04	ci right 1.640065e-04	k: 76	n:580000
Cons ci ratio: 7.650108e-03	ci left: 3.104323e-01	ci right 3.128179e-01	k: 180742	n:580000
KS ci ratio: 4.466954e-01	ci left: 1.032416e-04	ci right 1.640065e-04	k: 76	n:580000
C2CD3   580000 perm   312 sec   (1862 perm/sec)   p_kst 1.310345e-04   p_cons 3.116241e-01   p_joint 1.310345e-04

Joint ci ratio: 4.382392e-01	ci left: 1.060099e-04	ci right 1.668745e-04	k: 79	n:590000
Cons ci ratio: 7.585217e-03	ci left: 3.104301e-01	ci right 3.127954e-01	k: 183851	n:590000
KS ci ratio: 4.382392e-01	ci left: 1.060099e-04	ci right 1.668745e-04	k: 79	n:590000
C2CD3   590000 perm   319 sec   (1847 perm/sec)   p_kst 1.338983e-04   p_cons 3.116119e-01   p_joint 1.338983e-04

Joint ci ratio: 4.251532e-01	ci left: 1.116710e-04	ci right 1.733266e-04	k: 84	n:600000
Cons ci ratio: 7.520255e-03	ci left: 3.105247e-01	ci right 3.128704e-01	k: 187018	n:600000
KS ci ratio: 4.251532e-01	ci left: 1.116710e-04	ci right 1.733266e-04	k: 84	n:600000
C2CD3   600000 perm   327 sec   (1833 perm/sec)   p_kst 1.400000e-04   p_cons 3.116967e-01   p_joint 1.400000e-04

Joint ci ratio: 4.202378e-01	ci left: 1.127702e-04	ci right 1.741107e-04	k: 86	n:610000
Cons ci ratio: 7.458444e-03	ci left: 3.105295e-01	ci right 3.128559e-01	k: 190132	n:610000
KS ci ratio: 4.202378e-01	ci left: 1.127702e-04	ci right 1.741107e-04	k: 86	n:610000
C2CD3   610000 perm   335 sec   (1820 perm/sec)   p_kst 1.409836e-04   p_cons 3.116918e-01   p_joint 1.409836e-04

Joint ci ratio: 4.108972e-01	ci left: 1.167284e-04	ci right 1.784249e-04	k: 90	n:620000
Cons ci ratio: 7.399467e-03	ci left: 3.104569e-01	ci right 3.127642e-01	k: 193198	n:620000
KS ci ratio: 4.108972e-01	ci left: 1.167284e-04	ci right 1.784249e-04	k: 90	n:620000
C2CD3   620000 perm   343 sec   (1807 perm/sec)   p_kst 1.451613e-04   p_cons 3.116097e-01   p_joint 1.451613e-04

Joint ci ratio: 4.064547e-01	ci left: 1.177238e-04	ci right 1.790920e-04	k: 92	n:630000
Cons ci ratio: 7.339288e-03	ci left: 3.105373e-01	ci right 3.128264e-01	k: 196359	n:630000
KS ci ratio: 4.064547e-01	ci left: 1.177238e-04	ci right 1.790920e-04	k: 92	n:630000
C2CD3   630000 perm   351 sec   (1794 perm/sec)   p_kst 1.460317e-04   p_cons 3.116810e-01   p_joint 1.460317e-04

Joint ci ratio: 4.042871e-01	ci left: 1.172875e-04	ci right 1.780147e-04	k: 93	n:640000
Cons ci ratio: 7.283682e-03	ci left: 3.104310e-01	ci right 3.127019e-01	k: 199402	n:640000
KS ci ratio: 4.042871e-01	ci left: 1.172875e-04	ci right 1.780147e-04	k: 93	n:640000
C2CD3   640000 perm   359 sec   (1781 perm/sec)   p_kst 1.453125e-04   p_cons 3.115656e-01   p_joint 1.453125e-04

Joint ci ratio: 4.000535e-01	ci left: 1.182487e-04	ci right 1.786626e-04	k: 95	n:650000
Cons ci ratio: 7.227713e-03	ci left: 3.104234e-01	ci right 3.126767e-01	k: 202507	n:650000
KS ci ratio: 4.000535e-01	ci left: 1.182487e-04	ci right 1.786626e-04	k: 95	n:650000
C2CD3   650000 perm   368 sec   (1768 perm/sec)   p_kst 1.461538e-04   p_cons 3.115492e-01   p_joint 1.461538e-04

Joint ci ratio: 3.979861e-01	ci left: 1.178202e-04	ci right 1.776220e-04	k: 96	n:660000
Cons ci ratio: 7.171951e-03	ci left: 3.104797e-01	ci right 3.127159e-01	k: 205654	n:660000
KS ci ratio: 3.979861e-01	ci left: 1.178202e-04	ci right 1.776220e-04	k: 96	n:660000
C2CD3   660000 perm   376 sec   (1756 perm/sec)   p_kst 1.454545e-04   p_cons 3.115970e-01   p_joint 1.454545e-04

Joint ci ratio: 3.939454e-01	ci left: 1.187495e-04	ci right 1.782518e-04	k: 98	n:670000
Cons ci ratio: 7.116965e-03	ci left: 3.105641e-01	ci right 3.127838e-01	k: 208821	n:670000
KS ci ratio: 3.939454e-01	ci left: 1.187495e-04	ci right 1.782518e-04	k: 98	n:670000
C2CD3   670000 perm   384 sec   (1744 perm/sec)   p_kst 1.462687e-04   p_cons 3.116731e-01   p_joint 1.462687e-04

Joint ci ratio: 3.919709e-01	ci left: 1.183285e-04	ci right 1.772456e-04	k: 99	n:680000
Cons ci ratio: 7.065088e-03	ci left: 3.105330e-01	ci right 3.127362e-01	k: 211911	n:680000
KS ci ratio: 3.919709e-01	ci left: 1.183285e-04	ci right 1.772456e-04	k: 99	n:680000
C2CD3   680000 perm   393 sec   (1731 perm/sec)   p_kst 1.455882e-04   p_cons 3.116338e-01   p_joint 1.455882e-04

Joint ci ratio: 3.862200e-01	ci left: 1.205361e-04	ci right 1.794479e-04	k: 102	n:690000
Cons ci ratio: 7.013737e-03	ci left: 3.105391e-01	ci right 3.127262e-01	k: 215026	n:690000
KS ci ratio: 3.862200e-01	ci left: 1.205361e-04	ci right 1.794479e-04	k: 102	n:690000
C2CD3   690000 perm   401 sec   (1719 perm/sec)   p_kst 1.478261e-04   p_cons 3.116319e-01   p_joint 1.478261e-04

Joint ci ratio: 3.862204e-01	ci left: 1.188141e-04	ci right 1.768844e-04	k: 102	n:700000
Cons ci ratio: 6.963512e-03	ci left: 3.105436e-01	ci right 3.127151e-01	k: 218140	n:700000
KS ci ratio: 3.862204e-01	ci left: 1.188141e-04	ci right 1.768844e-04	k: 102	n:700000
C2CD3   700000 perm   410 sec   (1706 perm/sec)   p_kst 1.457143e-04   p_cons 3.116286e-01   p_joint 1.457143e-04

Joint ci ratio: 3.807154e-01	ci left: 1.209587e-04	ci right 1.790238e-04	k: 105	n:710000
Cons ci ratio: 6.914670e-03	ci left: 3.105284e-01	ci right 3.126844e-01	k: 221240	n:710000
KS ci ratio: 3.807154e-01	ci left: 1.209587e-04	ci right 1.790238e-04	k: 105	n:710000
C2CD3   710000 perm   419 sec   (1694 perm/sec)   p_kst 1.478873e-04   p_cons 3.116056e-01   p_joint 1.478873e-04

Joint ci ratio: 3.737285e-01	ci left: 1.243076e-04	ci right 1.826172e-04	k: 109	n:720000
Cons ci ratio: 6.866396e-03	ci left: 3.105414e-01	ci right 3.126824e-01	k: 224360	n:720000
KS ci ratio: 3.737285e-01	ci left: 1.243076e-04	ci right 1.826172e-04	k: 109	n:720000
C2CD3   720000 perm   428 sec   (1683 perm/sec)   p_kst 1.513889e-04   p_cons 3.116111e-01   p_joint 1.513889e-04

Joint ci ratio: 3.703765e-01	ci left: 1.250884e-04	ci right 1.831104e-04	k: 111	n:730000
Cons ci ratio: 6.819969e-03	ci left: 3.105007e-01	ci right 3.126269e-01	k: 227441	n:730000
KS ci ratio: 3.703765e-01	ci left: 1.250884e-04	ci right 1.831104e-04	k: 111	n:730000
C2CD3   730000 perm   437 sec   (1671 perm/sec)   p_kst 1.520548e-04   p_cons 3.115630e-01   p_joint 1.520548e-04

Joint ci ratio: 3.639341e-01	ci left: 1.283048e-04	ci right 1.865377e-04	k: 115	n:740000
Cons ci ratio: 6.774129e-03	ci left: 3.104827e-01	ci right 3.125944e-01	k: 230538	n:740000
KS ci ratio: 3.639341e-01	ci left: 1.283048e-04	ci right 1.865377e-04	k: 115	n:740000
C2CD3   740000 perm   446 sec   (1660 perm/sec)   p_kst 1.554054e-04   p_cons 3.115378e-01   p_joint 1.554054e-04

Joint ci ratio: 3.623756e-01	ci left: 1.278057e-04	ci right 1.855051e-04	k: 116	n:750000
Cons ci ratio: 6.728344e-03	ci left: 3.105199e-01	ci right 3.126175e-01	k: 233676	n:750000
KS ci ratio: 3.623756e-01	ci left: 1.278057e-04	ci right 1.855051e-04	k: 116	n:750000
C2CD3   750000 perm   455 sec   (1649 perm/sec)   p_kst 1.546667e-04   p_cons 3.115680e-01   p_joint 1.546667e-04

Joint ci ratio: 3.578169e-01	ci left: 1.297143e-04	ci right 1.873672e-04	k: 119	n:760000
Cons ci ratio: 6.682695e-03	ci left: 3.106061e-01	ci right 3.126900e-01	k: 236852	n:760000
KS ci ratio: 3.578169e-01	ci left: 1.297143e-04	ci right 1.873672e-04	k: 119	n:760000
C2CD3   760000 perm   464 sec   (1638 perm/sec)   p_kst 1.565789e-04   p_cons 3.116474e-01   p_joint 1.565789e-04

Joint ci ratio: 3.563354e-01	ci left: 1.292119e-04	ci right 1.863486e-04	k: 120	n:770000
Cons ci ratio: 6.638145e-03	ci left: 3.106785e-01	ci right 3.127489e-01	k: 240019	n:770000
KS ci ratio: 3.563354e-01	ci left: 1.292119e-04	ci right 1.863486e-04	k: 120	n:770000
C2CD3   770000 perm   473 sec   (1627 perm/sec)   p_kst 1.558442e-04   p_cons 3.117130e-01   p_joint 1.558442e-04

Joint ci ratio: 3.519982e-01	ci left: 1.310594e-04	ci right 1.881464e-04	k: 123	n:780000
Cons ci ratio: 6.595773e-03	ci left: 3.106645e-01	ci right 3.127216e-01	k: 243120	n:780000
KS ci ratio: 3.519982e-01	ci left: 1.310594e-04	ci right 1.881464e-04	k: 123	n:780000
C2CD3   780000 perm   483 sec   (1616 perm/sec)   p_kst 1.576923e-04   p_cons 3.116923e-01   p_joint 1.576923e-04

Joint ci ratio: 3.519985e-01	ci left: 1.294004e-04	ci right 1.857648e-04	k: 123	n:790000
Cons ci ratio: 6.553159e-03	ci left: 3.107191e-01	ci right 3.127633e-01	k: 246275	n:790000
KS ci ratio: 3.519985e-01	ci left: 1.294004e-04	ci right 1.857648e-04	k: 123	n:790000
C2CD3   790000 perm   492 sec   (1605 perm/sec)   p_kst 1.556962e-04   p_cons 3.117405e-01   p_joint 1.556962e-04

Joint ci ratio: 3.505878e-01	ci left: 1.289226e-04	ci right 1.848026e-04	k: 124	n:800000
Cons ci ratio: 6.513599e-03	ci left: 3.106251e-01	ci right 3.126562e-01	k: 249312	n:800000
KS ci ratio: 3.505878e-01	ci left: 1.289226e-04	ci right 1.848026e-04	k: 124	n:800000
C2CD3   800000 perm   502 sec   (1595 perm/sec)   p_kst 1.550000e-04   p_cons 3.116400e-01   p_joint 1.550000e-04

Joint ci ratio: 3.505882e-01	ci left: 1.273309e-04	ci right 1.825212e-04	k: 124	n:810000
Cons ci ratio: 6.474634e-03	ci left: 3.105409e-01	ci right 3.125592e-01	k: 252355	n:810000
KS ci ratio: 3.505882e-01	ci left: 1.273309e-04	ci right 1.825212e-04	k: 124	n:810000
C2CD3   810000 perm   511 sec   (1584 perm/sec)   p_kst 1.530864e-04   p_cons 3.115494e-01   p_joint 1.530864e-04

Joint ci ratio: 3.464551e-01	ci left: 1.291164e-04	ci right 1.842728e-04	k: 127	n:820000
Cons ci ratio: 6.435793e-03	ci left: 3.104965e-01	ci right 3.125024e-01	k: 255429	n:820000
KS ci ratio: 3.464551e-01	ci left: 1.291164e-04	ci right 1.842728e-04	k: 127	n:820000
C2CD3   820000 perm   521 sec   (1574 perm/sec)   p_kst 1.548780e-04   p_cons 3.114988e-01   p_joint 1.548780e-04

Joint ci ratio: 3.464554e-01	ci left: 1.275608e-04	ci right 1.820527e-04	k: 127	n:830000
Cons ci ratio: 6.396474e-03	ci left: 3.105314e-01	ci right 3.125253e-01	k: 258568	n:830000
KS ci ratio: 3.464554e-01	ci left: 1.275608e-04	ci right 1.820527e-04	k: 127	n:830000
C2CD3   830000 perm   531 sec   (1564 perm/sec)   p_kst 1.530120e-04   p_cons 3.115277e-01   p_joint 1.530120e-04

Joint ci ratio: 3.464557e-01	ci left: 1.260422e-04	ci right 1.798854e-04	k: 127	n:840000
Cons ci ratio: 6.357885e-03	ci left: 3.105644e-01	ci right 3.125464e-01	k: 261706	n:840000
KS ci ratio: 3.464557e-01	ci left: 1.260422e-04	ci right 1.798854e-04	k: 127	n:840000
C2CD3   840000 perm   541 sec   (1554 perm/sec)   p_kst 1.511905e-04   p_cons 3.115548e-01   p_joint 1.511905e-04

Joint ci ratio: 3.451104e-01	ci left: 1.256337e-04	ci right 1.790474e-04	k: 128	n:850000
Cons ci ratio: 6.319155e-03	ci left: 3.106531e-01	ci right 3.126235e-01	k: 264892	n:850000
KS ci ratio: 3.451104e-01	ci left: 1.256337e-04	ci right 1.790474e-04	k: 128	n:850000
C2CD3   850000 perm   550 sec   (1544 perm/sec)   p_kst 1.505882e-04   p_cons 3.116376e-01   p_joint 1.505882e-04

Joint ci ratio: 3.437806e-01	ci left: 1.252350e-04	ci right 1.782284e-04	k: 129	n:860000
Cons ci ratio: 6.282281e-03	ci left: 3.106607e-01	ci right 3.126196e-01	k: 268010	n:860000
KS ci ratio: 3.437806e-01	ci left: 1.252350e-04	ci right 1.782284e-04	k: 129	n:860000
C2CD3   860000 perm   560 sec   (1535 perm/sec)   p_kst 1.500000e-04   p_cons 3.116395e-01   p_joint 1.500000e-04

Joint ci ratio: 3.437809e-01	ci left: 1.237955e-04	ci right 1.761798e-04	k: 129	n:870000
Cons ci ratio: 6.245911e-03	ci left: 3.106774e-01	ci right 3.126250e-01	k: 271136	n:870000
KS ci ratio: 3.437809e-01	ci left: 1.237955e-04	ci right 1.761798e-04	k: 129	n:870000
C2CD3   870000 perm   570 sec   (1525 perm/sec)   p_kst 1.482759e-04   p_cons 3.116506e-01   p_joint 1.482759e-04

Joint ci ratio: 3.437812e-01	ci left: 1.223887e-04	ci right 1.741778e-04	k: 129	n:880000
Cons ci ratio: 6.209951e-03	ci left: 3.107085e-01	ci right 3.126451e-01	k: 274275	n:880000
KS ci ratio: 3.437812e-01	ci left: 1.223887e-04	ci right 1.741778e-04	k: 129	n:880000
C2CD3   880000 perm   581 sec   (1516 perm/sec)   p_kst 1.465909e-04   p_cons 3.116761e-01   p_joint 1.465909e-04

Joint ci ratio: 3.437814e-01	ci left: 1.210135e-04	ci right 1.722208e-04	k: 129	n:890000
Cons ci ratio: 6.174234e-03	ci left: 3.107647e-01	ci right 3.126905e-01	k: 277437	n:890000
KS ci ratio: 3.437814e-01	ci left: 1.210135e-04	ci right 1.722208e-04	k: 129	n:890000
C2CD3   890000 perm   591 sec   (1506 perm/sec)   p_kst 1.449438e-04   p_cons 3.117270e-01   p_joint 1.449438e-04

Joint ci ratio: 3.411670e-01	ci left: 1.217001e-04	ci right 1.727198e-04	k: 131	n:900000
Cons ci ratio: 6.139508e-03	ci left: 3.107931e-01	ci right 3.127081e-01	k: 280575	n:900000
KS ci ratio: 3.411670e-01	ci left: 1.217001e-04	ci right 1.727198e-04	k: 131	n:900000
C2CD3   900000 perm   601 sec   (1497 perm/sec)   p_kst 1.455556e-04   p_cons 3.117500e-01   p_joint 1.455556e-04

Joint ci ratio: 3.411673e-01	ci left: 1.203627e-04	ci right 1.708218e-04	k: 131	n:910000
Cons ci ratio: 6.105251e-03	ci left: 3.108285e-01	ci right 3.127331e-01	k: 283720	n:910000
KS ci ratio: 3.411673e-01	ci left: 1.203627e-04	ci right 1.708218e-04	k: 131	n:910000
C2CD3   910000 perm   612 sec   (1488 perm/sec)   p_kst 1.439560e-04   p_cons 3.117802e-01   p_joint 1.439560e-04

Joint ci ratio: 3.386116e-01	ci left: 1.210428e-04	ci right 1.713238e-04	k: 133	n:920000
Cons ci ratio: 6.072961e-03	ci left: 3.107644e-01	ci right 3.126585e-01	k: 286774	n:920000
KS ci ratio: 3.386116e-01	ci left: 1.210428e-04	ci right 1.713238e-04	k: 133	n:920000
C2CD3   920000 perm   622 sec   (1479 perm/sec)   p_kst 1.445652e-04   p_cons 3.117109e-01   p_joint 1.445652e-04

Joint ci ratio: 3.348834e-01	ci left: 1.226943e-04	ci right 1.729792e-04	k: 136	n:930000
Cons ci ratio: 6.039770e-03	ci left: 3.108016e-01	ci right 3.126855e-01	k: 289921	n:930000
KS ci ratio: 3.348834e-01	ci left: 1.226943e-04	ci right 1.729792e-04	k: 136	n:930000
C2CD3   930000 perm   633 sec   (1470 perm/sec)   p_kst 1.462366e-04   p_cons 3.117430e-01   p_joint 1.462366e-04

Joint ci ratio: 3.336679e-01	ci left: 1.223636e-04	ci right 1.722918e-04	k: 137	n:940000
Cons ci ratio: 6.008250e-03	ci left: 3.107573e-01	ci right 3.126311e-01	k: 292992	n:940000
KS ci ratio: 3.336679e-01	ci left: 1.223636e-04	ci right 1.722918e-04	k: 137	n:940000
C2CD3   940000 perm   643 sec   (1461 perm/sec)   p_kst 1.457447e-04   p_cons 3.116936e-01   p_joint 1.457447e-04

Joint ci ratio: 3.300989e-01	ci left: 1.239704e-04	ci right 1.738982e-04	k: 140	n:950000
Cons ci ratio: 5.976998e-03	ci left: 3.107297e-01	ci right 3.125935e-01	k: 296078	n:950000
KS ci ratio: 3.300989e-01	ci left: 1.239704e-04	ci right 1.738982e-04	k: 140	n:950000
C2CD3   950000 perm   654 sec   (1453 perm/sec)   p_kst 1.473684e-04   p_cons 3.116611e-01   p_joint 1.473684e-04

Joint ci ratio: 3.300991e-01	ci left: 1.226790e-04	ci right 1.720868e-04	k: 140	n:960000
Cons ci ratio: 5.944366e-03	ci left: 3.108370e-01	ci right 3.126912e-01	k: 299293	n:960000
KS ci ratio: 3.300991e-01	ci left: 1.226790e-04	ci right 1.720868e-04	k: 140	n:960000
C2CD3   960000 perm   665 sec   (1444 perm/sec)   p_kst 1.458333e-04   p_cons 3.117635e-01   p_joint 1.458333e-04

Joint ci ratio: 3.255138e-01	ci left: 1.251987e-04	ci right 1.747745e-04	k: 144	n:970000
Cons ci ratio: 5.913442e-03	ci left: 3.108566e-01	ci right 3.127013e-01	k: 302425	n:970000
KS ci ratio: 3.255138e-01	ci left: 1.251987e-04	ci right 1.747745e-04	k: 144	n:970000
C2CD3   970000 perm   676 sec   (1436 perm/sec)   p_kst 1.484536e-04   p_cons 3.117784e-01   p_joint 1.484536e-04

Joint ci ratio: 3.243972e-01	ci left: 1.248584e-04	ci right 1.740945e-04	k: 145	n:980000
Cons ci ratio: 5.882380e-03	ci left: 3.109206e-01	ci right 3.127560e-01	k: 305601	n:980000
KS ci ratio: 3.243972e-01	ci left: 1.248584e-04	ci right 1.740945e-04	k: 145	n:980000
C2CD3   980000 perm   687 sec   (1427 perm/sec)   p_kst 1.479592e-04   p_cons 3.118378e-01   p_joint 1.479592e-04

Joint ci ratio: 3.243974e-01	ci left: 1.235972e-04	ci right 1.723360e-04	k: 145	n:990000
Cons ci ratio: 5.852256e-03	ci left: 3.109501e-01	ci right 3.127762e-01	k: 308744	n:990000
KS ci ratio: 3.243974e-01	ci left: 1.235972e-04	ci right 1.723360e-04	k: 145	n:990000
C2CD3   990000 perm   698 sec   (1419 perm/sec)   p_kst 1.464646e-04   p_cons 3.118626e-01   p_joint 1.464646e-04

Joint ci ratio: 3.243977e-01	ci left: 1.223612e-04	ci right 1.706126e-04	k: 145	n:1000000
Cons ci ratio: 5.822862e-03	ci left: 3.109591e-01	ci right 3.127760e-01	k: 311867	n:1000000
KS ci ratio: 3.243977e-01	ci left: 1.223612e-04	ci right 1.706126e-04	k: 145	n:1000000
C2CD3   1000000 perm   709 sec   (1411 perm/sec)   p_kst 1.450000e-04   p_cons 3.118670e-01   p_joint 1.450000e-04

Joint ci ratio: 3.221982e-01	ci left: 1.229692e-04	ci right 1.710637e-04	k: 147	n:1010000
Cons ci ratio: 5.794294e-03	ci left: 3.109392e-01	ci right 3.127470e-01	k: 314961	n:1010000
KS ci ratio: 3.221982e-01	ci left: 1.229692e-04	ci right 1.710637e-04	k: 147	n:1010000
C2CD3   1010000 perm   720 sec   (1402 perm/sec)   p_kst 1.455446e-04   p_cons 3.118426e-01   p_joint 1.455446e-04

Joint ci ratio: 3.168893e-01	ci left: 1.262725e-04	ci right 1.746803e-04	k: 152	n:1020000
Cons ci ratio: 5.765142e-03	ci left: 3.109941e-01	ci right 3.127932e-01	k: 318131	n:1020000
KS ci ratio: 3.168893e-01	ci left: 1.262725e-04	ci right 1.746803e-04	k: 152	n:1020000
C2CD3   1020000 perm   731 sec   (1394 perm/sec)   p_kst 1.490196e-04   p_cons 3.118931e-01   p_joint 1.490196e-04

Joint ci ratio: 3.148381e-01	ci left: 1.268344e-04	ci right 1.750796e-04	k: 154	n:1030000
Cons ci ratio: 5.737762e-03	ci left: 3.109481e-01	ci right 3.127384e-01	k: 321198	n:1030000
KS ci ratio: 3.148381e-01	ci left: 1.268344e-04	ci right 1.750796e-04	k: 154	n:1030000
C2CD3   1030000 perm   743 sec   (1386 perm/sec)   p_kst 1.495146e-04   p_cons 3.118427e-01   p_joint 1.495146e-04

Joint ci ratio: 3.138275e-01	ci left: 1.265005e-04	ci right 1.744333e-04	k: 155	n:1040000
Cons ci ratio: 5.709795e-03	ci left: 3.109761e-01	ci right 3.127577e-01	k: 324341	n:1040000
KS ci ratio: 3.138275e-01	ci left: 1.265005e-04	ci right 1.744333e-04	k: 155	n:1040000
C2CD3   1040000 perm   754 sec   (1378 perm/sec)   p_kst 1.490385e-04   p_cons 3.118663e-01   p_joint 1.490385e-04

Joint ci ratio: 3.138277e-01	ci left: 1.252958e-04	ci right 1.727720e-04	k: 155	n:1050000
Cons ci ratio: 5.682764e-03	ci left: 3.109635e-01	ci right 3.127366e-01	k: 327442	n:1050000
KS ci ratio: 3.138277e-01	ci left: 1.252958e-04	ci right 1.727720e-04	k: 155	n:1050000
C2CD3   1050000 perm   767 sec   (1370 perm/sec)   p_kst 1.476190e-04   p_cons 3.118495e-01   p_joint 1.476190e-04

Joint ci ratio: 3.138279e-01	ci left: 1.241137e-04	ci right 1.711421e-04	k: 155	n:1060000
Cons ci ratio: 5.655466e-03	ci left: 3.110002e-01	ci right 3.127650e-01	k: 330595	n:1060000
KS ci ratio: 3.138279e-01	ci left: 1.241137e-04	ci right 1.711421e-04	k: 155	n:1060000
C2CD3   1060000 perm   778 sec   (1362 perm/sec)   p_kst 1.462264e-04   p_cons 3.118821e-01   p_joint 1.462264e-04

Joint ci ratio: 3.128270e-01	ci left: 1.238149e-04	ci right 1.705505e-04	k: 156	n:1070000
Cons ci ratio: 5.628938e-03	ci left: 3.110073e-01	ci right 3.127638e-01	k: 333717	n:1070000
KS ci ratio: 3.128270e-01	ci left: 1.238149e-04	ci right 1.705505e-04	k: 156	n:1070000
C2CD3   1070000 perm   790 sec   (1354 perm/sec)   p_kst 1.457944e-04   p_cons 3.118850e-01   p_joint 1.457944e-04

Joint ci ratio: 3.128272e-01	ci left: 1.226684e-04	ci right 1.689713e-04	k: 156	n:1080000
Cons ci ratio: 5.602864e-03	ci left: 3.110078e-01	ci right 3.127561e-01	k: 336832	n:1080000
KS ci ratio: 3.128272e-01	ci left: 1.226684e-04	ci right 1.689713e-04	k: 156	n:1080000
C2CD3   1080000 perm   802 sec   (1346 perm/sec)   p_kst 1.444444e-04   p_cons 3.118815e-01   p_joint 1.444444e-04

Joint ci ratio: 3.118357e-01	ci left: 1.223886e-04	ci right 1.684103e-04	k: 157	n:1090000
Cons ci ratio: 5.577602e-03	ci left: 3.109735e-01	ci right 3.127137e-01	k: 339909	n:1090000
KS ci ratio: 3.118357e-01	ci left: 1.223886e-04	ci right 1.684103e-04	k: 157	n:1090000
C2CD3   1090000 perm   814 sec   (1338 perm/sec)   p_kst 1.440367e-04   p_cons 3.118431e-01   p_joint 1.440367e-04

Joint ci ratio: 3.098805e-01	ci left: 1.229523e-04	ci right 1.688388e-04	k: 159	n:1100000
Cons ci ratio: 5.552643e-03	ci left: 3.109426e-01	ci right 3.126748e-01	k: 342989	n:1100000
KS ci ratio: 3.098805e-01	ci left: 1.229523e-04	ci right 1.688388e-04	k: 159	n:1100000
C2CD3   1100000 perm   827 sec   (1331 perm/sec)   p_kst 1.445455e-04   p_cons 3.118082e-01   p_joint 1.445455e-04

Joint ci ratio: 3.089167e-01	ci left: 1.226756e-04	ci right 1.682884e-04	k: 160	n:1110000
Cons ci ratio: 5.527530e-03	ci left: 3.109500e-01	ci right 3.126744e-01	k: 346111	n:1110000
KS ci ratio: 3.089167e-01	ci left: 1.226756e-04	ci right 1.682884e-04	k: 160	n:1110000
C2CD3   1110000 perm   839 sec   (1323 perm/sec)   p_kst 1.441441e-04   p_cons 3.118117e-01   p_joint 1.441441e-04

Joint ci ratio: 3.070156e-01	ci left: 1.232280e-04	ci right 1.687091e-04	k: 162	n:1120000
Cons ci ratio: 5.503509e-03	ci left: 3.108984e-01	ci right 3.126150e-01	k: 349167	n:1120000
KS ci ratio: 3.070156e-01	ci left: 1.232280e-04	ci right 1.687091e-04	k: 162	n:1120000
C2CD3   1120000 perm   851 sec   (1315 perm/sec)   p_kst 1.446429e-04   p_cons 3.117563e-01   p_joint 1.446429e-04

Joint ci ratio: 3.051492e-01	ci left: 1.237715e-04	ci right 1.691215e-04	k: 164	n:1130000
Cons ci ratio: 5.478522e-03	ci left: 3.109477e-01	ci right 3.126568e-01	k: 352336	n:1130000
KS ci ratio: 3.051492e-01	ci left: 1.237715e-04	ci right 1.691215e-04	k: 164	n:1130000
C2CD3   1130000 perm   864 sec   (1308 perm/sec)   p_kst 1.451327e-04   p_cons 3.118018e-01   p_joint 1.451327e-04

Joint ci ratio: 3.051494e-01	ci left: 1.226858e-04	ci right 1.676380e-04	k: 164	n:1140000
Cons ci ratio: 5.454095e-03	ci left: 3.109786e-01	ci right 3.126802e-01	k: 355485	n:1140000
KS ci ratio: 3.051494e-01	ci left: 1.226858e-04	ci right 1.676380e-04	k: 164	n:1140000
C2CD3   1140000 perm   876 sec   (1301 perm/sec)   p_kst 1.438596e-04   p_cons 3.118289e-01   p_joint 1.438596e-04

Joint ci ratio: 3.033165e-01	ci left: 1.232253e-04	ci right 1.680517e-04	k: 166	n:1150000
Cons ci ratio: 5.429673e-03	ci left: 3.110342e-01	ci right 3.127285e-01	k: 358663	n:1150000
KS ci ratio: 3.033165e-01	ci left: 1.232253e-04	ci right 1.680517e-04	k: 166	n:1150000
C2CD3   1150000 perm   889 sec   (1294 perm/sec)   p_kst 1.443478e-04   p_cons 3.118809e-01   p_joint 1.443478e-04

Joint ci ratio: 3.024125e-01	ci left: 1.229596e-04	ci right 1.675304e-04	k: 167	n:1160000
Cons ci ratio: 5.406315e-03	ci left: 3.110303e-01	ci right 3.127172e-01	k: 361773	n:1160000
KS ci ratio: 3.024125e-01	ci left: 1.229596e-04	ci right 1.675304e-04	k: 167	n:1160000
C2CD3   1160000 perm   901 sec   (1287 perm/sec)   p_kst 1.439655e-04   p_cons 3.118733e-01   p_joint 1.439655e-04

Joint ci ratio: 3.024127e-01	ci left: 1.219087e-04	ci right 1.660985e-04	k: 167	n:1170000
Cons ci ratio: 5.382751e-03	ci left: 3.110666e-01	ci right 3.127463e-01	k: 364930	n:1170000
KS ci ratio: 3.024127e-01	ci left: 1.219087e-04	ci right 1.660985e-04	k: 167	n:1170000
C2CD3   1170000 perm   914 sec   (1280 perm/sec)   p_kst 1.427350e-04   p_cons 3.119060e-01   p_joint 1.427350e-04

Joint ci ratio: 3.015167e-01	ci left: 1.216588e-04	ci right 1.656024e-04	k: 168	n:1180000
Cons ci ratio: 5.360075e-03	ci left: 3.110557e-01	ci right 3.127283e-01	k: 368032	n:1180000
KS ci ratio: 3.015167e-01	ci left: 1.216588e-04	ci right 1.656024e-04	k: 168	n:1180000
C2CD3   1180000 perm   927 sec   (1273 perm/sec)   p_kst 1.423729e-04   p_cons 3.118915e-01   p_joint 1.423729e-04

Joint ci ratio: 2.997482e-01	ci left: 1.221904e-04	ci right 1.660178e-04	k: 170	n:1190000
Cons ci ratio: 5.337045e-03	ci left: 3.110962e-01	ci right 3.127618e-01	k: 371195	n:1190000
KS ci ratio: 2.997482e-01	ci left: 1.221904e-04	ci right 1.660178e-04	k: 170	n:1190000
C2CD3   1190000 perm   940 sec   (1266 perm/sec)   p_kst 1.428571e-04   p_cons 3.119286e-01   p_joint 1.428571e-04

Joint ci ratio: 2.988757e-01	ci left: 1.219429e-04	ci right 1.655300e-04	k: 171	n:1200000
Cons ci ratio: 5.314671e-03	ci left: 3.111070e-01	ci right 3.127656e-01	k: 374323	n:1200000
KS ci ratio: 2.988757e-01	ci left: 1.219429e-04	ci right 1.655300e-04	k: 171	n:1200000
C2CD3   1200000 perm   953 sec   (1259 perm/sec)   p_kst 1.425000e-04   p_cons 3.119358e-01   p_joint 1.425000e-04

Joint ci ratio: 2.963026e-01	ci left: 1.232294e-04	ci right 1.668259e-04	k: 174	n:1210000
Cons ci ratio: 5.292546e-03	ci left: 3.111200e-01	ci right 3.127718e-01	k: 377454	n:1210000
KS ci ratio: 2.963026e-01	ci left: 1.232294e-04	ci right 1.668259e-04	k: 174	n:1210000
C2CD3   1210000 perm   966 sec   (1252 perm/sec)   p_kst 1.438017e-04   p_cons 3.119455e-01   p_joint 1.438017e-04

Joint ci ratio: 2.937949e-01	ci left: 1.244964e-04	ci right 1.680989e-04	k: 177	n:1220000
Cons ci ratio: 5.270795e-03	ci left: 3.111247e-01	ci right 3.127697e-01	k: 380575	n:1220000
KS ci ratio: 2.937949e-01	ci left: 1.244964e-04	ci right 1.680989e-04	k: 177	n:1220000
C2CD3   1220000 perm   979 sec   (1246 perm/sec)   p_kst 1.450820e-04   p_cons 3.119467e-01   p_joint 1.450820e-04

Joint ci ratio: 2.929731e-01	ci left: 1.242374e-04	ci right 1.676050e-04	k: 178	n:1230000
Cons ci ratio: 5.248823e-03	ci left: 3.111691e-01	ci right 3.128074e-01	k: 383745	n:1230000
KS ci ratio: 2.929731e-01	ci left: 1.242374e-04	ci right 1.676050e-04	k: 178	n:1230000
C2CD3   1230000 perm   993 sec   (1239 perm/sec)   p_kst 1.447154e-04   p_cons 3.119878e-01   p_joint 1.447154e-04

Joint ci ratio: 2.897532e-01	ci left: 1.262256e-04	ci right 1.697142e-04	k: 182	n:1240000
Cons ci ratio: 5.226868e-03	ci left: 3.112337e-01	ci right 3.128655e-01	k: 386941	n:1240000
KS ci ratio: 2.897532e-01	ci left: 1.262256e-04	ci right 1.697142e-04	k: 182	n:1240000
C2CD3   1240000 perm   1006 sec   (1232 perm/sec)   p_kst 1.467742e-04   p_cons 3.120492e-01   p_joint 1.467742e-04

Joint ci ratio: 2.889648e-01	ci left: 1.259577e-04	ci right 1.692144e-04	k: 183	n:1250000
Cons ci ratio: 5.206205e-03	ci left: 3.112134e-01	ci right 3.128387e-01	k: 390032	n:1250000
KS ci ratio: 2.889648e-01	ci left: 1.259577e-04	ci right 1.692144e-04	k: 183	n:1250000
C2CD3   1250000 perm   1019 sec   (1226 perm/sec)   p_kst 1.464000e-04   p_cons 3.120256e-01   p_joint 1.464000e-04

Joint ci ratio: 2.881829e-01	ci left: 1.256942e-04	ci right 1.687223e-04	k: 184	n:1260000
Cons ci ratio: 5.185670e-03	ci left: 3.112030e-01	ci right 3.128217e-01	k: 393135	n:1260000
KS ci ratio: 2.881829e-01	ci left: 1.256942e-04	ci right 1.687223e-04	k: 184	n:1260000
C2CD3   1260000 perm   1033 sec   (1220 perm/sec)   p_kst 1.460317e-04   p_cons 3.120119e-01   p_joint 1.460317e-04

Joint ci ratio: 2.843653e-01	ci left: 1.283589e-04	ci right 1.716127e-04	k: 189	n:1270000
Cons ci ratio: 5.165338e-03	ci left: 3.111958e-01	ci right 3.128082e-01	k: 396242	n:1270000
KS ci ratio: 2.843653e-01	ci left: 1.283589e-04	ci right 1.716127e-04	k: 189	n:1270000
C2CD3   1270000 perm   1046 sec   (1214 perm/sec)   p_kst 1.488189e-04   p_cons 3.120016e-01   p_joint 1.488189e-04

Joint ci ratio: 2.821464e-01	ci left: 1.295334e-04	ci right 1.727817e-04	k: 192	n:1280000
Cons ci ratio: 5.145683e-03	ci left: 3.111521e-01	ci right 3.127581e-01	k: 399302	n:1280000
KS ci ratio: 2.821464e-01	ci left: 1.295334e-04	ci right 1.727817e-04	k: 192	n:1280000
C2CD3   1280000 perm   1060 sec   (1208 perm/sec)   p_kst 1.500000e-04   p_cons 3.119547e-01   p_joint 1.500000e-04

Joint ci ratio: 2.806957e-01	ci left: 1.299703e-04	ci right 1.731018e-04	k: 194	n:1290000
Cons ci ratio: 5.125798e-03	ci left: 3.111471e-01	ci right 3.127468e-01	k: 402411	n:1290000
KS ci ratio: 2.806957e-01	ci left: 1.299703e-04	ci right 1.731018e-04	k: 194	n:1290000
C2CD3   1290000 perm   1073 sec   (1202 perm/sec)   p_kst 1.503876e-04   p_cons 3.119465e-01   p_joint 1.503876e-04

Joint ci ratio: 2.792672e-01	ci left: 1.304010e-04	ci right 1.734165e-04	k: 196	n:1300000
Cons ci ratio: 5.106397e-03	ci left: 3.111206e-01	ci right 3.127141e-01	k: 405492	n:1300000
KS ci ratio: 2.792672e-01	ci left: 1.304010e-04	ci right 1.734165e-04	k: 196	n:1300000
C2CD3   1300000 perm   1087 sec   (1196 perm/sec)   p_kst 1.507692e-04   p_cons 3.119169e-01   p_joint 1.507692e-04

Joint ci ratio: 2.757889e-01	ci left: 1.329568e-04	ci right 1.761744e-04	k: 201	n:1310000
Cons ci ratio: 5.087278e-03	ci left: 3.110892e-01	ci right 3.126765e-01	k: 408566	n:1310000
KS ci ratio: 2.757889e-01	ci left: 1.329568e-04	ci right 1.761744e-04	k: 201	n:1310000
C2CD3   1310000 perm   1101 sec   (1190 perm/sec)   p_kst 1.534351e-04   p_cons 3.118824e-01   p_joint 1.534351e-04

Joint ci ratio: 2.751088e-01	ci left: 1.326548e-04	ci right 1.756495e-04	k: 202	n:1320000
Cons ci ratio: 5.067970e-03	ci left: 3.110923e-01	ci right 3.126737e-01	k: 411685	n:1320000
KS ci ratio: 2.751088e-01	ci left: 1.326548e-04	ci right 1.756495e-04	k: 202	n:1320000
C2CD3   1320000 perm   1115 sec   (1184 perm/sec)   p_kst 1.530303e-04   p_cons 3.118826e-01   p_joint 1.530303e-04

Joint ci ratio: 2.744337e-01	ci left: 1.323574e-04	ci right 1.751324e-04	k: 203	n:1330000
Cons ci ratio: 5.049703e-03	ci left: 3.110255e-01	ci right 3.126008e-01	k: 414711	n:1330000
KS ci ratio: 2.744337e-01	ci left: 1.323574e-04	ci right 1.751324e-04	k: 203	n:1330000
C2CD3   1330000 perm   1129 sec   (1178 perm/sec)   p_kst 1.526316e-04   p_cons 3.118128e-01   p_joint 1.526316e-04

Joint ci ratio: 2.737636e-01	ci left: 1.320647e-04	ci right 1.746228e-04	k: 204	n:1340000
Cons ci ratio: 5.030407e-03	ci left: 3.110642e-01	ci right 3.126336e-01	k: 417877	n:1340000
KS ci ratio: 2.737636e-01	ci left: 1.320647e-04	ci right 1.746228e-04	k: 204	n:1340000
C2CD3   1340000 perm   1143 sec   (1172 perm/sec)   p_kst 1.522388e-04   p_cons 3.118485e-01   p_joint 1.522388e-04

Joint ci ratio: 2.717821e-01	ci left: 1.331567e-04	ci right 1.757032e-04	k: 207	n:1350000
Cons ci ratio: 5.011010e-03	ci left: 3.111297e-01	ci right 3.126934e-01	k: 421080	n:1350000
KS ci ratio: 2.717821e-01	ci left: 1.331567e-04	ci right 1.757032e-04	k: 207	n:1350000
C2CD3   1350000 perm   1157 sec   (1167 perm/sec)   p_kst 1.533333e-04   p_cons 3.119111e-01   p_joint 1.533333e-04

Joint ci ratio: 2.704847e-01	ci left: 1.335482e-04	ci right 1.759815e-04	k: 209	n:1360000
Cons ci ratio: 4.820074e-03	ci left: 3.264100e-01	ci right 3.279878e-01	k: 444990	n:1360000
KS ci ratio: 2.704847e-01	ci left: 1.335482e-04	ci right 1.759815e-04	k: 209	n:1360000
C2CD3   1360000 perm   1172 sec   (1161 perm/sec)   p_kst 1.536765e-04   p_cons 3.271985e-01   p_joint 1.536765e-04

Joint ci ratio: 2.692058e-01	ci left: 1.339345e-04	ci right 1.762554e-04	k: 211	n:1370000
Cons ci ratio: 4.802243e-03	ci left: 3.264318e-01	ci right 3.280039e-01	k: 448288	n:1370000
KS ci ratio: 2.692058e-01	ci left: 1.339345e-04	ci right 1.762554e-04	k: 211	n:1370000
C2CD3   1370000 perm   1186 sec   (1155 perm/sec)   p_kst 1.540146e-04   p_cons 3.272175e-01   p_joint 1.540146e-04

Joint ci ratio: 2.679448e-01	ci left: 1.343157e-04	ci right 1.765248e-04	k: 213	n:1380000
Cons ci ratio: 4.784467e-03	ci left: 3.264664e-01	ci right 3.280328e-01	k: 451604	n:1380000
KS ci ratio: 2.679448e-01	ci left: 1.343157e-04	ci right 1.765248e-04	k: 213	n:1380000
C2CD3   1380000 perm   1200 sec   (1150 perm/sec)   p_kst 1.543478e-04   p_cons 3.272493e-01   p_joint 1.543478e-04

Joint ci ratio: 2.673210e-01	ci left: 1.340206e-04	ci right 1.760224e-04	k: 214	n:1390000
Cons ci ratio: 4.766567e-03	ci left: 3.265300e-01	ci right 3.280909e-01	k: 454961	n:1390000
KS ci ratio: 2.673210e-01	ci left: 1.340206e-04	ci right 1.760224e-04	k: 214	n:1390000
C2CD3   1390000 perm   1215 sec   (1144 perm/sec)   p_kst 1.539568e-04   p_cons 3.273101e-01   p_joint 1.539568e-04

Joint ci ratio: 2.667015e-01	ci left: 1.337297e-04	ci right 1.755271e-04	k: 215	n:1400000
Cons ci ratio: 4.749637e-03	ci left: 3.265213e-01	ci right 3.280765e-01	k: 458218	n:1400000
KS ci ratio: 2.667015e-01	ci left: 1.337297e-04	ci right 1.755271e-04	k: 215	n:1400000
C2CD3   1400000 perm   1229 sec   (1139 perm/sec)   p_kst 1.535714e-04   p_cons 3.272986e-01   p_joint 1.535714e-04

Joint ci ratio: 2.667017e-01	ci left: 1.327813e-04	ci right 1.742822e-04	k: 215	n:1410000
Cons ci ratio: 4.732780e-03	ci left: 3.265227e-01	ci right 3.280724e-01	k: 461489	n:1410000
KS ci ratio: 2.667017e-01	ci left: 1.327813e-04	ci right 1.742822e-04	k: 215	n:1410000
C2CD3   1410000 perm   1244 sec   (1134 perm/sec)   p_kst 1.524823e-04   p_cons 3.272972e-01   p_joint 1.524823e-04

Joint ci ratio: 2.667018e-01	ci left: 1.318462e-04	ci right 1.730549e-04	k: 215	n:1420000
Cons ci ratio: 4.715905e-03	ci left: 3.265423e-01	ci right 3.280866e-01	k: 464786	n:1420000
KS ci ratio: 2.667018e-01	ci left: 1.318462e-04	ci right 1.730549e-04	k: 215	n:1420000
C2CD3   1420000 perm   1259 sec   (1128 perm/sec)   p_kst 1.514085e-04   p_cons 3.273141e-01   p_joint 1.514085e-04

Joint ci ratio: 2.648687e-01	ci left: 1.328823e-04	ci right 1.740821e-04	k: 218	n:1430000
Cons ci ratio: 4.699940e-03	ci left: 3.264932e-01	ci right 3.280320e-01	k: 467985	n:1430000
KS ci ratio: 2.648687e-01	ci left: 1.328823e-04	ci right 1.740821e-04	k: 218	n:1430000
C2CD3   1430000 perm   1274 sec   (1123 perm/sec)   p_kst 1.524476e-04   p_cons 3.272622e-01   p_joint 1.524476e-04

Joint ci ratio: 2.642661e-01	ci left: 1.326079e-04	ci right 1.736136e-04	k: 219	n:1440000
Cons ci ratio: 4.683220e-03	ci left: 3.265308e-01	ci right 3.280643e-01	k: 471308	n:1440000
KS ci ratio: 2.642661e-01	ci left: 1.326079e-04	ci right 1.736136e-04	k: 219	n:1440000
C2CD3   1440000 perm   1289 sec   (1117 perm/sec)   p_kst 1.520833e-04   p_cons 3.272972e-01   p_joint 1.520833e-04

Joint ci ratio: 2.636675e-01	ci left: 1.323374e-04	ci right 1.731514e-04	k: 220	n:1450000
Cons ci ratio: 4.667065e-03	ci left: 3.265314e-01	ci right 3.280596e-01	k: 474578	n:1450000
KS ci ratio: 2.636675e-01	ci left: 1.323374e-04	ci right 1.731514e-04	k: 220	n:1450000
C2CD3   1450000 perm   1304 sec   (1112 perm/sec)   p_kst 1.517241e-04   p_cons 3.272952e-01   p_joint 1.517241e-04

Joint ci ratio: 2.630731e-01	ci left: 1.320707e-04	ci right 1.726955e-04	k: 221	n:1460000
Cons ci ratio: 4.651467e-03	ci left: 3.264951e-01	ci right 3.280179e-01	k: 477794	n:1460000
KS ci ratio: 2.630731e-01	ci left: 1.320707e-04	ci right 1.726955e-04	k: 221	n:1460000
C2CD3   1460000 perm   1319 sec   (1107 perm/sec)   p_kst 1.513699e-04   p_cons 3.272562e-01   p_joint 1.513699e-04

Joint ci ratio: 2.613132e-01	ci left: 1.330790e-04	ci right 1.736953e-04	k: 224	n:1470000
Cons ci ratio: 4.635587e-03	ci left: 3.265007e-01	ci right 3.280184e-01	k: 481071	n:1470000
KS ci ratio: 2.613132e-01	ci left: 1.330790e-04	ci right 1.736953e-04	k: 224	n:1470000
C2CD3   1470000 perm   1334 sec   (1102 perm/sec)   p_kst 1.523810e-04   p_cons 3.272592e-01   p_joint 1.523810e-04

Joint ci ratio: 2.607345e-01	ci left: 1.328113e-04	ci right 1.732415e-04	k: 225	n:1480000
Cons ci ratio: 4.620003e-03	ci left: 3.264934e-01	ci right 3.280059e-01	k: 484329	n:1480000
KS ci ratio: 2.607345e-01	ci left: 1.328113e-04	ci right 1.732415e-04	k: 225	n:1480000
C2CD3   1480000 perm   1350 sec   (1097 perm/sec)   p_kst 1.520270e-04   p_cons 3.272493e-01   p_joint 1.520270e-04

Joint ci ratio: 2.584571e-01	ci left: 1.344298e-04	ci right 1.749376e-04	k: 229	n:1490000
Cons ci ratio: 4.604743e-03	ci left: 3.264701e-01	ci right 3.279775e-01	k: 487563	n:1490000
KS ci ratio: 2.584571e-01	ci left: 1.344298e-04	ci right 1.749376e-04	k: 229	n:1490000
C2CD3   1490000 perm   1365 sec   (1092 perm/sec)   p_kst 1.536913e-04   p_cons 3.272235e-01   p_joint 1.536913e-04

Joint ci ratio: 2.578971e-01	ci left: 1.341571e-04	ci right 1.744811e-04	k: 230	n:1500000
Cons ci ratio: 4.589697e-03	ci left: 3.264412e-01	ci right 3.279435e-01	k: 490788	n:1500000
KS ci ratio: 2.578971e-01	ci left: 1.341571e-04	ci right 1.744811e-04	k: 230	n:1500000
C2CD3   1500000 perm   1380 sec   (1087 perm/sec)   p_kst 1.533333e-04   p_cons 3.271920e-01   p_joint 1.533333e-04

Joint ci ratio: 2.578973e-01	ci left: 1.332687e-04	ci right 1.733256e-04	k: 230	n:1510000
Cons ci ratio: 4.574501e-03	ci left: 3.264411e-01	ci right 3.279384e-01	k: 494056	n:1510000
KS ci ratio: 2.578973e-01	ci left: 1.332687e-04	ci right 1.733256e-04	k: 230	n:1510000
C2CD3   1510000 perm   1396 sec   (1082 perm/sec)   p_kst 1.523179e-04   p_cons 3.271894e-01   p_joint 1.523179e-04

Joint ci ratio: 2.573409e-01	ci left: 1.330073e-04	ci right 1.728856e-04	k: 231	n:1520000
Cons ci ratio: 4.559332e-03	ci left: 3.264528e-01	ci right 3.279452e-01	k: 497342	n:1520000
KS ci ratio: 2.573409e-01	ci left: 1.330073e-04	ci right 1.728856e-04	k: 231	n:1520000
C2CD3   1520000 perm   1412 sec   (1076 perm/sec)   p_kst 1.519737e-04   p_cons 3.271987e-01   p_joint 1.519737e-04

Joint ci ratio: 2.567881e-01	ci left: 1.327495e-04	ci right 1.724512e-04	k: 232	n:1530000
Cons ci ratio: 4.543842e-03	ci left: 3.265101e-01	ci right 3.279977e-01	k: 500698	n:1530000
KS ci ratio: 2.567881e-01	ci left: 1.327495e-04	ci right 1.724512e-04	k: 232	n:1530000
C2CD3   1530000 perm   1428 sec   (1072 perm/sec)   p_kst 1.516340e-04   p_cons 3.272536e-01   p_joint 1.516340e-04

Joint ci ratio: 2.556930e-01	ci left: 1.331028e-04	ci right 1.727134e-04	k: 234	n:1540000
Cons ci ratio: 4.528942e-03	ci left: 3.265245e-01	ci right 3.280073e-01	k: 503989	n:1540000
KS ci ratio: 2.556930e-01	ci left: 1.331028e-04	ci right 1.727134e-04	k: 234	n:1540000
C2CD3   1540000 perm   1445 sec   (1066 perm/sec)   p_kst 1.519481e-04   p_cons 3.272656e-01   p_joint 1.519481e-04

Joint ci ratio: 2.556931e-01	ci left: 1.322440e-04	ci right 1.715991e-04	k: 234	n:1550000
Cons ci ratio: 4.514696e-03	ci left: 3.264891e-01	ci right 3.279670e-01	k: 507203	n:1550000
KS ci ratio: 2.556931e-01	ci left: 1.322440e-04	ci right 1.715991e-04	k: 234	n:1550000
C2CD3   1550000 perm   1461 sec   (1061 perm/sec)   p_kst 1.509677e-04   p_cons 3.272277e-01   p_joint 1.509677e-04

Joint ci ratio: 2.540764e-01	ci left: 1.331966e-04	ci right 1.725447e-04	k: 237	n:1560000
Cons ci ratio: 4.500487e-03	ci left: 3.264637e-01	ci right 3.279369e-01	k: 510432	n:1560000
KS ci ratio: 2.540764e-01	ci left: 1.331966e-04	ci right 1.725447e-04	k: 237	n:1560000
C2CD3   1560000 perm   1477 sec   (1056 perm/sec)   p_kst 1.519231e-04   p_cons 3.272000e-01   p_joint 1.519231e-04

Joint ci ratio: 2.535443e-01	ci left: 1.329446e-04	ci right 1.721231e-04	k: 238	n:1570000
Cons ci ratio: 4.486163e-03	ci left: 3.264629e-01	ci right 3.279314e-01	k: 513699	n:1570000
KS ci ratio: 2.535443e-01	ci left: 1.329446e-04	ci right 1.721231e-04	k: 238	n:1570000
C2CD3   1570000 perm   1493 sec   (1051 perm/sec)   p_kst 1.515924e-04   p_cons 3.271968e-01   p_joint 1.515924e-04

Joint ci ratio: 2.524901e-01	ci left: 1.332887e-04	ci right 1.723796e-04	k: 240	n:1580000
Cons ci ratio: 4.472163e-03	ci left: 3.264437e-01	ci right 3.279075e-01	k: 516937	n:1580000
KS ci ratio: 2.524901e-01	ci left: 1.332887e-04	ci right 1.723796e-04	k: 240	n:1580000
C2CD3   1580000 perm   1509 sec   (1047 perm/sec)   p_kst 1.518987e-04   p_cons 3.271753e-01   p_joint 1.518987e-04

Joint ci ratio: 2.519679e-01	ci left: 1.330396e-04	ci right 1.719641e-04	k: 241	n:1590000
Cons ci ratio: 4.458400e-03	ci left: 3.264141e-01	ci right 3.278733e-01	k: 520158	n:1590000
KS ci ratio: 2.519679e-01	ci left: 1.330396e-04	ci right 1.719641e-04	k: 241	n:1590000
C2CD3   1590000 perm   1527 sec   (1042 perm/sec)   p_kst 1.515723e-04   p_cons 3.271434e-01   p_joint 1.515723e-04

Joint ci ratio: 2.514489e-01	ci left: 1.327937e-04	ci right 1.715537e-04	k: 242	n:1600000
Cons ci ratio: 4.444424e-03	ci left: 3.264187e-01	ci right 3.278732e-01	k: 523433	n:1600000
KS ci ratio: 2.514489e-01	ci left: 1.327937e-04	ci right 1.715537e-04	k: 242	n:1600000
C2CD3   1600000 perm   1543 sec   (1037 perm/sec)   p_kst 1.512500e-04   p_cons 3.271456e-01   p_joint 1.512500e-04

Joint ci ratio: 2.509332e-01	ci left: 1.325509e-04	ci right 1.711483e-04	k: 243	n:1610000
Cons ci ratio: 4.430340e-03	ci left: 3.264467e-01	ci right 3.278968e-01	k: 526746	n:1610000
KS ci ratio: 2.509332e-01	ci left: 1.325509e-04	ci right 1.711483e-04	k: 243	n:1610000
C2CD3   1610000 perm   1559 sec   (1032 perm/sec)   p_kst 1.509317e-04   p_cons 3.271714e-01   p_joint 1.509317e-04

Joint ci ratio: 2.489011e-01	ci left: 1.340472e-04	ci right 1.727152e-04	k: 247	n:1620000
Cons ci ratio: 4.416711e-03	ci left: 3.264423e-01	ci right 3.278879e-01	k: 530007	n:1620000
KS ci ratio: 2.489011e-01	ci left: 1.340472e-04	ci right 1.727152e-04	k: 247	n:1620000
C2CD3   1620000 perm   1576 sec   (1028 perm/sec)   p_kst 1.524691e-04   p_cons 3.271648e-01   p_joint 1.524691e-04

Joint ci ratio: 2.479035e-01	ci left: 1.343755e-04	ci right 1.729588e-04	k: 249	n:1630000
Cons ci ratio: 4.403557e-03	ci left: 3.264031e-01	ci right 3.278442e-01	k: 533211	n:1630000
KS ci ratio: 2.479035e-01	ci left: 1.343755e-04	ci right 1.729588e-04	k: 249	n:1630000
C2CD3   1630000 perm   1593 sec   (1024 perm/sec)   p_kst 1.527607e-04   p_cons 3.271233e-01   p_joint 1.527607e-04

Joint ci ratio: 2.469177e-01	ci left: 1.347000e-04	ci right 1.731992e-04	k: 251	n:1640000
Cons ci ratio: 4.389900e-03	ci left: 3.264265e-01	ci right 3.278632e-01	k: 536517	n:1640000
KS ci ratio: 2.469177e-01	ci left: 1.347000e-04	ci right 1.731992e-04	k: 251	n:1640000
C2CD3   1640000 perm   1609 sec   (1019 perm/sec)   p_kst 1.530488e-04   p_cons 3.271445e-01   p_joint 1.530488e-04

Joint ci ratio: 2.464293e-01	ci left: 1.344522e-04	ci right 1.727929e-04	k: 252	n:1650000
Cons ci ratio: 4.376562e-03	ci left: 3.264302e-01	ci right 3.278625e-01	k: 539791	n:1650000
KS ci ratio: 2.464293e-01	ci left: 1.344522e-04	ci right 1.727929e-04	k: 252	n:1650000
C2CD3   1650000 perm   1626 sec   (1015 perm/sec)   p_kst 1.527273e-04   p_cons 3.271461e-01   p_joint 1.527273e-04

Joint ci ratio: 2.464294e-01	ci left: 1.336423e-04	ci right 1.717520e-04	k: 252	n:1660000
Cons ci ratio: 4.363314e-03	ci left: 3.264369e-01	ci right 3.278649e-01	k: 543070	n:1660000
KS ci ratio: 2.464294e-01	ci left: 1.336423e-04	ci right 1.717520e-04	k: 252	n:1660000
C2CD3   1660000 perm   1643 sec   (1010 perm/sec)   p_kst 1.518072e-04   p_cons 3.271506e-01   p_joint 1.518072e-04

Joint ci ratio: 2.454611e-01	ci left: 1.339658e-04	ci right 1.719948e-04	k: 254	n:1670000
Cons ci ratio: 4.350234e-03	ci left: 3.264387e-01	ci right 3.278625e-01	k: 546341	n:1670000
KS ci ratio: 2.454611e-01	ci left: 1.339658e-04	ci right 1.719948e-04	k: 254	n:1670000
C2CD3   1670000 perm   1660 sec   (1006 perm/sec)   p_kst 1.520958e-04   p_cons 3.271503e-01   p_joint 1.520958e-04

Joint ci ratio: 2.454612e-01	ci left: 1.331684e-04	ci right 1.709711e-04	k: 254	n:1680000
Cons ci ratio: 4.337147e-03	ci left: 3.264530e-01	ci right 3.278726e-01	k: 549633	n:1680000
KS ci ratio: 2.454612e-01	ci left: 1.331684e-04	ci right 1.709711e-04	k: 254	n:1680000
C2CD3   1680000 perm   1677 sec   (1002 perm/sec)   p_kst 1.511905e-04   p_cons 3.271625e-01   p_joint 1.511905e-04

Joint ci ratio: 2.454613e-01	ci left: 1.323804e-04	ci right 1.699594e-04	k: 254	n:1690000
Cons ci ratio: 4.324597e-03	ci left: 3.264246e-01	ci right 3.278399e-01	k: 552853	n:1690000
KS ci ratio: 2.454613e-01	ci left: 1.323804e-04	ci right 1.699594e-04	k: 254	n:1690000
C2CD3   1690000 perm   1695 sec   (997 perm/sec)   p_kst 1.502959e-04   p_cons 3.271320e-01   p_joint 1.502959e-04

Joint ci ratio: 2.435583e-01	ci left: 1.338105e-04	ci right 1.714565e-04	k: 258	n:1700000
Cons ci ratio: 4.311808e-03	ci left: 3.264318e-01	ci right 3.278429e-01	k: 556133	n:1700000
KS ci ratio: 2.435583e-01	ci left: 1.338105e-04	ci right 1.714565e-04	k: 258	n:1700000
C2CD3   1700000 perm   1713 sec   (992 perm/sec)   p_kst 1.517647e-04   p_cons 3.271371e-01   p_joint 1.517647e-04

Joint ci ratio: 2.426233e-01	ci left: 1.341264e-04	ci right 1.716945e-04	k: 260	n:1710000
Cons ci ratio: 4.298482e-03	ci left: 3.265055e-01	ci right 3.279126e-01	k: 559527	n:1710000
KS ci ratio: 2.426233e-01	ci left: 1.341264e-04	ci right 1.716945e-04	k: 260	n:1710000
C2CD3   1710000 perm   1731 sec   (988 perm/sec)   p_kst 1.520468e-04   p_cons 3.272088e-01   p_joint 1.520468e-04

Joint ci ratio: 2.412407e-01	ci left: 1.349850e-04	ci right 1.725460e-04	k: 263	n:1720000
Cons ci ratio: 4.285233e-03	ci left: 3.265831e-01	ci right 3.279861e-01	k: 562929	n:1720000
KS ci ratio: 2.412407e-01	ci left: 1.349850e-04	ci right 1.725460e-04	k: 263	n:1720000
C2CD3   1720000 perm   1749 sec   (984 perm/sec)   p_kst 1.529070e-04   p_cons 3.272843e-01   p_joint 1.529070e-04

Joint ci ratio: 2.412408e-01	ci left: 1.342047e-04	ci right 1.715486e-04	k: 263	n:1730000
Cons ci ratio: 4.272958e-03	ci left: 3.265719e-01	ci right 3.279709e-01	k: 566179	n:1730000
KS ci ratio: 2.412408e-01	ci left: 1.342047e-04	ci right 1.715486e-04	k: 263	n:1730000
C2CD3   1730000 perm   1767 sec   (979 perm/sec)   p_kst 1.520231e-04   p_cons 3.272711e-01   p_joint 1.520231e-04

Joint ci ratio: 2.403322e-01	ci left: 1.345135e-04	ci right 1.717813e-04	k: 265	n:1740000
Cons ci ratio: 4.260694e-03	ci left: 3.265706e-01	ci right 3.279656e-01	k: 569446	n:1740000
KS ci ratio: 2.403322e-01	ci left: 1.345135e-04	ci right 1.717813e-04	k: 265	n:1740000
C2CD3   1740000 perm   1785 sec   (975 perm/sec)   p_kst 1.522989e-04   p_cons 3.272678e-01   p_joint 1.522989e-04

Joint ci ratio: 2.403323e-01	ci left: 1.337449e-04	ci right 1.707997e-04	k: 265	n:1750000
Cons ci ratio: 4.248595e-03	ci left: 3.265631e-01	ci right 3.279540e-01	k: 572702	n:1750000
KS ci ratio: 2.403323e-01	ci left: 1.337449e-04	ci right 1.707997e-04	k: 265	n:1750000
C2CD3   1750000 perm   1802 sec   (971 perm/sec)   p_kst 1.514286e-04   p_cons 3.272583e-01   p_joint 1.514286e-04

Joint ci ratio: 2.403324e-01	ci left: 1.329850e-04	ci right 1.698293e-04	k: 265	n:1760000
Cons ci ratio: 4.236446e-03	ci left: 3.265716e-01	ci right 3.279585e-01	k: 575986	n:1760000
KS ci ratio: 2.403324e-01	ci left: 1.329850e-04	ci right 1.698293e-04	k: 265	n:1760000
C2CD3   1760000 perm   1821 sec   (967 perm/sec)   p_kst 1.505682e-04   p_cons 3.272648e-01   p_joint 1.505682e-04

Joint ci ratio: 2.389884e-01	ci left: 1.338268e-04	ci right 1.706663e-04	k: 268	n:1770000
Cons ci ratio: 4.224486e-03	ci left: 3.265709e-01	ci right 3.279540e-01	k: 579254	n:1770000
KS ci ratio: 2.389884e-01	ci left: 1.338268e-04	ci right 1.706663e-04	k: 268	n:1770000
C2CD3   1770000 perm   1839 sec   (963 perm/sec)   p_kst 1.514124e-04   p_cons 3.272621e-01   p_joint 1.514124e-04

Joint ci ratio: 2.385454e-01	ci left: 1.336031e-04	ci right 1.703028e-04	k: 269	n:1780000
Cons ci ratio: 4.212424e-03	ci left: 3.265916e-01	ci right 3.279708e-01	k: 582560	n:1780000
KS ci ratio: 2.385454e-01	ci left: 1.336031e-04	ci right 1.703028e-04	k: 269	n:1780000
C2CD3   1780000 perm   1857 sec   (958 perm/sec)   p_kst 1.511236e-04   p_cons 3.272809e-01   p_joint 1.511236e-04

Joint ci ratio: 2.385455e-01	ci left: 1.328567e-04	ci right 1.693514e-04	k: 269	n:1790000
Cons ci ratio: 4.200848e-03	ci left: 3.265718e-01	ci right 3.279471e-01	k: 585794	n:1790000
KS ci ratio: 2.385455e-01	ci left: 1.328567e-04	ci right 1.693514e-04	k: 269	n:1790000
C2CD3   1790000 perm   1876 sec   (954 perm/sec)   p_kst 1.502793e-04   p_cons 3.272592e-01   p_joint 1.502793e-04

Joint ci ratio: 2.385456e-01	ci left: 1.321187e-04	ci right 1.684106e-04	k: 269	n:1800000
Cons ci ratio: 4.189292e-03	ci left: 3.265601e-01	ci right 3.279316e-01	k: 589042	n:1800000
KS ci ratio: 2.385456e-01	ci left: 1.321187e-04	ci right 1.684106e-04	k: 269	n:1800000
C2CD3   1800000 perm   1894 sec   (951 perm/sec)   p_kst 1.494444e-04   p_cons 3.272456e-01   p_joint 1.494444e-04

Joint ci ratio: 2.376670e-01	ci left: 1.324278e-04	ci right 1.686509e-04	k: 271	n:1810000
Cons ci ratio: 4.177769e-03	ci left: 3.265551e-01	ci right 3.279228e-01	k: 592302	n:1810000
KS ci ratio: 2.376670e-01	ci left: 1.324278e-04	ci right 1.686509e-04	k: 271	n:1810000
C2CD3   1810000 perm   1912 sec   (947 perm/sec)   p_kst 1.497238e-04   p_cons 3.272387e-01   p_joint 1.497238e-04

Joint ci ratio: 2.376671e-01	ci left: 1.317001e-04	ci right 1.677243e-04	k: 271	n:1820000
Cons ci ratio: 4.166694e-03	ci left: 3.265129e-01	ci right 3.278767e-01	k: 595494	n:1820000
KS ci ratio: 2.376671e-01	ci left: 1.317001e-04	ci right 1.677243e-04	k: 271	n:1820000
C2CD3   1820000 perm   1930 sec   (943 perm/sec)   p_kst 1.489011e-04   p_cons 3.271945e-01   p_joint 1.489011e-04

Joint ci ratio: 2.376672e-01	ci left: 1.309805e-04	ci right 1.668077e-04	k: 271	n:1830000
Cons ci ratio: 4.155304e-03	ci left: 3.265137e-01	ci right 3.278738e-01	k: 598764	n:1830000
KS ci ratio: 2.376672e-01	ci left: 1.309805e-04	ci right 1.668077e-04	k: 271	n:1830000
C2CD3   1830000 perm   1949 sec   (939 perm/sec)   p_kst 1.480874e-04   p_cons 3.271934e-01   p_joint 1.480874e-04

Joint ci ratio: 2.376673e-01	ci left: 1.302686e-04	ci right 1.659012e-04	k: 271	n:1840000
Cons ci ratio: 4.144283e-03	ci left: 3.264851e-01	ci right 3.278415e-01	k: 601980	n:1840000
KS ci ratio: 2.376673e-01	ci left: 1.302686e-04	ci right 1.659012e-04	k: 271	n:1840000
C2CD3   1840000 perm   1967 sec   (935 perm/sec)   p_kst 1.472826e-04   p_cons 3.271630e-01   p_joint 1.472826e-04

Joint ci ratio: 2.376674e-01	ci left: 1.295644e-04	ci right 1.650044e-04	k: 271	n:1850000
Cons ci ratio: 4.132918e-03	ci left: 3.265028e-01	ci right 3.278555e-01	k: 605281	n:1850000
KS ci ratio: 2.376674e-01	ci left: 1.295644e-04	ci right 1.650044e-04	k: 271	n:1850000
C2CD3   1850000 perm   1986 sec   (932 perm/sec)   p_kst 1.464865e-04   p_cons 3.271789e-01   p_joint 1.464865e-04

Joint ci ratio: 2.376675e-01	ci left: 1.288679e-04	ci right 1.641173e-04	k: 271	n:1860000
Cons ci ratio: 4.121707e-03	ci left: 3.265139e-01	ci right 3.278630e-01	k: 608570	n:1860000
KS ci ratio: 2.376675e-01	ci left: 1.288679e-04	ci right 1.641173e-04	k: 271	n:1860000
C2CD3   1860000 perm   2004 sec   (928 perm/sec)   p_kst 1.456989e-04   p_cons 3.271882e-01   p_joint 1.456989e-04

Joint ci ratio: 2.376676e-01	ci left: 1.281787e-04	ci right 1.632397e-04	k: 271	n:1870000
Cons ci ratio: 4.110097e-03	ci left: 3.265772e-01	ci right 3.279228e-01	k: 611957	n:1870000
KS ci ratio: 2.376676e-01	ci left: 1.281787e-04	ci right 1.632397e-04	k: 271	n:1870000
C2CD3   1870000 perm   2023 sec   (924 perm/sec)   p_kst 1.449198e-04   p_cons 3.272497e-01   p_joint 1.449198e-04

Joint ci ratio: 2.372319e-01	ci left: 1.279972e-04	ci right 1.629349e-04	k: 272	n:1880000
Cons ci ratio: 4.099163e-03	ci left: 3.265777e-01	ci right 3.279196e-01	k: 615227	n:1880000
KS ci ratio: 2.372319e-01	ci left: 1.279972e-04	ci right 1.629349e-04	k: 272	n:1880000
C2CD3   1880000 perm   2042 sec   (921 perm/sec)   p_kst 1.446809e-04   p_cons 3.272484e-01   p_joint 1.446809e-04

Joint ci ratio: 2.372320e-01	ci left: 1.273199e-04	ci right 1.620728e-04	k: 272	n:1890000
Cons ci ratio: 4.088381e-03	ci left: 3.265713e-01	ci right 3.279097e-01	k: 618484	n:1890000
KS ci ratio: 2.372320e-01	ci left: 1.273199e-04	ci right 1.620728e-04	k: 272	n:1890000
C2CD3   1890000 perm   2061 sec   (917 perm/sec)   p_kst 1.439153e-04   p_cons 3.272402e-01   p_joint 1.439153e-04

Joint ci ratio: 2.367987e-01	ci left: 1.271449e-04	ci right 1.617773e-04	k: 273	n:1900000
Cons ci ratio: 4.077580e-03	ci left: 3.265760e-01	ci right 3.279109e-01	k: 621762	n:1900000
KS ci ratio: 2.367987e-01	ci left: 1.271449e-04	ci right 1.617773e-04	k: 273	n:1900000
C2CD3   1900000 perm   2079 sec   (914 perm/sec)   p_kst 1.436842e-04   p_cons 3.272432e-01   p_joint 1.436842e-04

Joint ci ratio: 2.355128e-01	ci left: 1.279570e-04	ci right 1.625938e-04	k: 276	n:1910000
Cons ci ratio: 4.066991e-03	ci left: 3.265670e-01	ci right 3.278984e-01	k: 625014	n:1910000
KS ci ratio: 2.355128e-01	ci left: 1.279570e-04	ci right 1.625938e-04	k: 276	n:1910000
C2CD3   1910000 perm   2098 sec   (910 perm/sec)   p_kst 1.445026e-04   p_cons 3.272325e-01   p_joint 1.445026e-04

Joint ci ratio: 2.342477e-01	ci left: 1.287611e-04	ci right 1.634012e-04	k: 279	n:1920000
Cons ci ratio: 4.056080e-03	ci left: 3.266019e-01	ci right 3.279298e-01	k: 628350	n:1920000
KS ci ratio: 2.342477e-01	ci left: 1.287611e-04	ci right 1.634012e-04	k: 279	n:1920000
C2CD3   1920000 perm   2117 sec   (907 perm/sec)   p_kst 1.453125e-04   p_cons 3.272656e-01   p_joint 1.453125e-04

Joint ci ratio: 2.342478e-01	ci left: 1.280939e-04	ci right 1.625546e-04	k: 279	n:1930000
Cons ci ratio: 4.045714e-03	ci left: 3.265867e-01	ci right 3.279112e-01	k: 631590	n:1930000
KS ci ratio: 2.342478e-01	ci left: 1.280939e-04	ci right 1.625546e-04	k: 279	n:1930000
C2CD3   1930000 perm   2136 sec   (903 perm/sec)   p_kst 1.445596e-04   p_cons 3.272487e-01   p_joint 1.445596e-04

Joint ci ratio: 2.342478e-01	ci left: 1.274337e-04	ci right 1.617167e-04	k: 279	n:1940000
Cons ci ratio: 4.035276e-03	ci left: 3.265882e-01	ci right 3.279092e-01	k: 634862	n:1940000
KS ci ratio: 2.342478e-01	ci left: 1.274337e-04	ci right 1.617167e-04	k: 279	n:1940000
C2CD3   1940000 perm   2156 sec   (900 perm/sec)   p_kst 1.438144e-04   p_cons 3.272485e-01   p_joint 1.438144e-04

Joint ci ratio: 2.334157e-01	ci left: 1.277457e-04	ci right 1.619729e-04	k: 281	n:1950000
Cons ci ratio: 4.024843e-03	ci left: 3.265978e-01	ci right 3.279155e-01	k: 638150	n:1950000
KS ci ratio: 2.334157e-01	ci left: 1.277457e-04	ci right 1.619729e-04	k: 281	n:1950000
C2CD3   1950000 perm   2175 sec   (897 perm/sec)   p_kst 1.441026e-04   p_cons 3.272564e-01   p_joint 1.441026e-04

Joint ci ratio: 2.334158e-01	ci left: 1.270939e-04	ci right 1.611466e-04	k: 281	n:1960000
Cons ci ratio: 4.014444e-03	ci left: 3.266125e-01	ci right 3.279268e-01	k: 641448	n:1960000
KS ci ratio: 2.334158e-01	ci left: 1.270939e-04	ci right 1.611466e-04	k: 281	n:1960000
C2CD3   1960000 perm   2194 sec   (893 perm/sec)   p_kst 1.433673e-04   p_cons 3.272694e-01   p_joint 1.433673e-04

Joint ci ratio: 2.334158e-01	ci left: 1.264488e-04	ci right 1.603286e-04	k: 281	n:1970000
Cons ci ratio: 4.004675e-03	ci left: 3.265666e-01	ci right 3.278775e-01	k: 644627	n:1970000
KS ci ratio: 2.334158e-01	ci left: 1.264488e-04	ci right 1.603286e-04	k: 281	n:1970000
C2CD3   1970000 perm   2213 sec   (890 perm/sec)   p_kst 1.426396e-04   p_cons 3.272218e-01   p_joint 1.426396e-04

Joint ci ratio: 2.330031e-01	ci left: 1.262857e-04	ci right 1.600533e-04	k: 282	n:1980000
Cons ci ratio: 3.994569e-03	ci left: 3.265662e-01	ci right 3.278737e-01	k: 647895	n:1980000
KS ci ratio: 2.330031e-01	ci left: 1.262857e-04	ci right 1.600533e-04	k: 282	n:1980000
C2CD3   1980000 perm   2233 sec   (887 perm/sec)   p_kst 1.424242e-04   p_cons 3.272197e-01   p_joint 1.424242e-04

Joint ci ratio: 2.325925e-01	ci left: 1.261243e-04	ci right 1.597808e-04	k: 283	n:1990000
Cons ci ratio: 3.984670e-03	ci left: 3.265511e-01	ci right 3.278554e-01	k: 651134	n:1990000
KS ci ratio: 2.325925e-01	ci left: 1.261243e-04	ci right 1.597808e-04	k: 283	n:1990000
C2CD3   1990000 perm   2253 sec   (883 perm/sec)   p_kst 1.422111e-04   p_cons 3.272030e-01   p_joint 1.422111e-04

Joint ci ratio: 2.317778e-01	ci left: 1.264355e-04	ci right 1.600400e-04	k: 285	n:2000000
Cons ci ratio: 3.974462e-03	ci left: 3.265787e-01	ci right 3.278798e-01	k: 654458	n:2000000
KS ci ratio: 2.317778e-01	ci left: 1.264355e-04	ci right 1.600400e-04	k: 285	n:2000000
C2CD3   2000000 perm   2272 sec   (880 perm/sec)   p_kst 1.425000e-04   p_cons 3.272290e-01   p_joint 1.425000e-04

Joint ci ratio: 2.317779e-01	ci left: 1.258065e-04	ci right 1.592438e-04	k: 285	n:2010000
Cons ci ratio: 3.964215e-03	ci left: 3.266190e-01	ci right 3.279168e-01	k: 657808	n:2010000
KS ci ratio: 2.317779e-01	ci left: 1.258065e-04	ci right 1.592438e-04	k: 285	n:2010000
C2CD3   2010000 perm   2292 sec   (877 perm/sec)   p_kst 1.417910e-04   p_cons 3.272677e-01   p_joint 1.417910e-04

Joint ci ratio: 2.309717e-01	ci left: 1.261164e-04	ci right 1.595028e-04	k: 287	n:2020000
Cons ci ratio: 3.954282e-03	ci left: 3.266326e-01	ci right 3.279273e-01	k: 661105	n:2020000
KS ci ratio: 2.309717e-01	ci left: 1.261164e-04	ci right 1.595028e-04	k: 287	n:2020000
C2CD3   2020000 perm   2312 sec   (874 perm/sec)   p_kst 1.420792e-04   p_cons 3.272797e-01   p_joint 1.420792e-04

Joint ci ratio: 2.301738e-01	ci left: 1.264235e-04	ci right 1.597591e-04	k: 289	n:2030000
Cons ci ratio: 3.944397e-03	ci left: 3.266491e-01	ci right 3.279406e-01	k: 664408	n:2030000
KS ci ratio: 2.301738e-01	ci left: 1.264235e-04	ci right 1.597591e-04	k: 289	n:2030000
C2CD3   2030000 perm   2332 sec   (871 perm/sec)   p_kst 1.423645e-04   p_cons 3.272946e-01   p_joint 1.423645e-04

Joint ci ratio: 2.293842e-01	ci left: 1.267277e-04	ci right 1.600127e-04	k: 291	n:2040000
Cons ci ratio: 3.934713e-03	ci left: 3.266512e-01	ci right 3.279395e-01	k: 667682	n:2040000
KS ci ratio: 2.293842e-01	ci left: 1.267277e-04	ci right 1.600127e-04	k: 291	n:2040000
C2CD3   2040000 perm   2352 sec   (867 perm/sec)   p_kst 1.426471e-04   p_cons 3.272951e-01   p_joint 1.426471e-04

Joint ci ratio: 2.289924e-01	ci left: 1.265693e-04	ci right 1.597479e-04	k: 292	n:2050000
Cons ci ratio: 3.925217e-03	ci left: 3.266401e-01	ci right 3.279252e-01	k: 670929	n:2050000
KS ci ratio: 2.289924e-01	ci left: 1.265693e-04	ci right 1.597479e-04	k: 292	n:2050000
C2CD3   2050000 perm   2372 sec   (864 perm/sec)   p_kst 1.424390e-04   p_cons 3.272824e-01   p_joint 1.424390e-04

Joint ci ratio: 2.278289e-01	ci left: 1.273279e-04	ci right 1.605119e-04	k: 295	n:2060000
Cons ci ratio: 3.915371e-03	ci left: 3.266762e-01	ci right 3.279582e-01	k: 674273	n:2060000
KS ci ratio: 2.278289e-01	ci left: 1.273279e-04	ci right 1.605119e-04	k: 295	n:2060000
C2CD3   2060000 perm   2392 sec   (861 perm/sec)   p_kst 1.432039e-04   p_cons 3.273170e-01   p_joint 1.432039e-04

Joint ci ratio: 2.274451e-01	ci left: 1.271683e-04	ci right 1.602471e-04	k: 296	n:2070000
Cons ci ratio: 3.905672e-03	ci left: 3.267038e-01	ci right 3.279827e-01	k: 677600	n:2070000
KS ci ratio: 2.274451e-01	ci left: 1.271683e-04	ci right 1.602471e-04	k: 296	n:2070000
C2CD3   2070000 perm   2413 sec   (858 perm/sec)   p_kst 1.429952e-04   p_cons 3.273430e-01   p_joint 1.429952e-04

Joint ci ratio: 2.274452e-01	ci left: 1.265569e-04	ci right 1.594767e-04	k: 296	n:2080000
Cons ci ratio: 3.896580e-03	ci left: 3.266705e-01	ci right 3.279463e-01	k: 680801	n:2080000
KS ci ratio: 2.274452e-01	ci left: 1.265569e-04	ci right 1.594767e-04	k: 296	n:2080000
C2CD3   2080000 perm   2433 sec   (855 perm/sec)   p_kst 1.423077e-04   p_cons 3.273082e-01   p_joint 1.423077e-04

Joint ci ratio: 2.263050e-01	ci left: 1.273052e-04	ci right 1.602305e-04	k: 299	n:2090000
Cons ci ratio: 3.887213e-03	ci left: 3.266758e-01	ci right 3.279486e-01	k: 684082	n:2090000
KS ci ratio: 2.263050e-01	ci left: 1.273052e-04	ci right 1.602305e-04	k: 299	n:2090000
C2CD3   2090000 perm   2453 sec   (852 perm/sec)   p_kst 1.430622e-04   p_cons 3.273120e-01   p_joint 1.430622e-04

Joint ci ratio: 2.259288e-01	ci left: 1.271482e-04	ci right 1.599706e-04	k: 300	n:2100000
Cons ci ratio: 3.877914e-03	ci left: 3.266811e-01	ci right 3.279508e-01	k: 687363	n:2100000
KS ci ratio: 2.259288e-01	ci left: 1.271482e-04	ci right 1.599706e-04	k: 300	n:2100000
C2CD3   2100000 perm   2474 sec   (849 perm/sec)   p_kst 1.428571e-04   p_cons 3.273157e-01   p_joint 1.428571e-04

Joint ci ratio: 2.255545e-01	ci left: 1.269928e-04	ci right 1.597131e-04	k: 301	n:2110000
Cons ci ratio: 3.868460e-03	ci left: 3.267114e-01	ci right 3.279782e-01	k: 690697	n:2110000
KS ci ratio: 2.255545e-01	ci left: 1.269928e-04	ci right 1.597131e-04	k: 301	n:2110000
C2CD3   2110000 perm   2494 sec   (846 perm/sec)   p_kst 1.426540e-04   p_cons 3.273445e-01   p_joint 1.426540e-04

Joint ci ratio: 2.251820e-01	ci left: 1.268388e-04	ci right 1.594581e-04	k: 302	n:2120000
Cons ci ratio: 3.859290e-03	ci left: 3.267169e-01	ci right 3.279807e-01	k: 693979	n:2120000
KS ci ratio: 2.251820e-01	ci left: 1.268388e-04	ci right 1.594581e-04	k: 302	n:2120000
C2CD3   2120000 perm   2515 sec   (843 perm/sec)   p_kst 1.424528e-04   p_cons 3.273486e-01   p_joint 1.424528e-04

Joint ci ratio: 2.251820e-01	ci left: 1.262433e-04	ci right 1.587094e-04	k: 302	n:2130000
Cons ci ratio: 3.850210e-03	ci left: 3.267196e-01	ci right 3.279804e-01	k: 697255	n:2130000
KS ci ratio: 2.251820e-01	ci left: 1.262433e-04	ci right 1.587094e-04	k: 302	n:2130000
C2CD3   2130000 perm   2536 sec   (840 perm/sec)   p_kst 1.417840e-04   p_cons 3.273498e-01   p_joint 1.417840e-04

Joint ci ratio: 2.251821e-01	ci left: 1.256534e-04	ci right 1.579678e-04	k: 302	n:2140000
Cons ci ratio: 3.841389e-03	ci left: 3.266998e-01	ci right 3.279577e-01	k: 700483	n:2140000
KS ci ratio: 2.251821e-01	ci left: 1.256534e-04	ci right 1.579678e-04	k: 302	n:2140000
C2CD3   2140000 perm   2556 sec   (837 perm/sec)   p_kst 1.411215e-04   p_cons 3.273285e-01   p_joint 1.411215e-04

Joint ci ratio: 2.248115e-01	ci left: 1.255079e-04	ci right 1.577244e-04	k: 303	n:2150000
Cons ci ratio: 3.832366e-03	ci left: 3.267104e-01	ci right 3.279654e-01	k: 703776	n:2150000
KS ci ratio: 2.248115e-01	ci left: 1.255079e-04	ci right 1.577244e-04	k: 303	n:2150000
C2CD3   2150000 perm   2578 sec   (834 perm/sec)   p_kst 1.409302e-04   p_cons 3.273377e-01   p_joint 1.409302e-04

Joint ci ratio: 2.240756e-01	ci left: 1.258007e-04	ci right 1.579720e-04	k: 305	n:2160000
Cons ci ratio: 3.823277e-03	ci left: 3.267358e-01	ci right 3.279878e-01	k: 707101	n:2160000
KS ci ratio: 2.240756e-01	ci left: 1.258007e-04	ci right 1.579720e-04	k: 305	n:2160000
C2CD3   2160000 perm   2599 sec   (831 perm/sec)   p_kst 1.412037e-04   p_cons 3.273616e-01   p_joint 1.412037e-04

Joint ci ratio: 2.233468e-01	ci left: 1.260910e-04	ci right 1.582173e-04	k: 307	n:2170000
Cons ci ratio: 3.814236e-03	ci left: 3.267627e-01	ci right 3.280119e-01	k: 710430	n:2170000
KS ci ratio: 2.233468e-01	ci left: 1.260910e-04	ci right 1.582173e-04	k: 307	n:2170000
C2CD3   2170000 perm   2620 sec   (828 perm/sec)   p_kst 1.414747e-04   p_cons 3.273871e-01   p_joint 1.414747e-04

Joint ci ratio: 2.229852e-01	ci left: 1.259457e-04	ci right 1.579758e-04	k: 308	n:2180000
Cons ci ratio: 3.805477e-03	ci left: 3.267642e-01	ci right 3.280105e-01	k: 713704	n:2180000
KS ci ratio: 2.229852e-01	ci left: 1.259457e-04	ci right 1.579758e-04	k: 308	n:2180000
C2CD3   2180000 perm   2641 sec   (825 perm/sec)   p_kst 1.412844e-04   p_cons 3.273872e-01   p_joint 1.412844e-04

Joint ci ratio: 2.222670e-01	ci left: 1.262329e-04	ci right 1.582186e-04	k: 310	n:2190000
Cons ci ratio: 3.796613e-03	ci left: 3.267849e-01	ci right 3.280284e-01	k: 717020	n:2190000
KS ci ratio: 2.222670e-01	ci left: 1.262329e-04	ci right 1.582186e-04	k: 310	n:2190000
C2CD3   2190000 perm   2663 sec   (823 perm/sec)   p_kst 1.415525e-04   p_cons 3.274064e-01   p_joint 1.415525e-04

Joint ci ratio: 2.219105e-01	ci left: 1.260884e-04	ci right 1.579792e-04	k: 311	n:2200000
Cons ci ratio: 3.787901e-03	ci left: 3.267949e-01	ci right 3.280356e-01	k: 720313	n:2200000
KS ci ratio: 2.219105e-01	ci left: 1.260884e-04	ci right 1.579792e-04	k: 311	n:2200000
C2CD3   2200000 perm   2684 sec   (820 perm/sec)   p_kst 1.413636e-04   p_cons 3.274150e-01   p_joint 1.413636e-04

Joint ci ratio: 2.212026e-01	ci left: 1.263726e-04	ci right 1.582195e-04	k: 313	n:2210000
Cons ci ratio: 3.779302e-03	ci left: 3.267985e-01	ci right 3.280363e-01	k: 723592	n:2210000
KS ci ratio: 2.212026e-01	ci left: 1.263726e-04	ci right 1.582195e-04	k: 313	n:2210000
C2CD3   2210000 perm   2705 sec   (817 perm/sec)   p_kst 1.416290e-04   p_cons 3.274172e-01   p_joint 1.416290e-04

Joint ci ratio: 2.205015e-01	ci left: 1.266544e-04	ci right 1.584574e-04	k: 315	n:2220000
Cons ci ratio: 3.770928e-03	ci left: 3.267827e-01	ci right 3.280177e-01	k: 726828	n:2220000
KS ci ratio: 2.205015e-01	ci left: 1.266544e-04	ci right 1.584574e-04	k: 315	n:2220000
C2CD3   2220000 perm   2727 sec   (814 perm/sec)   p_kst 1.418919e-04   p_cons 3.274000e-01   p_joint 1.418919e-04

Joint ci ratio: 2.205016e-01	ci left: 1.260864e-04	ci right 1.577468e-04	k: 315	n:2230000
Cons ci ratio: 3.762364e-03	ci left: 3.267957e-01	ci right 3.280280e-01	k: 730128	n:2230000
KS ci ratio: 2.205016e-01	ci left: 1.260864e-04	ci right 1.577468e-04	k: 315	n:2230000
C2CD3   2230000 perm   2748 sec   (811 perm/sec)   p_kst 1.412556e-04   p_cons 3.274117e-01   p_joint 1.412556e-04

Joint ci ratio: 2.201535e-01	ci left: 1.259454e-04	ci right 1.575136e-04	k: 316	n:2240000
Cons ci ratio: 3.754189e-03	ci left: 3.267699e-01	ci right 3.279993e-01	k: 733341	n:2240000
KS ci ratio: 2.201535e-01	ci left: 1.259454e-04	ci right 1.575136e-04	k: 316	n:2240000
C2CD3   2240000 perm   2770 sec   (809 perm/sec)   p_kst 1.410714e-04   p_cons 3.273844e-01   p_joint 1.410714e-04

Joint ci ratio: 2.191190e-01	ci left: 1.266456e-04	ci right 1.582201e-04	k: 319	n:2250000
Cons ci ratio: 3.745870e-03	ci left: 3.267673e-01	ci right 3.279940e-01	k: 736606	n:2250000
KS ci ratio: 2.191190e-01	ci left: 1.266456e-04	ci right 1.582201e-04	k: 319	n:2250000
C2CD3   2250000 perm   2791 sec   (806 perm/sec)   p_kst 1.417778e-04   p_cons 3.273804e-01   p_joint 1.417778e-04

Joint ci ratio: 2.187775e-01	ci left: 1.265034e-04	ci right 1.579868e-04	k: 320	n:2260000
Cons ci ratio: 3.737772e-03	ci left: 3.267453e-01	ci right 3.279693e-01	k: 739827	n:2260000
KS ci ratio: 2.187775e-01	ci left: 1.265034e-04	ci right 1.579868e-04	k: 320	n:2260000
C2CD3   2260000 perm   2813 sec   (803 perm/sec)   p_kst 1.415929e-04   p_cons 3.273571e-01   p_joint 1.415929e-04

Joint ci ratio: 2.180991e-01	ci left: 1.267790e-04	ci right 1.582200e-04	k: 322	n:2270000
Cons ci ratio: 3.729607e-03	ci left: 3.267376e-01	ci right 3.279589e-01	k: 743080	n:2270000
KS ci ratio: 2.180991e-01	ci left: 1.267790e-04	ci right 1.582200e-04	k: 322	n:2270000
C2CD3   2270000 perm   2835 sec   (801 perm/sec)   p_kst 1.418502e-04   p_cons 3.273480e-01   p_joint 1.418502e-04

Joint ci ratio: 2.177623e-01	ci left: 1.266376e-04	ci right 1.579885e-04	k: 323	n:2280000
Cons ci ratio: 3.721532e-03	ci left: 3.267256e-01	ci right 3.279442e-01	k: 746323	n:2280000
KS ci ratio: 2.177623e-01	ci left: 1.266376e-04	ci right 1.579885e-04	k: 323	n:2280000
C2CD3   2280000 perm   2857 sec   (798 perm/sec)   p_kst 1.416667e-04   p_cons 3.273346e-01   p_joint 1.416667e-04

Joint ci ratio: 2.164302e-01	ci left: 1.277364e-04	ci right 1.591401e-04	k: 327	n:2290000
Cons ci ratio: 3.713693e-03	ci left: 3.266918e-01	ci right 3.279077e-01	k: 749516	n:2290000
KS ci ratio: 2.164302e-01	ci left: 1.277364e-04	ci right 1.591401e-04	k: 327	n:2290000
C2CD3   2290000 perm   2879 sec   (796 perm/sec)   p_kst 1.427948e-04   p_cons 3.272996e-01   p_joint 1.427948e-04

Joint ci ratio: 2.161011e-01	ci left: 1.275922e-04	ci right 1.589065e-04	k: 328	n:2300000
Cons ci ratio: 3.705604e-03	ci left: 3.266940e-01	ci right 3.279073e-01	k: 752791	n:2300000
KS ci ratio: 2.161011e-01	ci left: 1.275922e-04	ci right 1.589065e-04	k: 328	n:2300000
C2CD3   2300000 perm   2901 sec   (793 perm/sec)   p_kst 1.426087e-04   p_cons 3.273004e-01   p_joint 1.426087e-04

Joint ci ratio: 2.161012e-01	ci left: 1.270399e-04	ci right 1.582186e-04	k: 328	n:2310000
Cons ci ratio: 3.697734e-03	ci left: 3.266763e-01	ci right 3.278869e-01	k: 756020	n:2310000
KS ci ratio: 2.161012e-01	ci left: 1.270399e-04	ci right 1.582186e-04	k: 328	n:2310000
C2CD3   2310000 perm   2923 sec   (790 perm/sec)   p_kst 1.419913e-04   p_cons 3.272814e-01   p_joint 1.419913e-04

Joint ci ratio: 2.157735e-01	ci left: 1.269000e-04	ci right 1.579910e-04	k: 329	n:2320000
Cons ci ratio: 3.689828e-03	ci left: 3.266691e-01	ci right 3.278771e-01	k: 759273	n:2320000
KS ci ratio: 2.157735e-01	ci left: 1.269000e-04	ci right 1.579910e-04	k: 329	n:2320000
C2CD3   2320000 perm   2946 sec   (787 perm/sec)   p_kst 1.418103e-04   p_cons 3.272728e-01   p_joint 1.418103e-04

Joint ci ratio: 2.151226e-01	ci left: 1.271674e-04	ci right 1.582175e-04	k: 331	n:2330000
Cons ci ratio: 3.681858e-03	ci left: 3.266756e-01	ci right 3.278810e-01	k: 762558	n:2330000
KS ci ratio: 2.151226e-01	ci left: 1.271674e-04	ci right 1.582175e-04	k: 331	n:2330000
C2CD3   2330000 perm   2969 sec   (785 perm/sec)   p_kst 1.420601e-04   p_cons 3.272781e-01   p_joint 1.420601e-04

Joint ci ratio: 2.144775e-01	ci left: 1.274327e-04	ci right 1.584420e-04	k: 333	n:2340000
Cons ci ratio: 3.674152e-03	ci left: 3.266565e-01	ci right 3.278593e-01	k: 765783	n:2340000
KS ci ratio: 2.144775e-01	ci left: 1.274327e-04	ci right 1.584420e-04	k: 333	n:2340000
C2CD3   2340000 perm   2991 sec   (782 perm/sec)   p_kst 1.423077e-04   p_cons 3.272577e-01   p_joint 1.423077e-04

Joint ci ratio: 2.144776e-01	ci left: 1.268904e-04	ci right 1.577678e-04	k: 333	n:2350000
Cons ci ratio: 3.666591e-03	ci left: 3.266261e-01	ci right 3.278263e-01	k: 768981	n:2350000
KS ci ratio: 2.144776e-01	ci left: 1.268904e-04	ci right 1.577678e-04	k: 333	n:2350000
C2CD3   2350000 perm   3013 sec   (780 perm/sec)   p_kst 1.417021e-04   p_cons 3.272260e-01   p_joint 1.417021e-04

Joint ci ratio: 2.144776e-01	ci left: 1.263528e-04	ci right 1.570992e-04	k: 333	n:2360000
Cons ci ratio: 3.658822e-03	ci left: 3.266264e-01	ci right 3.278240e-01	k: 772251	n:2360000
KS ci ratio: 2.144776e-01	ci left: 1.263528e-04	ci right 1.570992e-04	k: 333	n:2360000
C2CD3   2360000 perm   3036 sec   (777 perm/sec)   p_kst 1.411017e-04   p_cons 3.272250e-01   p_joint 1.411017e-04

Joint ci ratio: 2.132046e-01	ci left: 1.274170e-04	ci right 1.582144e-04	k: 337	n:2370000
Cons ci ratio: 3.651292e-03	ci left: 3.266039e-01	ci right 3.277990e-01	k: 775467	n:2370000
KS ci ratio: 2.132046e-01	ci left: 1.274170e-04	ci right 1.582144e-04	k: 337	n:2370000
C2CD3   2370000 perm   3059 sec   (775 perm/sec)   p_kst 1.421941e-04   p_cons 3.272013e-01   p_joint 1.421941e-04

Joint ci ratio: 2.132047e-01	ci left: 1.268816e-04	ci right 1.575496e-04	k: 337	n:2380000
Cons ci ratio: 3.643648e-03	ci left: 3.266010e-01	ci right 3.277936e-01	k: 778729	n:2380000
KS ci ratio: 2.132047e-01	ci left: 1.268816e-04	ci right 1.575496e-04	k: 337	n:2380000
C2CD3   2380000 perm   3082 sec   (772 perm/sec)   p_kst 1.415966e-04   p_cons 3.271971e-01   p_joint 1.415966e-04

Joint ci ratio: 2.132048e-01	ci left: 1.263508e-04	ci right 1.568904e-04	k: 337	n:2390000
Cons ci ratio: 3.635938e-03	ci left: 3.266119e-01	ci right 3.278020e-01	k: 782024	n:2390000
KS ci ratio: 2.132048e-01	ci left: 1.263508e-04	ci right 1.568904e-04	k: 337	n:2390000
C2CD3   2390000 perm   3105 sec   (770 perm/sec)   p_kst 1.410042e-04   p_cons 3.272067e-01   p_joint 1.410042e-04

Joint ci ratio: 2.128901e-01	ci left: 1.262187e-04	ci right 1.566756e-04	k: 338	n:2400000
Cons ci ratio: 3.628214e-03	ci left: 3.266301e-01	ci right 3.278178e-01	k: 785337	n:2400000
KS ci ratio: 2.128901e-01	ci left: 1.262187e-04	ci right 1.566756e-04	k: 338	n:2400000
C2CD3   2400000 perm   3129 sec   (767 perm/sec)   p_kst 1.408333e-04   p_cons 3.272237e-01   p_joint 1.408333e-04

Joint ci ratio: 2.122648e-01	ci left: 1.264807e-04	ci right 1.568995e-04	k: 340	n:2410000
Cons ci ratio: 3.620564e-03	ci left: 3.266454e-01	ci right 3.278306e-01	k: 788643	n:2410000
KS ci ratio: 2.122648e-01	ci left: 1.264807e-04	ci right 1.568995e-04	k: 340	n:2410000
C2CD3   2410000 perm   3152 sec   (765 perm/sec)   p_kst 1.410788e-04   p_cons 3.272378e-01   p_joint 1.410788e-04

Joint ci ratio: 2.110306e-01	ci left: 1.275233e-04	ci right 1.579915e-04	k: 344	n:2420000
Cons ci ratio: 3.612972e-03	ci left: 3.266593e-01	ci right 3.278420e-01	k: 791946	n:2420000
KS ci ratio: 2.110306e-01	ci left: 1.275233e-04	ci right 1.579915e-04	k: 344	n:2420000
C2CD3   2420000 perm   3176 sec   (762 perm/sec)   p_kst 1.421488e-04   p_cons 3.272504e-01   p_joint 1.421488e-04

Joint ci ratio: 2.107255e-01	ci left: 1.273883e-04	ci right 1.577745e-04	k: 345	n:2430000
Cons ci ratio: 3.605680e-03	ci left: 3.266422e-01	ci right 3.278224e-01	k: 795174	n:2430000
KS ci ratio: 2.107255e-01	ci left: 1.273883e-04	ci right 1.577745e-04	k: 345	n:2430000
C2CD3   2430000 perm   3199 sec   (760 perm/sec)   p_kst 1.419753e-04   p_cons 3.272321e-01   p_joint 1.419753e-04

Joint ci ratio: 2.107255e-01	ci left: 1.268663e-04	ci right 1.571279e-04	k: 345	n:2440000
Cons ci ratio: 3.598258e-03	ci left: 3.266465e-01	ci right 3.278244e-01	k: 798454	n:2440000
KS ci ratio: 2.107255e-01	ci left: 1.268663e-04	ci right 1.571279e-04	k: 345	n:2440000
C2CD3   2440000 perm   3223 sec   (757 perm/sec)   p_kst 1.413934e-04   p_cons 3.272352e-01   p_joint 1.413934e-04

Joint ci ratio: 2.104217e-01	ci left: 1.267351e-04	ci right 1.569162e-04	k: 346	n:2450000
Cons ci ratio: 3.590832e-03	ci left: 3.266570e-01	ci right 3.278324e-01	k: 801749	n:2450000
KS ci ratio: 2.104217e-01	ci left: 1.267351e-04	ci right 1.569162e-04	k: 346	n:2450000
C2CD3   2450000 perm   3246 sec   (755 perm/sec)   p_kst 1.412245e-04   p_cons 3.272445e-01   p_joint 1.412245e-04

Joint ci ratio: 2.101192e-01	ci left: 1.266050e-04	ci right 1.567063e-04	k: 347	n:2460000
Cons ci ratio: 3.583571e-03	ci left: 3.266527e-01	ci right 3.278258e-01	k: 805008	n:2460000
KS ci ratio: 2.101192e-01	ci left: 1.266050e-04	ci right 1.567063e-04	k: 347	n:2460000
C2CD3   2460000 perm   3270 sec   (752 perm/sec)   p_kst 1.410569e-04   p_cons 3.272390e-01   p_joint 1.410569e-04

Joint ci ratio: 2.101192e-01	ci left: 1.260924e-04	ci right 1.560718e-04	k: 347	n:2470000
Cons ci ratio: 3.576346e-03	ci left: 3.266493e-01	ci right 3.278200e-01	k: 808269	n:2470000
KS ci ratio: 2.101192e-01	ci left: 1.260924e-04	ci right 1.560718e-04	k: 347	n:2470000
C2CD3   2470000 perm   3294 sec   (750 perm/sec)   p_kst 1.404858e-04   p_cons 3.272344e-01   p_joint 1.404858e-04

Joint ci ratio: 2.098180e-01	ci left: 1.259660e-04	ci right 1.558669e-04	k: 348	n:2480000
Cons ci ratio: 3.569097e-03	ci left: 3.266543e-01	ci right 3.278227e-01	k: 811551	n:2480000
KS ci ratio: 2.098180e-01	ci left: 1.259660e-04	ci right 1.558669e-04	k: 348	n:2480000
C2CD3   2480000 perm   3318 sec   (748 perm/sec)   p_kst 1.403226e-04   p_cons 3.272383e-01   p_joint 1.403226e-04

Joint ci ratio: 2.098180e-01	ci left: 1.254601e-04	ci right 1.552409e-04	k: 348	n:2490000
Cons ci ratio: 3.561808e-03	ci left: 3.266698e-01	ci right 3.278358e-01	k: 814859	n:2490000
KS ci ratio: 2.098180e-01	ci left: 1.254601e-04	ci right 1.552409e-04	k: 348	n:2490000
C2CD3   2490000 perm   3342 sec   (745 perm/sec)   p_kst 1.397590e-04   p_cons 3.272526e-01   p_joint 1.397590e-04

Joint ci ratio: 2.095181e-01	ci left: 1.253373e-04	ci right 1.550409e-04	k: 349	n:2500000
Cons ci ratio: 3.554821e-03	ci left: 3.266532e-01	ci right 3.278168e-01	k: 818087	n:2500000
KS ci ratio: 2.095181e-01	ci left: 1.253373e-04	ci right 1.550409e-04	k: 349	n:2500000
C2CD3   2500000 perm   3366 sec   (743 perm/sec)   p_kst 1.396000e-04   p_cons 3.272348e-01   p_joint 1.396000e-04

Joint ci ratio: 2.086258e-01	ci left: 1.259706e-04	ci right 1.556809e-04	k: 352	n:2510000
Cons ci ratio: 3.547781e-03	ci left: 3.266482e-01	ci right 3.278095e-01	k: 821344	n:2510000
KS ci ratio: 2.086258e-01	ci left: 1.259706e-04	ci right 1.556809e-04	k: 352	n:2510000
C2CD3   2510000 perm   3390 sec   (740 perm/sec)   p_kst 1.402390e-04   p_cons 3.272287e-01   p_joint 1.402390e-04

Joint ci ratio: 2.080373e-01	ci left: 1.262229e-04	ci right 1.558982e-04	k: 354	n:2520000
Cons ci ratio: 3.540707e-03	ci left: 3.266528e-01	ci right 3.278118e-01	k: 824625	n:2520000
KS ci ratio: 2.080373e-01	ci left: 1.262229e-04	ci right 1.558982e-04	k: 354	n:2520000
C2CD3   2520000 perm   3414 sec   (738 perm/sec)   p_kst 1.404762e-04   p_cons 3.272321e-01   p_joint 1.404762e-04

Joint ci ratio: 2.077449e-01	ci left: 1.260987e-04	ci right 1.556978e-04	k: 355	n:2530000
Cons ci ratio: 3.533593e-03	ci left: 3.266677e-01	ci right 3.278244e-01	k: 827932	n:2530000
KS ci ratio: 2.077449e-01	ci left: 1.260987e-04	ci right 1.556978e-04	k: 355	n:2530000
C2CD3   2530000 perm   3439 sec   (736 perm/sec)   p_kst 1.403162e-04   p_cons 3.272458e-01   p_joint 1.403162e-04

Joint ci ratio: 2.074538e-01	ci left: 1.259755e-04	ci right 1.554989e-04	k: 356	n:2540000
Cons ci ratio: 3.526515e-03	ci left: 3.266832e-01	ci right 3.278377e-01	k: 831241	n:2540000
KS ci ratio: 2.074538e-01	ci left: 1.259755e-04	ci right 1.554989e-04	k: 356	n:2540000
C2CD3   2540000 perm   3463 sec   (733 perm/sec)   p_kst 1.401575e-04   p_cons 3.272602e-01   p_joint 1.401575e-04

Joint ci ratio: 2.071639e-01	ci left: 1.258533e-04	ci right 1.553016e-04	k: 357	n:2550000
Cons ci ratio: 3.519721e-03	ci left: 3.266684e-01	ci right 3.278206e-01	k: 834473	n:2550000
KS ci ratio: 2.071639e-01	ci left: 1.258533e-04	ci right 1.553016e-04	k: 357	n:2550000
C2CD3   2550000 perm   3488 sec   (731 perm/sec)   p_kst 1.400000e-04   p_cons 3.272443e-01   p_joint 1.400000e-04

Joint ci ratio: 2.068751e-01	ci left: 1.257320e-04	ci right 1.551058e-04	k: 358	n:2560000
Cons ci ratio: 3.512732e-03	ci left: 3.266830e-01	ci right 3.278330e-01	k: 837780	n:2560000
KS ci ratio: 2.068751e-01	ci left: 1.257320e-04	ci right 1.551058e-04	k: 358	n:2560000
C2CD3   2560000 perm   3513 sec   (729 perm/sec)   p_kst 1.398437e-04   p_cons 3.272578e-01   p_joint 1.398437e-04

Joint ci ratio: 2.057321e-01	ci left: 1.267188e-04	ci right 1.561390e-04	k: 362	n:2570000
Cons ci ratio: 3.505909e-03	ci left: 3.266820e-01	ci right 3.278297e-01	k: 841047	n:2570000
KS ci ratio: 2.057321e-01	ci left: 1.267188e-04	ci right 1.561390e-04	k: 362	n:2570000
C2CD3   2570000 perm   3538 sec   (726 perm/sec)   p_kst 1.408560e-04   p_cons 3.272556e-01   p_joint 1.408560e-04

Joint ci ratio: 2.054493e-01	ci left: 1.265953e-04	ci right 1.559413e-04	k: 363	n:2580000
Cons ci ratio: 3.499152e-03	ci left: 3.266775e-01	ci right 3.278229e-01	k: 844305	n:2580000
KS ci ratio: 2.054493e-01	ci left: 1.265953e-04	ci right 1.559413e-04	k: 363	n:2580000
C2CD3   2580000 perm   3562 sec   (724 perm/sec)   p_kst 1.406977e-04   p_cons 3.272500e-01   p_joint 1.406977e-04

Joint ci ratio: 2.054493e-01	ci left: 1.261065e-04	ci right 1.553392e-04	k: 363	n:2590000
Cons ci ratio: 3.492472e-03	ci left: 3.266683e-01	ci right 3.278116e-01	k: 847551	n:2590000
KS ci ratio: 2.054493e-01	ci left: 1.261065e-04	ci right 1.553392e-04	k: 363	n:2590000
C2CD3   2590000 perm   3587 sec   (722 perm/sec)   p_kst 1.401544e-04   p_cons 3.272398e-01   p_joint 1.401544e-04

Joint ci ratio: 2.048872e-01	ci left: 1.263512e-04	ci right 1.555505e-04	k: 365	n:2600000
Cons ci ratio: 3.485555e-03	ci left: 3.266939e-01	ci right 3.278350e-01	k: 850887	n:2600000
KS ci ratio: 2.048872e-01	ci left: 1.263512e-04	ci right 1.555505e-04	k: 365	n:2600000
C2CD3   2600000 perm   3612 sec   (720 perm/sec)   p_kst 1.403846e-04   p_cons 3.272642e-01   p_joint 1.403846e-04

Joint ci ratio: 2.043297e-01	ci left: 1.265941e-04	ci right 1.557600e-04	k: 367	n:2610000
Cons ci ratio: 3.479176e-03	ci left: 3.266564e-01	ci right 3.277953e-01	k: 854059	n:2610000
KS ci ratio: 2.043297e-01	ci left: 1.265941e-04	ci right 1.557600e-04	k: 367	n:2610000
C2CD3   2610000 perm   3637 sec   (718 perm/sec)   p_kst 1.406130e-04   p_cons 3.272257e-01   p_joint 1.406130e-04

Joint ci ratio: 2.040526e-01	ci left: 1.264731e-04	ci right 1.555666e-04	k: 368	n:2620000
Cons ci ratio: 3.472709e-03	ci left: 3.266349e-01	ci right 3.277716e-01	k: 857272	n:2620000
KS ci ratio: 2.040526e-01	ci left: 1.264731e-04	ci right 1.555666e-04	k: 368	n:2620000
C2CD3   2620000 perm   3661 sec   (716 perm/sec)   p_kst 1.404580e-04   p_cons 3.272031e-01   p_joint 1.404580e-04

Joint ci ratio: 2.035019e-01	ci left: 1.267139e-04	ci right 1.557743e-04	k: 370	n:2630000
Cons ci ratio: 3.466107e-03	ci left: 3.266352e-01	ci right 3.277697e-01	k: 860542	n:2630000
KS ci ratio: 2.035019e-01	ci left: 1.267139e-04	ci right 1.557743e-04	k: 370	n:2630000
C2CD3   2630000 perm   3687 sec   (713 perm/sec)   p_kst 1.406844e-04   p_cons 3.272023e-01   p_joint 1.406844e-04

Joint ci ratio: 2.032282e-01	ci left: 1.265934e-04	ci right 1.555823e-04	k: 371	n:2640000
Cons ci ratio: 3.459485e-03	ci left: 3.266427e-01	ci right 3.277751e-01	k: 863831	n:2640000
KS ci ratio: 2.032282e-01	ci left: 1.265934e-04	ci right 1.555823e-04	k: 371	n:2640000
C2CD3   2640000 perm   3712 sec   (711 perm/sec)   p_kst 1.405303e-04   p_cons 3.272087e-01   p_joint 1.405303e-04

Joint ci ratio: 2.032282e-01	ci left: 1.261157e-04	ci right 1.549952e-04	k: 371	n:2650000
Cons ci ratio: 3.452973e-03	ci left: 3.266411e-01	ci right 3.277713e-01	k: 867096	n:2650000
KS ci ratio: 2.032282e-01	ci left: 1.261157e-04	ci right 1.549952e-04	k: 371	n:2650000
C2CD3   2650000 perm   3738 sec   (709 perm/sec)   p_kst 1.400000e-04   p_cons 3.272060e-01   p_joint 1.400000e-04

Joint ci ratio: 2.029556e-01	ci left: 1.259984e-04	ci right 1.548076e-04	k: 372	n:2660000
Cons ci ratio: 3.446520e-03	ci left: 3.266365e-01	ci right 3.277646e-01	k: 870353	n:2660000
KS ci ratio: 2.029556e-01	ci left: 1.259984e-04	ci right 1.548076e-04	k: 372	n:2660000
C2CD3   2660000 perm   3763 sec   (707 perm/sec)   p_kst 1.398496e-04   p_cons 3.272004e-01   p_joint 1.398496e-04

Joint ci ratio: 2.024137e-01	ci left: 1.262375e-04	ci right 1.550148e-04	k: 374	n:2670000
Cons ci ratio: 3.440233e-03	ci left: 3.266155e-01	ci right 3.277414e-01	k: 873566	n:2670000
KS ci ratio: 2.024137e-01	ci left: 1.262375e-04	ci right 1.550148e-04	k: 374	n:2670000
C2CD3   2670000 perm   3788 sec   (705 perm/sec)   p_kst 1.400749e-04   p_cons 3.271783e-01   p_joint 1.400749e-04

Joint ci ratio: 2.016088e-01	ci left: 1.268293e-04	ci right 1.556123e-04	k: 377	n:2680000
Cons ci ratio: 3.433758e-03	ci left: 3.266230e-01	ci right 3.277468e-01	k: 876855	n:2680000
KS ci ratio: 2.016088e-01	ci left: 1.268293e-04	ci right 1.556123e-04	k: 377	n:2680000
C2CD3   2680000 perm   3814 sec   (703 perm/sec)   p_kst 1.406716e-04   p_cons 3.271847e-01   p_joint 1.406716e-04

Joint ci ratio: 2.013427e-01	ci left: 1.267108e-04	ci right 1.554243e-04	k: 378	n:2690000
Cons ci ratio: 3.427179e-03	ci left: 3.266486e-01	ci right 3.277704e-01	k: 880193	n:2690000
KS ci ratio: 2.013427e-01	ci left: 1.267108e-04	ci right 1.554243e-04	k: 378	n:2690000
C2CD3   2690000 perm   3840 sec   (701 perm/sec)   p_kst 1.405204e-04   p_cons 3.272093e-01   p_joint 1.405204e-04

Joint ci ratio: 2.010776e-01	ci left: 1.265932e-04	ci right 1.552377e-04	k: 379	n:2700000
Cons ci ratio: 3.420752e-03	ci left: 3.266592e-01	ci right 3.277789e-01	k: 883491	n:2700000
KS ci ratio: 2.010776e-01	ci left: 1.265932e-04	ci right 1.552377e-04	k: 379	n:2700000
C2CD3   2700000 perm   3866 sec   (698 perm/sec)   p_kst 1.403704e-04   p_cons 3.272189e-01   p_joint 1.403704e-04

Joint ci ratio: 2.010776e-01	ci left: 1.261261e-04	ci right 1.546649e-04	k: 379	n:2710000
Cons ci ratio: 3.414443e-03	ci left: 3.266591e-01	ci right 3.277767e-01	k: 886760	n:2710000
KS ci ratio: 2.010776e-01	ci left: 1.261261e-04	ci right 1.546649e-04	k: 379	n:2710000
C2CD3   2710000 perm   3892 sec   (696 perm/sec)   p_kst 1.398524e-04   p_cons 3.272177e-01   p_joint 1.398524e-04

Joint ci ratio: 2.008136e-01	ci left: 1.260115e-04	ci right 1.544824e-04	k: 380	n:2720000
Cons ci ratio: 3.408207e-03	ci left: 3.266542e-01	ci right 3.277697e-01	k: 890016	n:2720000
KS ci ratio: 2.008136e-01	ci left: 1.260115e-04	ci right 1.544824e-04	k: 380	n:2720000
C2CD3   2720000 perm   3917 sec   (694 perm/sec)   p_kst 1.397059e-04   p_cons 3.272118e-01   p_joint 1.397059e-04

Joint ci ratio: 2.008136e-01	ci left: 1.255499e-04	ci right 1.539165e-04	k: 380	n:2730000
Cons ci ratio: 3.401965e-03	ci left: 3.266544e-01	ci right 3.277679e-01	k: 893286	n:2730000
KS ci ratio: 2.008136e-01	ci left: 1.255499e-04	ci right 1.539165e-04	k: 380	n:2730000
C2CD3   2730000 perm   3943 sec   (692 perm/sec)   p_kst 1.391941e-04   p_cons 3.272110e-01   p_joint 1.391941e-04

Joint ci ratio: 2.005506e-01	ci left: 1.254384e-04	ci right 1.537380e-04	k: 381	n:2740000
Cons ci ratio: 3.395828e-03	ci left: 3.266455e-01	ci right 3.277570e-01	k: 896531	n:2740000
KS ci ratio: 2.005506e-01	ci left: 1.254384e-04	ci right 1.537380e-04	k: 381	n:2740000
C2CD3   2740000 perm   3969 sec   (690 perm/sec)   p_kst 1.390511e-04   p_cons 3.272011e-01   p_joint 1.390511e-04

Joint ci ratio: 1.995087e-01	ci left: 1.263639e-04	ci right 1.547063e-04	k: 385	n:2750000
Cons ci ratio: 3.389629e-03	ci left: 3.266491e-01	ci right 3.277585e-01	k: 899810	n:2750000
KS ci ratio: 1.995087e-01	ci left: 1.263639e-04	ci right 1.547063e-04	k: 385	n:2750000
C2CD3   2750000 perm   3995 sec   (688 perm/sec)   p_kst 1.400000e-04   p_cons 3.272036e-01   p_joint 1.400000e-04

Joint ci ratio: 1.987378e-01	ci left: 1.269388e-04	ci right 1.552868e-04	k: 388	n:2760000
Cons ci ratio: 3.383586e-03	ci left: 3.266367e-01	ci right 3.277441e-01	k: 903045	n:2760000
KS ci ratio: 1.987378e-01	ci left: 1.269388e-04	ci right 1.552868e-04	k: 388	n:2760000
C2CD3   2760000 perm   4021 sec   (686 perm/sec)   p_kst 1.405797e-04   p_cons 3.271902e-01   p_joint 1.405797e-04

Joint ci ratio: 1.987379e-01	ci left: 1.264806e-04	ci right 1.547262e-04	k: 388	n:2770000
Cons ci ratio: 3.377818e-03	ci left: 3.265926e-01	ci right 3.276980e-01	k: 906192	n:2770000
KS ci ratio: 1.987379e-01	ci left: 1.264806e-04	ci right 1.547262e-04	k: 388	n:2770000
C2CD3   2770000 perm   4049 sec   (684 perm/sec)   p_kst 1.400722e-04   p_cons 3.271451e-01   p_joint 1.400722e-04

Joint ci ratio: 2.484087e-01	ci left: 7.845086e-05	ci right 1.010295e-04	k: 248	n:2780000
Cons ci ratio: 3.371585e-03	ci left: 3.266136e-01	ci right 3.277170e-01	k: 909519	n:2780000
KS ci ratio: 1.979759e-01	ci left: 1.270512e-04	ci right 1.553023e-04	k: 391	n:2780000
C2CD3   2780000 perm   4076 sec   (682 perm/sec)   p_kst 1.406475e-04   p_cons 3.271651e-01   p_joint 8.920863e-05

Joint ci ratio: 2.479114e-01	ci left: 7.850580e-05	ci right 1.010481e-04	k: 249	n:2790000
Cons ci ratio: 3.365747e-03	ci left: 3.265871e-01	ci right 3.276885e-01	k: 912714	n:2790000
KS ci ratio: 1.977239e-01	ci left: 1.269364e-04	ci right 1.551218e-04	k: 392	n:2790000
C2CD3   2790000 perm   4102 sec   (680 perm/sec)   p_kst 1.405018e-04   p_cons 3.271376e-01   p_joint 8.924731e-05

Joint ci ratio: 2.479115e-01	ci left: 7.822543e-05	ci right 1.006872e-04	k: 249	n:2800000
Cons ci ratio: 3.359912e-03	ci left: 3.265644e-01	ci right 3.276638e-01	k: 915919	n:2800000
KS ci ratio: 1.977239e-01	ci left: 1.264831e-04	ci right 1.545678e-04	k: 392	n:2800000
C2CD3   2800000 perm   4129 sec   (678 perm/sec)   p_kst 1.400000e-04   p_cons 3.271139e-01   p_joint 8.892857e-05

Joint ci ratio: 2.479115e-01	ci left: 7.794704e-05	ci right 1.003289e-04	k: 249	n:2810000
Cons ci ratio: 3.353853e-03	ci left: 3.265753e-01	ci right 3.276728e-01	k: 919218	n:2810000
KS ci ratio: 1.977240e-01	ci left: 1.260330e-04	ci right 1.540178e-04	k: 392	n:2810000
C2CD3   2810000 perm   4155 sec   (676 perm/sec)   p_kst 1.395018e-04   p_cons 3.271238e-01   p_joint 8.861210e-05

Joint ci ratio: 2.474172e-01	ci left: 7.800324e-05	ci right 1.003497e-04	k: 250	n:2820000
Cons ci ratio: 3.347851e-03	ci left: 3.265829e-01	ci right 3.276784e-01	k: 922508	n:2820000
KS ci ratio: 1.974729e-01	ci left: 1.259231e-04	ci right 1.538437e-04	k: 393	n:2820000
C2CD3   2820000 perm   4182 sec   (674 perm/sec)   p_kst 1.393617e-04   p_cons 3.271305e-01   p_joint 8.865248e-05

Joint ci ratio: 2.474172e-01	ci left: 7.772761e-05	ci right 9.999507e-05	k: 250	n:2830000
Cons ci ratio: 3.341620e-03	ci left: 3.266247e-01	ci right 3.277184e-01	k: 925895	n:2830000
KS ci ratio: 1.974730e-01	ci left: 1.254782e-04	ci right 1.533001e-04	k: 393	n:2830000
C2CD3   2830000 perm   4209 sec   (672 perm/sec)   p_kst 1.388693e-04   p_cons 3.271714e-01   p_joint 8.833922e-05

Joint ci ratio: 2.469258e-01	ci left: 7.778422e-05	ci right 1.000169e-04	k: 251	n:2840000
Cons ci ratio: 3.335862e-03	ci left: 3.266086e-01	ci right 3.277002e-01	k: 929118	n:2840000
KS ci ratio: 1.967254e-01	ci left: 1.260405e-04	ci right 1.538687e-04	k: 396	n:2840000
C2CD3   2840000 perm   4235 sec   (671 perm/sec)   p_kst 1.394366e-04   p_cons 3.271542e-01   p_joint 8.838028e-05

Joint ci ratio: 2.464373e-01	ci left: 7.784048e-05	ci right 1.000384e-04	k: 252	n:2850000
Cons ci ratio: 3.329756e-03	ci left: 3.266423e-01	ci right 3.277321e-01	k: 932483	n:2850000
KS ci ratio: 1.964781e-01	ci left: 1.259319e-04	ci right 1.536970e-04	k: 397	n:2850000
C2CD3   2850000 perm   4262 sec   (669 perm/sec)   p_kst 1.392982e-04   p_cons 3.271870e-01   p_joint 8.842105e-05

Joint ci ratio: 2.459517e-01	ci left: 7.789639e-05	ci right 1.000598e-04	k: 253	n:2860000
Cons ci ratio: 3.323972e-03	ci left: 3.266377e-01	ci right 3.277256e-01	k: 935739	n:2860000
KS ci ratio: 1.962317e-01	ci left: 1.258240e-04	ci right 1.535264e-04	k: 398	n:2860000
C2CD3   2860000 perm   4289 sec   (667 perm/sec)   p_kst 1.391608e-04   p_cons 3.271815e-01   p_joint 8.846154e-05

Joint ci ratio: 2.454690e-01	ci left: 7.795196e-05	ci right 1.000810e-04	k: 254	n:2870000
Cons ci ratio: 3.318157e-03	ci left: 3.266412e-01	ci right 3.277271e-01	k: 939018	n:2870000
KS ci ratio: 1.959863e-01	ci left: 1.257170e-04	ci right 1.533570e-04	k: 399	n:2870000
C2CD3   2870000 perm   4316 sec   (665 perm/sec)   p_kst 1.390244e-04   p_cons 3.271840e-01   p_joint 8.850174e-05

Joint ci ratio: 2.454690e-01	ci left: 7.768129e-05	ci right 9.973354e-05	k: 254	n:2880000
Cons ci ratio: 3.312474e-03	ci left: 3.266311e-01	ci right 3.277151e-01	k: 942258	n:2880000
KS ci ratio: 1.959864e-01	ci left: 1.252804e-04	ci right 1.528245e-04	k: 399	n:2880000
C2CD3   2880000 perm   4343 sec   (663 perm/sec)   p_kst 1.385417e-04   p_cons 3.271729e-01   p_joint 8.819444e-05

Joint ci ratio: 2.449891e-01	ci left: 7.773726e-05	ci right 9.975568e-05	k: 255	n:2890000
Cons ci ratio: 3.306876e-03	ci left: 3.266138e-01	ci right 3.276959e-01	k: 945477	n:2890000
KS ci ratio: 1.954982e-01	ci left: 1.255051e-04	ci right 1.530216e-04	k: 401	n:2890000
C2CD3   2890000 perm   4372 sec   (661 perm/sec)   p_kst 1.387543e-04   p_cons 3.271547e-01   p_joint 8.823529e-05

Joint ci ratio: 2.449891e-01	ci left: 7.746920e-05	ci right 9.941170e-05	k: 255	n:2900000
Cons ci ratio: 3.301163e-03	ci left: 3.266155e-01	ci right 3.276958e-01	k: 948751	n:2900000
KS ci ratio: 1.952555e-01	ci left: 1.254003e-04	ci right 1.528556e-04	k: 402	n:2900000
C2CD3   2900000 perm   4401 sec   (659 perm/sec)   p_kst 1.386207e-04   p_cons 3.271555e-01   p_joint 8.793103e-05

Joint ci ratio: 2.449892e-01	ci left: 7.720298e-05	ci right 9.907008e-05	k: 255	n:2910000
Cons ci ratio: 3.295528e-03	ci left: 3.266108e-01	ci right 3.276892e-01	k: 952006	n:2910000
KS ci ratio: 1.952556e-01	ci left: 1.249693e-04	ci right 1.523303e-04	k: 402	n:2910000
C2CD3   2910000 perm   4429 sec   (657 perm/sec)   p_kst 1.381443e-04   p_cons 3.271498e-01   p_joint 8.762887e-05

Joint ci ratio: 2.440377e-01	ci left: 7.758155e-05	ci right 9.945761e-05	k: 257	n:2920000
Cons ci ratio: 3.289887e-03	ci left: 3.266108e-01	ci right 3.276874e-01	k: 955275	n:2920000
KS ci ratio: 1.945328e-01	ci left: 1.255186e-04	ci right 1.528861e-04	k: 405	n:2920000
C2CD3   2920000 perm   4457 sec   (655 perm/sec)   p_kst 1.386986e-04   p_cons 3.271490e-01   p_joint 8.801370e-05

Joint ci ratio: 2.440378e-01	ci left: 7.731677e-05	ci right 9.911816e-05	k: 257	n:2930000
Cons ci ratio: 3.284295e-03	ci left: 3.266082e-01	ci right 3.276829e-01	k: 958536	n:2930000
KS ci ratio: 1.945328e-01	ci left: 1.250902e-04	ci right 1.523643e-04	k: 405	n:2930000
C2CD3   2930000 perm   4484 sec   (653 perm/sec)   p_kst 1.382253e-04   p_cons 3.271454e-01   p_joint 8.771331e-05

Joint ci ratio: 2.430973e-01	ci left: 7.769254e-05	ci right 9.950273e-05	k: 259	n:2940000
Cons ci ratio: 3.278703e-03	ci left: 3.266093e-01	ci right 3.276822e-01	k: 961808	n:2940000
KS ci ratio: 1.940554e-01	ci left: 1.253119e-04	ci right 1.525594e-04	k: 407	n:2940000
C2CD3   2940000 perm   4512 sec   (652 perm/sec)   p_kst 1.384354e-04   p_cons 3.271456e-01   p_joint 8.809524e-05

Joint ci ratio: 2.421676e-01	ci left: 7.806593e-05	ci right 9.988454e-05	k: 261	n:2950000
Cons ci ratio: 3.273110e-03	ci left: 3.266144e-01	ci right 3.276856e-01	k: 965092	n:2950000
KS ci ratio: 1.935815e-01	ci left: 1.255322e-04	ci right 1.527531e-04	k: 409	n:2950000
C2CD3   2950000 perm   4540 sec   (650 perm/sec)   p_kst 1.386441e-04   p_cons 3.271498e-01   p_joint 8.847458e-05

Joint ci ratio: 2.421676e-01	ci left: 7.780219e-05	ci right 9.954709e-05	k: 261	n:2960000
Cons ci ratio: 3.267352e-03	ci left: 3.266456e-01	ci right 3.277149e-01	k: 968453	n:2960000
KS ci ratio: 1.931111e-01	ci left: 1.257511e-04	ci right 1.529454e-04	k: 411	n:2960000
C2CD3   2960000 perm   4569 sec   (648 perm/sec)   p_kst 1.388514e-04   p_cons 3.271801e-01   p_joint 8.817568e-05

Joint ci ratio: 2.421677e-01	ci left: 7.754023e-05	ci right 9.921192e-05	k: 261	n:2970000
Cons ci ratio: 3.261883e-03	ci left: 3.266415e-01	ci right 3.277090e-01	k: 971710	n:2970000
KS ci ratio: 1.931111e-01	ci left: 1.253277e-04	ci right 1.524304e-04	k: 411	n:2970000
C2CD3   2970000 perm   4597 sec   (646 perm/sec)   p_kst 1.383838e-04   p_cons 3.271751e-01   p_joint 8.787879e-05

Joint ci ratio: 2.421677e-01	ci left: 7.728003e-05	ci right 9.887899e-05	k: 261	n:2980000
Cons ci ratio: 3.256365e-03	ci left: 3.266478e-01	ci right 3.277136e-01	k: 974998	n:2980000
KS ci ratio: 1.931112e-01	ci left: 1.249071e-04	ci right 1.519189e-04	k: 411	n:2980000
C2CD3   2980000 perm   4625 sec   (644 perm/sec)   p_kst 1.379195e-04   p_cons 3.271805e-01   p_joint 8.758389e-05

Joint ci ratio: 2.417069e-01	ci left: 7.733574e-05	ci right 9.890298e-05	k: 262	n:2990000
Cons ci ratio: 3.250945e-03	ci left: 3.266448e-01	ci right 3.277087e-01	k: 978258	n:2990000
KS ci ratio: 1.926441e-01	ci left: 1.251260e-04	ci right 1.521119e-04	k: 413	n:2990000
C2CD3   2990000 perm   4653 sec   (643 perm/sec)   p_kst 1.381271e-04   p_cons 3.271766e-01   p_joint 8.762542e-05

Joint ci ratio: 2.403399e-01	ci left: 7.801757e-05	ci right 9.963357e-05	k: 265	n:3000000
Cons ci ratio: 3.245649e-03	ci left: 3.266284e-01	ci right 3.276906e-01	k: 981478	n:3000000
KS ci ratio: 1.919499e-01	ci left: 1.256607e-04	ci right 1.526530e-04	k: 416	n:3000000
C2CD3   3000000 perm   4681 sec   (641 perm/sec)   p_kst 1.386667e-04   p_cons 3.271593e-01   p_joint 8.833333e-05

Joint ci ratio: 2.398894e-01	ci left: 7.807062e-05	ci right 9.965474e-05	k: 266	n:3010000
Cons ci ratio: 3.240428e-03	ci left: 3.266055e-01	ci right 3.276659e-01	k: 984678	n:3010000
KS ci ratio: 1.914912e-01	ci left: 1.258758e-04	ci right 1.528421e-04	k: 418	n:3010000
C2CD3   3010000 perm   4710 sec   (639 perm/sec)   p_kst 1.388704e-04   p_cons 3.271355e-01   p_joint 8.837209e-05

Joint ci ratio: 2.398895e-01	ci left: 7.781210e-05	ci right 9.932476e-05	k: 266	n:3020000
Cons ci ratio: 3.235045e-03	ci left: 3.266083e-01	ci right 3.276669e-01	k: 987955	n:3020000
KS ci ratio: 1.914912e-01	ci left: 1.254590e-04	ci right 1.523360e-04	k: 418	n:3020000
C2CD3   3020000 perm   4738 sec   (637 perm/sec)   p_kst 1.384106e-04   p_cons 3.271374e-01   p_joint 8.807947e-05

Joint ci ratio: 2.398895e-01	ci left: 7.755530e-05	ci right 9.899696e-05	k: 266	n:3030000
Cons ci ratio: 3.229667e-03	ci left: 3.266140e-01	ci right 3.276708e-01	k: 991241	n:3030000
KS ci ratio: 1.914913e-01	ci left: 1.250450e-04	ci right 1.518333e-04	k: 418	n:3030000
C2CD3   3030000 perm   4766 sec   (636 perm/sec)   p_kst 1.379538e-04   p_cons 3.271422e-01   p_joint 8.778878e-05

Joint ci ratio: 2.398895e-01	ci left: 7.730018e-05	ci right 9.867131e-05	k: 266	n:3040000
Cons ci ratio: 3.224422e-03	ci left: 3.266052e-01	ci right 3.276603e-01	k: 994483	n:3040000
KS ci ratio: 1.914913e-01	ci left: 1.246336e-04	ci right 1.513338e-04	k: 418	n:3040000
C2CD3   3040000 perm   4795 sec   (634 perm/sec)   p_kst 1.375000e-04   p_cons 3.271326e-01   p_joint 8.750000e-05

Joint ci ratio: 2.398896e-01	ci left: 7.704674e-05	ci right 9.834780e-05	k: 266	n:3050000
Cons ci ratio: 3.219156e-03	ci left: 3.266027e-01	ci right 3.276560e-01	k: 997744	n:3050000
KS ci ratio: 1.914913e-01	ci left: 1.242250e-04	ci right 1.508377e-04	k: 418	n:3050000
C2CD3   3050000 perm   4823 sec   (632 perm/sec)   p_kst 1.370492e-04   p_cons 3.271292e-01   p_joint 8.721311e-05

Joint ci ratio: 2.394416e-01	ci left: 7.710212e-05	ci right 9.837278e-05	k: 267	n:3060000
Cons ci ratio: 3.214078e-03	ci left: 3.265779e-01	ci right 3.276296e-01	k: 1000937	n:3060000
KS ci ratio: 1.910359e-01	ci left: 1.244413e-04	ci right 1.510296e-04	k: 420	n:3060000
C2CD3   3060000 perm   4852 sec   (631 perm/sec)   p_kst 1.372549e-04   p_cons 3.271036e-01   p_joint 8.725490e-05

Joint ci ratio: 2.394416e-01	ci left: 7.685098e-05	ci right 9.805235e-05	k: 267	n:3070000
Cons ci ratio: 3.208927e-03	ci left: 3.265667e-01	ci right 3.276167e-01	k: 1004171	n:3070000
KS ci ratio: 1.910360e-01	ci left: 1.240360e-04	ci right 1.505376e-04	k: 420	n:3070000
C2CD3   3070000 perm   4881 sec   (629 perm/sec)   p_kst 1.368078e-04   p_cons 3.270915e-01   p_joint 8.697068e-05

Joint ci ratio: 2.389961e-01	ci left: 7.690668e-05	ci right 9.807810e-05	k: 268	n:3080000
Cons ci ratio: 3.203822e-03	ci left: 3.265527e-01	ci right 3.276009e-01	k: 1007396	n:3080000
KS ci ratio: 1.908095e-01	ci left: 1.239424e-04	ci right 1.503891e-04	k: 421	n:3080000
C2CD3   3080000 perm   4910 sec   (627 perm/sec)   p_kst 1.366883e-04   p_cons 3.270766e-01   p_joint 8.701299e-05

Joint ci ratio: 2.389962e-01	ci left: 7.665779e-05	ci right 9.776070e-05	k: 268	n:3090000
Cons ci ratio: 3.198572e-03	ci left: 3.265620e-01	ci right 3.276085e-01	k: 1010693	n:3090000
KS ci ratio: 1.905838e-01	ci left: 1.238495e-04	ci right 1.502414e-04	k: 422	n:3090000
C2CD3   3090000 perm   4939 sec   (626 perm/sec)   p_kst 1.365696e-04   p_cons 3.270851e-01   p_joint 8.673139e-05

Joint ci ratio: 2.385532e-01	ci left: 7.671379e-05	ci right 9.778718e-05	k: 269	n:3100000
Cons ci ratio: 3.193332e-03	ci left: 3.265736e-01	ci right 3.276184e-01	k: 1013997	n:3100000
KS ci ratio: 1.903590e-01	ci left: 1.237572e-04	ci right 1.500947e-04	k: 423	n:3100000
C2CD3   3100000 perm   4969 sec   (624 perm/sec)   p_kst 1.364516e-04   p_cons 3.270958e-01   p_joint 8.677419e-05

Joint ci ratio: 2.381126e-01	ci left: 7.676946e-05	ci right 9.781346e-05	k: 270	n:3110000
Cons ci ratio: 3.188105e-03	ci left: 3.265866e-01	ci right 3.276298e-01	k: 1017306	n:3110000
KS ci ratio: 1.896890e-01	ci left: 1.242780e-04	ci right 1.506226e-04	k: 426	n:3110000
C2CD3   3110000 perm   4998 sec   (622 perm/sec)   p_kst 1.369775e-04   p_cons 3.271080e-01   p_joint 8.681672e-05

Joint ci ratio: 2.381127e-01	ci left: 7.652340e-05	ci right 9.749996e-05	k: 270	n:3120000
Cons ci ratio: 3.182860e-03	ci left: 3.266057e-01	ci right 3.276472e-01	k: 1020634	n:3120000
KS ci ratio: 1.896891e-01	ci left: 1.238796e-04	ci right 1.501398e-04	k: 426	n:3120000
C2CD3   3120000 perm   5027 sec   (621 perm/sec)   p_kst 1.365385e-04   p_cons 3.271263e-01   p_joint 8.653846e-05

Joint ci ratio: 2.381127e-01	ci left: 7.627892e-05	ci right 9.718846e-05	k: 270	n:3130000
Cons ci ratio: 3.177843e-03	ci left: 3.265965e-01	ci right 3.276364e-01	k: 1023874	n:3130000
KS ci ratio: 1.896891e-01	ci left: 1.234839e-04	ci right 1.496601e-04	k: 426	n:3130000
C2CD3   3130000 perm   5057 sec   (619 perm/sec)   p_kst 1.361022e-04   p_cons 3.271163e-01   p_joint 8.626198e-05

Joint ci ratio: 2.376746e-01	ci left: 7.633548e-05	ci right 9.721636e-05	k: 271	n:3140000
Cons ci ratio: 3.172736e-03	ci left: 3.266034e-01	ci right 3.276415e-01	k: 1027164	n:3140000
KS ci ratio: 1.892464e-01	ci left: 1.236973e-04	ci right 1.498506e-04	k: 428	n:3140000
C2CD3   3140000 perm   5086 sec   (617 perm/sec)   p_kst 1.363057e-04   p_cons 3.271223e-01   p_joint 8.630573e-05

Joint ci ratio: 2.372389e-01	ci left: 7.639172e-05	ci right 9.724405e-05	k: 272	n:3150000
Cons ci ratio: 3.167783e-03	ci left: 3.265921e-01	ci right 3.276286e-01	k: 1030397	n:3150000
KS ci ratio: 1.890263e-01	ci left: 1.236071e-04	ci right 1.497074e-04	k: 429	n:3150000
C2CD3   3150000 perm   5115 sec   (616 perm/sec)   p_kst 1.361905e-04   p_cons 3.271102e-01   p_joint 8.634921e-05

Joint ci ratio: 2.368056e-01	ci left: 7.644764e-05	ci right 9.727153e-05	k: 273	n:3160000
Cons ci ratio: 3.162781e-03	ci left: 3.265910e-01	ci right 3.276258e-01	k: 1033662	n:3160000
KS ci ratio: 1.888068e-01	ci left: 1.235174e-04	ci right 1.495650e-04	k: 430	n:3160000
C2CD3   3160000 perm   5145 sec   (614 perm/sec)   p_kst 1.360759e-04   p_cons 3.271082e-01   p_joint 8.639241e-05

Joint ci ratio: 2.363746e-01	ci left: 7.650324e-05	ci right 9.729880e-05	k: 274	n:3170000
Cons ci ratio: 3.157727e-03	ci left: 3.266003e-01	ci right 3.276335e-01	k: 1036960	n:3170000
KS ci ratio: 1.885882e-01	ci left: 1.234283e-04	ci right 1.494235e-04	k: 431	n:3170000
C2CD3   3170000 perm   5175 sec   (613 perm/sec)   p_kst 1.359621e-04   p_cons 3.271167e-01   p_joint 8.643533e-05

Joint ci ratio: 2.363746e-01	ci left: 7.626266e-05	ci right 9.699283e-05	k: 274	n:3180000
Cons ci ratio: 3.152952e-03	ci left: 3.265740e-01	ci right 3.276056e-01	k: 1040145	n:3180000
KS ci ratio: 1.883703e-01	ci left: 1.233398e-04	ci right 1.492829e-04	k: 432	n:3180000
C2CD3   3180000 perm   5204 sec   (611 perm/sec)   p_kst 1.358491e-04   p_cons 3.270896e-01   p_joint 8.616352e-05

Joint ci ratio: 2.355197e-01	ci left: 7.661350e-05	ci right 9.735273e-05	k: 276	n:3190000
Cons ci ratio: 3.147874e-03	ci left: 3.265933e-01	ci right 3.276233e-01	k: 1043475	n:3190000
KS ci ratio: 1.879368e-01	ci left: 1.235506e-04	ci right 1.494714e-04	k: 434	n:3190000
C2CD3   3190000 perm   5234 sec   (609 perm/sec)   p_kst 1.360502e-04   p_cons 3.271082e-01   p_joint 8.652038e-05

Joint ci ratio: 2.346740e-01	ci left: 7.696227e-05	ci right 9.771024e-05	k: 278	n:3200000
Cons ci ratio: 3.142988e-03	ci left: 3.265891e-01	ci right 3.276175e-01	k: 1046730	n:3200000
KS ci ratio: 1.872920e-01	ci left: 1.240580e-04	ci right 1.499858e-04	k: 437	n:3200000
C2CD3   3200000 perm   5264 sec   (608 perm/sec)   p_kst 1.365625e-04   p_cons 3.271031e-01   p_joint 8.687500e-05

Joint ci ratio: 2.346740e-01	ci left: 7.672251e-05	ci right 9.740585e-05	k: 278	n:3210000
Cons ci ratio: 3.137988e-03	ci left: 3.266039e-01	ci right 3.276307e-01	k: 1050046	n:3210000
KS ci ratio: 1.870786e-01	ci left: 1.239684e-04	ci right 1.498447e-04	k: 438	n:3210000
C2CD3   3210000 perm   5295 sec   (606 perm/sec)   p_kst 1.364486e-04   p_cons 3.271171e-01   p_joint 8.660436e-05

Joint ci ratio: 2.338374e-01	ci left: 7.706891e-05	ci right 9.776085e-05	k: 280	n:3220000
Cons ci ratio: 3.133163e-03	ci left: 3.265975e-01	ci right 3.276227e-01	k: 1053294	n:3220000
KS ci ratio: 1.864426e-01	ci left: 1.244715e-04	ci right 1.503545e-04	k: 441	n:3220000
C2CD3   3220000 perm   5326 sec   (605 perm/sec)   p_kst 1.369565e-04   p_cons 3.271099e-01   p_joint 8.695652e-05

Joint ci ratio: 2.330096e-01	ci left: 7.741330e-05	ci right 9.811352e-05	k: 282	n:3230000
Cons ci ratio: 3.128184e-03	ci left: 3.266159e-01	ci right 3.276395e-01	k: 1056622	n:3230000
KS ci ratio: 1.860222e-01	ci left: 1.246765e-04	ci right 1.505370e-04	k: 443	n:3230000
C2CD3   3230000 perm   5357 sec   (603 perm/sec)   p_kst 1.371517e-04   p_cons 3.271276e-01   p_joint 8.730650e-05

Joint ci ratio: 2.321905e-01	ci left: 7.775568e-05	ci right 9.846389e-05	k: 284	n:3240000
Cons ci ratio: 3.123472e-03	ci left: 3.266000e-01	ci right 3.276220e-01	k: 1059839	n:3240000
KS ci ratio: 1.856046e-01	ci left: 1.248803e-04	ci right 1.507184e-04	k: 445	n:3240000
C2CD3   3240000 perm   5387 sec   (601 perm/sec)   p_kst 1.373457e-04   p_cons 3.271108e-01   p_joint 8.765432e-05

Joint ci ratio: 2.313800e-01	ci left: 7.809609e-05	ci right 9.881198e-05	k: 286	n:3250000
Cons ci ratio: 3.118720e-03	ci left: 3.265927e-01	ci right 3.276131e-01	k: 1063084	n:3250000
KS ci ratio: 1.849834e-01	ci left: 1.253763e-04	ci right 1.512205e-04	k: 448	n:3250000
C2CD3   3250000 perm   5417 sec   (600 perm/sec)   p_kst 1.378462e-04   p_cons 3.271028e-01   p_joint 8.800000e-05

Joint ci ratio: 2.313801e-01	ci left: 7.785653e-05	ci right 9.850888e-05	k: 286	n:3260000
Cons ci ratio: 3.114011e-03	ci left: 3.265824e-01	ci right 3.276013e-01	k: 1066319	n:3260000
KS ci ratio: 1.847778e-01	ci left: 1.252843e-04	ci right 1.510775e-04	k: 449	n:3260000
C2CD3   3260000 perm   5448 sec   (598 perm/sec)   p_kst 1.377301e-04   p_cons 3.270917e-01   p_joint 8.773006e-05

Joint ci ratio: 2.305780e-01	ci left: 7.819467e-05	ci right 9.885457e-05	k: 288	n:3270000
Cons ci ratio: 3.109017e-03	ci left: 3.266157e-01	ci right 3.276330e-01	k: 1069696	n:3270000
KS ci ratio: 1.843685e-01	ci left: 1.254845e-04	ci right 1.512554e-04	k: 451	n:3270000
C2CD3   3270000 perm   5479 sec   (597 perm/sec)   p_kst 1.379205e-04   p_cons 3.271242e-01   p_joint 8.807339e-05

Joint ci ratio: 2.305780e-01	ci left: 7.795627e-05	ci right 9.855319e-05	k: 288	n:3280000
Cons ci ratio: 3.104315e-03	ci left: 3.266106e-01	ci right 3.276263e-01	k: 1072948	n:3280000
KS ci ratio: 1.843686e-01	ci left: 1.251019e-04	ci right 1.507942e-04	k: 451	n:3280000
C2CD3   3280000 perm   5509 sec   (595 perm/sec)   p_kst 1.375000e-04   p_cons 3.271183e-01   p_joint 8.780488e-05

Joint ci ratio: 2.305781e-01	ci left: 7.771932e-05	ci right 9.825364e-05	k: 288	n:3290000
Cons ci ratio: 3.099568e-03	ci left: 3.266149e-01	ci right 3.276291e-01	k: 1076231	n:3290000
KS ci ratio: 1.839620e-01	ci left: 1.253015e-04	ci right 1.509718e-04	k: 453	n:3290000
C2CD3   3290000 perm   5540 sec   (594 perm/sec)   p_kst 1.376900e-04   p_cons 3.271219e-01   p_joint 8.753799e-05

Joint ci ratio: 2.305781e-01	ci left: 7.748381e-05	ci right 9.795590e-05	k: 288	n:3300000
Cons ci ratio: 3.094797e-03	ci left: 3.266259e-01	ci right 3.276386e-01	k: 1079536	n:3300000
KS ci ratio: 1.837597e-01	ci left: 1.252109e-04	ci right 1.508312e-04	k: 454	n:3300000
C2CD3   3300000 perm   5571 sec   (592 perm/sec)   p_kst 1.375758e-04   p_cons 3.271321e-01   p_joint 8.727273e-05

Joint ci ratio: 2.301802e-01	ci left: 7.753440e-05	ci right 9.797948e-05	k: 289	n:3310000
Cons ci ratio: 3.090235e-03	ci left: 3.266100e-01	ci right 3.276211e-01	k: 1082752	n:3310000
KS ci ratio: 1.833572e-01	ci left: 1.254091e-04	ci right 1.510075e-04	k: 456	n:3310000
C2CD3   3310000 perm   5602 sec   (591 perm/sec)   p_kst 1.377644e-04   p_cons 3.271154e-01   p_joint 8.731118e-05

Joint ci ratio: 2.297844e-01	ci left: 7.758471e-05	ci right 9.800289e-05	k: 290	n:3320000
Cons ci ratio: 3.085597e-03	ci left: 3.266080e-01	ci right 3.276176e-01	k: 1086014	n:3320000
KS ci ratio: 1.831569e-01	ci left: 1.253188e-04	ci right 1.508677e-04	k: 457	n:3320000
C2CD3   3320000 perm   5633 sec   (589 perm/sec)   p_kst 1.376506e-04   p_cons 3.271127e-01   p_joint 8.734940e-05

Joint ci ratio: 2.282211e-01	ci left: 7.848403e-05	ci right 9.897857e-05	k: 294	n:3330000
Cons ci ratio: 3.081032e-03	ci left: 3.265985e-01	ci right 3.276066e-01	k: 1089251	n:3330000
KS ci ratio: 1.823622e-01	ci left: 1.260887e-04	ci right 1.516707e-04	k: 461	n:3330000
C2CD3   3330000 perm   5664 sec   (588 perm/sec)   p_kst 1.384384e-04   p_cons 3.271024e-01   p_joint 8.828829e-05

Joint ci ratio: 2.278352e-01	ci left: 7.853134e-05	ci right 9.899870e-05	k: 295	n:3340000
Cons ci ratio: 3.076494e-03	ci left: 3.265882e-01	ci right 3.275948e-01	k: 1092485	n:3340000
KS ci ratio: 1.821652e-01	ci left: 1.259969e-04	ci right 1.515297e-04	k: 462	n:3340000
C2CD3   3340000 perm   5695 sec   (586 perm/sec)   p_kst 1.383234e-04   p_cons 3.270913e-01   p_joint 8.832335e-05

Joint ci ratio: 2.278353e-01	ci left: 7.829692e-05	ci right 9.870319e-05	k: 295	n:3350000
Cons ci ratio: 3.071886e-03	ci left: 3.265907e-01	ci right 3.275958e-01	k: 1095762	n:3350000
KS ci ratio: 1.821652e-01	ci left: 1.256208e-04	ci right 1.510773e-04	k: 462	n:3350000
C2CD3   3350000 perm   5726 sec   (585 perm/sec)   p_kst 1.379104e-04   p_cons 3.270931e-01   p_joint 8.805970e-05

Joint ci ratio: 2.274514e-01	ci left: 7.834454e-05	ci right 9.872399e-05	k: 296	n:3360000
Cons ci ratio: 3.067208e-03	ci left: 3.266064e-01	ci right 3.276100e-01	k: 1099083	n:3360000
KS ci ratio: 1.817730e-01	ci left: 1.258151e-04	ci right 1.512500e-04	k: 464	n:3360000
C2CD3   3360000 perm   5757 sec   (584 perm/sec)   p_kst 1.380952e-04   p_cons 3.271080e-01   p_joint 8.809524e-05

Joint ci ratio: 2.274514e-01	ci left: 7.811206e-05	ci right 9.843104e-05	k: 296	n:3370000
Cons ci ratio: 3.062794e-03	ci left: 3.265869e-01	ci right 3.275890e-01	k: 1102286	n:3370000
KS ci ratio: 1.817731e-01	ci left: 1.254417e-04	ci right 1.508012e-04	k: 464	n:3370000
C2CD3   3370000 perm   5789 sec   (582 perm/sec)   p_kst 1.376855e-04   p_cons 3.270878e-01   p_joint 8.783383e-05

Joint ci ratio: 2.270695e-01	ci left: 7.815998e-05	ci right 9.845249e-05	k: 297	n:3380000
Cons ci ratio: 3.058301e-03	ci left: 3.265818e-01	ci right 3.275824e-01	k: 1105537	n:3380000
KS ci ratio: 1.811895e-01	ci left: 1.259178e-04	ci right 1.512829e-04	k: 467	n:3380000
C2CD3   3380000 perm   5820 sec   (581 perm/sec)   p_kst 1.381657e-04   p_cons 3.270820e-01   p_joint 8.786982e-05

Joint ci ratio: 2.266894e-01	ci left: 7.820764e-05	ci right 9.847380e-05	k: 298	n:3390000
Cons ci ratio: 3.053709e-03	ci left: 3.265938e-01	ci right 3.275929e-01	k: 1108846	n:3390000
KS ci ratio: 1.806115e-01	ci left: 1.263913e-04	ci right 1.517616e-04	k: 470	n:3390000
C2CD3   3390000 perm   5852 sec   (579 perm/sec)   p_kst 1.386431e-04   p_cons 3.270932e-01   p_joint 8.790560e-05

Joint ci ratio: 2.263113e-01	ci left: 7.825505e-05	ci right 9.849494e-05	k: 299	n:3400000
Cons ci ratio: 3.049367e-03	ci left: 3.265725e-01	ci right 3.275701e-01	k: 1112042	n:3400000
KS ci ratio: 1.804201e-01	ci left: 1.263004e-04	ci right 1.516227e-04	k: 471	n:3400000
C2CD3   3400000 perm   5883 sec   (578 perm/sec)   p_kst 1.385294e-04   p_cons 3.270712e-01   p_joint 8.794118e-05

Joint ci ratio: 2.259350e-01	ci left: 7.830221e-05	ci right 9.851594e-05	k: 300	n:3410000
Cons ci ratio: 3.044965e-03	ci left: 3.265628e-01	ci right 3.275589e-01	k: 1115277	n:3410000
KS ci ratio: 1.802293e-01	ci left: 1.262100e-04	ci right 1.514845e-04	k: 472	n:3410000
C2CD3   3410000 perm   5915 sec   (577 perm/sec)   p_kst 1.384164e-04   p_cons 3.270607e-01   p_joint 8.797654e-05

Joint ci ratio: 2.259351e-01	ci left: 7.807325e-05	ci right 9.822788e-05	k: 300	n:3420000
Cons ci ratio: 3.040588e-03	ci left: 3.265522e-01	ci right 3.275469e-01	k: 1118509	n:3420000
KS ci ratio: 1.802293e-01	ci left: 1.258410e-04	ci right 1.510416e-04	k: 472	n:3420000
C2CD3   3420000 perm   5947 sec   (575 perm/sec)   p_kst 1.380117e-04   p_cons 3.270494e-01   p_joint 8.771930e-05

Joint ci ratio: 2.251881e-01	ci left: 7.839578e-05	ci right 9.855748e-05	k: 302	n:3430000
Cons ci ratio: 3.036107e-03	ci left: 3.265595e-01	ci right 3.275527e-01	k: 1121802	n:3430000
KS ci ratio: 1.796604e-01	ci left: 1.263093e-04	ci right 1.515152e-04	k: 475	n:3430000
C2CD3   3430000 perm   5979 sec   (574 perm/sec)   p_kst 1.384840e-04   p_cons 3.270560e-01   p_joint 8.804665e-05

Joint ci ratio: 2.248175e-01	ci left: 7.844220e-05	ci right 9.857803e-05	k: 303	n:3440000
Cons ci ratio: 3.031618e-03	ci left: 3.265708e-01	ci right 3.275626e-01	k: 1125109	n:3440000
KS ci ratio: 1.789102e-01	ci left: 1.270528e-04	ci right 1.522897e-04	k: 479	n:3440000
C2CD3   3440000 perm   6010 sec   (572 perm/sec)   p_kst 1.392442e-04   p_cons 3.270666e-01   p_joint 8.808140e-05

Joint ci ratio: 2.248175e-01	ci left: 7.821483e-05	ci right 9.829230e-05	k: 303	n:3450000
Cons ci ratio: 3.027241e-03	ci left: 3.265687e-01	ci right 3.275591e-01	k: 1128370	n:3450000
KS ci ratio: 1.789102e-01	ci left: 1.266845e-04	ci right 1.518482e-04	k: 479	n:3450000
C2CD3   3450000 perm   6043 sec   (571 perm/sec)   p_kst 1.388406e-04   p_cons 3.270638e-01   p_joint 8.782609e-05

Joint ci ratio: 2.244486e-01	ci left: 7.826153e-05	ci right 9.831347e-05	k: 304	n:3460000
Cons ci ratio: 3.022771e-03	ci left: 3.265828e-01	ci right 3.275718e-01	k: 1131687	n:3460000
KS ci ratio: 1.787242e-01	ci left: 1.265944e-04	ci right 1.517113e-04	k: 480	n:3460000
C2CD3   3460000 perm   6074 sec   (570 perm/sec)   p_kst 1.387283e-04   p_cons 3.270772e-01   p_joint 8.786127e-05

Joint ci ratio: 2.237163e-01	ci left: 7.858002e-05	ci right 9.863881e-05	k: 306	n:3470000
Cons ci ratio: 3.018264e-03	ci left: 3.266052e-01	ci right 3.275928e-01	k: 1135033	n:3470000
KS ci ratio: 1.783537e-01	ci left: 1.267802e-04	ci right 1.518762e-04	k: 482	n:3470000
C2CD3   3470000 perm   6107 sec   (568 perm/sec)   p_kst 1.389049e-04   p_cons 3.270988e-01   p_joint 8.818444e-05

Joint ci ratio: 2.229911e-01	ci left: 7.889677e-05	ci right 9.896218e-05	k: 308	n:3480000
Cons ci ratio: 3.014016e-03	ci left: 3.265924e-01	ci right 3.275785e-01	k: 1138257	n:3480000
KS ci ratio: 1.779856e-01	ci left: 1.269650e-04	ci right 1.520401e-04	k: 484	n:3480000
C2CD3   3480000 perm   6140 sec   (567 perm/sec)   p_kst 1.390805e-04   p_cons 3.270853e-01   p_joint 8.850575e-05

Joint ci ratio: 2.226311e-01	ci left: 7.894125e-05	ci right 9.898112e-05	k: 309	n:3490000
Cons ci ratio: 3.009595e-03	ci left: 3.266078e-01	ci right 3.275925e-01	k: 1141579	n:3490000
KS ci ratio: 1.776197e-01	ci left: 1.271488e-04	ci right 1.522030e-04	k: 486	n:3490000
C2CD3   3490000 perm   6172 sec   (565 perm/sec)   p_kst 1.392550e-04   p_cons 3.271000e-01   p_joint 8.853868e-05

Joint ci ratio: 2.222729e-01	ci left: 7.898550e-05	ci right 9.899992e-05	k: 310	n:3500000
Cons ci ratio: 3.005417e-03	ci left: 3.265902e-01	ci right 3.275735e-01	k: 1144786	n:3500000
KS ci ratio: 1.768947e-01	ci left: 1.278777e-04	ci right 1.529616e-04	k: 490	n:3500000
C2CD3   3500000 perm   6204 sec   (564 perm/sec)   p_kst 1.400000e-04   p_cons 3.270817e-01   p_joint 8.857143e-05

Joint ci ratio: 2.222729e-01	ci left: 7.876047e-05	ci right 9.871787e-05	k: 310	n:3510000
Cons ci ratio: 3.001160e-03	ci left: 3.265870e-01	ci right 3.275689e-01	k: 1148043	n:3510000
KS ci ratio: 1.768947e-01	ci left: 1.275133e-04	ci right 1.525258e-04	k: 490	n:3510000
C2CD3   3510000 perm   6236 sec   (563 perm/sec)   p_kst 1.396011e-04   p_cons 3.270778e-01   p_joint 8.831909e-05

Joint ci ratio: 2.222730e-01	ci left: 7.853672e-05	ci right 9.843742e-05	k: 310	n:3520000
Cons ci ratio: 2.996752e-03	ci left: 3.266085e-01	ci right 3.275890e-01	k: 1151387	n:3520000
KS ci ratio: 1.767149e-01	ci left: 1.274226e-04	ci right 1.523892e-04	k: 491	n:3520000
C2CD3   3520000 perm   6269 sec   (561 perm/sec)   p_kst 1.394886e-04   p_cons 3.270986e-01   p_joint 8.806818e-05

Joint ci ratio: 2.215616e-01	ci left: 7.884932e-05	ci right 9.875658e-05	k: 312	n:3530000
Cons ci ratio: 2.992533e-03	ci left: 3.266049e-01	ci right 3.275840e-01	k: 1154643	n:3530000
KS ci ratio: 1.760008e-01	ci left: 1.281447e-04	ci right 1.531406e-04	k: 495	n:3530000
C2CD3   3530000 perm   6302 sec   (560 perm/sec)   p_kst 1.402266e-04   p_cons 3.270943e-01   p_joint 8.838527e-05

Joint ci ratio: 2.212086e-01	ci left: 7.889340e-05	ci right 9.877573e-05	k: 313	n:3540000
Cons ci ratio: 2.988300e-03	ci left: 3.266062e-01	ci right 3.275839e-01	k: 1157916	n:3540000
KS ci ratio: 1.758237e-01	ci left: 1.280528e-04	ci right 1.530029e-04	k: 496	n:3540000
C2CD3   3540000 perm   6335 sec   (559 perm/sec)   p_kst 1.401130e-04   p_cons 3.270949e-01   p_joint 8.841808e-05

Joint ci ratio: 2.212086e-01	ci left: 7.867116e-05	ci right 9.849749e-05	k: 313	n:3550000
Cons ci ratio: 2.984214e-03	ci left: 3.265883e-01	ci right 3.275646e-01	k: 1161121	n:3550000
KS ci ratio: 1.758237e-01	ci left: 1.276921e-04	ci right 1.525719e-04	k: 496	n:3550000
C2CD3   3550000 perm   6368 sec   (557 perm/sec)   p_kst 1.397183e-04   p_cons 3.270763e-01   p_joint 8.816901e-05

Joint ci ratio: 2.212086e-01	ci left: 7.845018e-05	ci right 9.822081e-05	k: 313	n:3560000
Cons ci ratio: 2.979947e-03	ci left: 3.265997e-01	ci right 3.275747e-01	k: 1164430	n:3560000
KS ci ratio: 1.758237e-01	ci left: 1.273334e-04	ci right 1.521433e-04	k: 496	n:3560000
C2CD3   3560000 perm   6400 sec   (556 perm/sec)   p_kst 1.393258e-04   p_cons 3.270871e-01   p_joint 8.792135e-05

Joint ci ratio: 2.208572e-01	ci left: 7.849503e-05	ci right 9.824128e-05	k: 314	n:3570000
Cons ci ratio: 2.975922e-03	ci left: 3.265781e-01	ci right 3.275516e-01	k: 1167621	n:3570000
KS ci ratio: 1.756471e-01	ci left: 1.272445e-04	ci right 1.520096e-04	k: 497	n:3570000
C2CD3   3570000 perm   6433 sec   (555 perm/sec)   p_kst 1.392157e-04   p_cons 3.270647e-01   p_joint 8.795518e-05

Joint ci ratio: 2.208572e-01	ci left: 7.827577e-05	ci right 9.796686e-05	k: 314	n:3580000
Cons ci ratio: 2.971743e-03	ci left: 3.265816e-01	ci right 3.275538e-01	k: 1170902	n:3580000
KS ci ratio: 1.754710e-01	ci left: 1.271561e-04	ci right 1.518766e-04	k: 498	n:3580000
C2CD3   3580000 perm   6467 sec   (554 perm/sec)   p_kst 1.391061e-04   p_cons 3.270676e-01   p_joint 8.770950e-05

Joint ci ratio: 2.208573e-01	ci left: 7.805773e-05	ci right 9.769397e-05	k: 314	n:3590000
Cons ci ratio: 2.967448e-03	ci left: 3.266049e-01	ci right 3.275758e-01	k: 1174254	n:3590000
KS ci ratio: 1.752955e-01	ci left: 1.270683e-04	ci right 1.517443e-04	k: 499	n:3590000
C2CD3   3590000 perm   6500 sec   (552 perm/sec)   p_kst 1.389972e-04   p_cons 3.270903e-01   p_joint 8.746518e-05

Joint ci ratio: 2.205075e-01	ci left: 7.810333e-05	ci right 9.771571e-05	k: 315	n:3600000
Cons ci ratio: 2.963328e-03	ci left: 3.266051e-01	ci right 3.275746e-01	k: 1177523	n:3600000
KS ci ratio: 1.749459e-01	ci left: 1.272465e-04	ci right 1.519027e-04	k: 501	n:3600000
C2CD3   3600000 perm   6533 sec   (551 perm/sec)   p_kst 1.391667e-04   p_cons 3.270897e-01   p_joint 8.750000e-05

Joint ci ratio: 2.205075e-01	ci left: 7.788698e-05	ci right 9.744503e-05	k: 315	n:3610000
Cons ci ratio: 2.959068e-03	ci left: 3.266285e-01	ci right 3.275967e-01	k: 1180876	n:3610000
KS ci ratio: 1.747720e-01	ci left: 1.271589e-04	ci right 1.517710e-04	k: 502	n:3610000
C2CD3   3610000 perm   6566 sec   (550 perm/sec)   p_kst 1.390582e-04   p_cons 3.271125e-01   p_joint 8.725762e-05

Joint ci ratio: 2.194682e-01	ci left: 7.845489e-05	ci right 9.805016e-05	k: 318	n:3620000
Cons ci ratio: 2.955098e-03	ci left: 3.266112e-01	ci right 3.275780e-01	k: 1184082	n:3620000
KS ci ratio: 1.742531e-01	ci left: 1.276002e-04	ci right 1.522166e-04	k: 505	n:3620000
C2CD3   3620000 perm   6599 sec   (549 perm/sec)   p_kst 1.395028e-04   p_cons 3.270945e-01   p_joint 8.784530e-05

Joint ci ratio: 2.191250e-01	ci left: 7.849911e-05	ci right 9.807064e-05	k: 319	n:3630000
Cons ci ratio: 2.951034e-03	ci left: 3.266105e-01	ci right 3.275760e-01	k: 1187348	n:3630000
KS ci ratio: 1.740811e-01	ci left: 1.275121e-04	ci right 1.520848e-04	k: 506	n:3630000
C2CD3   3630000 perm   6632 sec   (547 perm/sec)   p_kst 1.393939e-04   p_cons 3.270931e-01   p_joint 8.787879e-05

Joint ci ratio: 2.184434e-01	ci left: 7.880280e-05	ci right 9.838072e-05	k: 321	n:3640000
Cons ci ratio: 2.946980e-03	ci left: 3.266109e-01	ci right 3.275751e-01	k: 1190618	n:3640000
KS ci ratio: 1.737388e-01	ci left: 1.276874e-04	ci right 1.522403e-04	k: 508	n:3640000
C2CD3   3640000 perm   6665 sec   (546 perm/sec)   p_kst 1.395604e-04   p_cons 3.270929e-01   p_joint 8.818681e-05

Joint ci ratio: 2.184434e-01	ci left: 7.858690e-05	ci right 9.811119e-05	k: 321	n:3650000
Cons ci ratio: 2.942905e-03	ci left: 3.266168e-01	ci right 3.275797e-01	k: 1193908	n:3650000
KS ci ratio: 1.735684e-01	ci left: 1.275996e-04	ci right 1.521091e-04	k: 509	n:3650000
C2CD3   3650000 perm   6699 sec   (545 perm/sec)   p_kst 1.394521e-04   p_cons 3.270981e-01   p_joint 8.794521e-05

Joint ci ratio: 2.181050e-01	ci left: 7.863047e-05	ci right 9.813126e-05	k: 322	n:3660000
Cons ci ratio: 2.938997e-03	ci left: 3.266002e-01	ci right 3.275618e-01	k: 1197116	n:3660000
KS ci ratio: 1.733985e-01	ci left: 1.275123e-04	ci right 1.519785e-04	k: 510	n:3660000
C2CD3   3660000 perm   6733 sec   (544 perm/sec)   p_kst 1.393443e-04   p_cons 3.270809e-01   p_joint 8.797814e-05

Joint ci ratio: 2.181050e-01	ci left: 7.841622e-05	ci right 9.786388e-05	k: 322	n:3670000
Cons ci ratio: 2.935021e-03	ci left: 3.265963e-01	ci right 3.275565e-01	k: 1200370	n:3670000
KS ci ratio: 1.733985e-01	ci left: 1.271649e-04	ci right 1.515644e-04	k: 510	n:3670000
C2CD3   3670000 perm   6766 sec   (542 perm/sec)   p_kst 1.389646e-04   p_cons 3.270763e-01   p_joint 8.773842e-05

Joint ci ratio: 2.181050e-01	ci left: 7.820313e-05	ci right 9.759794e-05	k: 322	n:3680000
Cons ci ratio: 2.931062e-03	ci left: 3.265921e-01	ci right 3.275511e-01	k: 1203623	n:3680000
KS ci ratio: 1.733985e-01	ci left: 1.268193e-04	ci right 1.511526e-04	k: 510	n:3680000
C2CD3   3680000 perm   6800 sec   (541 perm/sec)   p_kst 1.385870e-04   p_cons 3.270715e-01   p_joint 8.750000e-05

Joint ci ratio: 2.177682e-01	ci left: 7.824741e-05	ci right 9.761922e-05	k: 323	n:3690000
Cons ci ratio: 2.927030e-03	ci left: 3.266015e-01	ci right 3.275592e-01	k: 1206926	n:3690000
KS ci ratio: 1.730602e-01	ci left: 1.269941e-04	ci right 1.513084e-04	k: 512	n:3690000
C2CD3   3690000 perm   6834 sec   (540 perm/sec)   p_kst 1.387534e-04   p_cons 3.270802e-01   p_joint 8.753388e-05

Joint ci ratio: 2.177682e-01	ci left: 7.803593e-05	ci right 9.735539e-05	k: 323	n:3700000
Cons ci ratio: 2.923055e-03	ci left: 3.266047e-01	ci right 3.275610e-01	k: 1210206	n:3700000
KS ci ratio: 1.728918e-01	ci left: 1.269095e-04	ci right 1.511815e-04	k: 513	n:3700000
C2CD3   3700000 perm   6868 sec   (539 perm/sec)   p_kst 1.386486e-04   p_cons 3.270827e-01   p_joint 8.729730e-05

Joint ci ratio: 2.167669e-01	ci left: 7.859022e-05	ci right 9.794553e-05	k: 326	n:3710000
Cons ci ratio: 2.919039e-03	ci left: 3.266164e-01	ci right 3.275715e-01	k: 1213518	n:3710000
KS ci ratio: 1.723894e-01	ci left: 1.273411e-04	ci right 1.516175e-04	k: 516	n:3710000
C2CD3   3710000 perm   6902 sec   (538 perm/sec)   p_kst 1.390836e-04   p_cons 3.270938e-01   p_joint 8.787062e-05

Joint ci ratio: 2.164362e-01	ci left: 7.863319e-05	ci right 9.796561e-05	k: 327	n:3720000
Cons ci ratio: 2.915037e-03	ci left: 3.266286e-01	ci right 3.275824e-01	k: 1216832	n:3720000
KS ci ratio: 1.720569e-01	ci left: 1.275132e-04	ci right 1.517707e-04	k: 518	n:3720000
C2CD3   3720000 perm   6936 sec   (536 perm/sec)   p_kst 1.392473e-04   p_cons 3.271054e-01   p_joint 8.790323e-05

Joint ci ratio: 2.161070e-01	ci left: 7.867595e-05	ci right 9.798557e-05	k: 328	n:3730000
Cons ci ratio: 2.911109e-03	ci left: 3.266319e-01	ci right 3.275844e-01	k: 1220113	n:3730000
KS ci ratio: 1.718914e-01	ci left: 1.274279e-04	ci right 1.516434e-04	k: 519	n:3730000
C2CD3   3730000 perm   6971 sec   (535 perm/sec)   p_kst 1.391421e-04   p_cons 3.271080e-01   p_joint 8.793566e-05

Joint ci ratio: 2.157793e-01	ci left: 7.871851e-05	ci right 9.800539e-05	k: 329	n:3740000
Cons ci ratio: 2.907172e-03	ci left: 3.266390e-01	ci right 3.275902e-01	k: 1223408	n:3740000
KS ci ratio: 1.717263e-01	ci left: 1.273431e-04	ci right 1.515168e-04	k: 520	n:3740000
C2CD3   3740000 perm   7005 sec   (534 perm/sec)   p_kst 1.390374e-04   p_cons 3.271144e-01   p_joint 8.796791e-05

Joint ci ratio: 2.154531e-01	ci left: 7.876086e-05	ci right 9.802509e-05	k: 330	n:3750000
Cons ci ratio: 2.903288e-03	ci left: 3.266404e-01	ci right 3.275903e-01	k: 1226682	n:3750000
KS ci ratio: 1.715618e-01	ci left: 1.272587e-04	ci right 1.513909e-04	k: 521	n:3750000
C2CD3   3750000 perm   7039 sec   (533 perm/sec)   p_kst 1.389333e-04   p_cons 3.271152e-01   p_joint 8.800000e-05

Joint ci ratio: 2.154532e-01	ci left: 7.855139e-05	ci right 9.776438e-05	k: 330	n:3760000
Cons ci ratio: 2.899446e-03	ci left: 3.266378e-01	ci right 3.275864e-01	k: 1229941	n:3760000
KS ci ratio: 1.715618e-01	ci left: 1.269203e-04	ci right 1.509883e-04	k: 521	n:3760000
C2CD3   3760000 perm   7074 sec   (531 perm/sec)   p_kst 1.385638e-04   p_cons 3.271120e-01   p_joint 8.776596e-05

Joint ci ratio: 2.151284e-01	ci left: 7.859398e-05	ci right 9.778459e-05	k: 331	n:3770000
Cons ci ratio: 2.895658e-03	ci left: 3.266293e-01	ci right 3.275768e-01	k: 1233178	n:3770000
KS ci ratio: 1.713977e-01	ci left: 1.268375e-04	ci right 1.508644e-04	k: 522	n:3770000
C2CD3   3770000 perm   7109 sec   (530 perm/sec)   p_kst 1.384615e-04   p_cons 3.271029e-01   p_joint 8.779841e-05

Joint ci ratio: 2.151285e-01	ci left: 7.838606e-05	ci right 9.752591e-05	k: 331	n:3780000
Cons ci ratio: 2.891818e-03	ci left: 3.266310e-01	ci right 3.275772e-01	k: 1236453	n:3780000
KS ci ratio: 1.712341e-01	ci left: 1.267551e-04	ci right 1.507412e-04	k: 523	n:3780000
C2CD3   3780000 perm   7144 sec   (529 perm/sec)   p_kst 1.383598e-04   p_cons 3.271040e-01   p_joint 8.756614e-05

Joint ci ratio: 2.148052e-01	ci left: 7.842888e-05	ci right 9.754662e-05	k: 332	n:3790000
Cons ci ratio: 2.888011e-03	ci left: 3.266300e-01	ci right 3.275750e-01	k: 1239718	n:3790000
KS ci ratio: 1.710710e-01	ci left: 1.266733e-04	ci right 1.506186e-04	k: 524	n:3790000
C2CD3   3790000 perm   7178 sec   (528 perm/sec)   p_kst 1.382586e-04   p_cons 3.271024e-01   p_joint 8.759894e-05

Joint ci ratio: 2.144834e-01	ci left: 7.847150e-05	ci right 9.756720e-05	k: 333	n:3800000
Cons ci ratio: 2.884341e-03	ci left: 3.266104e-01	ci right 3.275541e-01	k: 1242912	n:3800000
KS ci ratio: 1.709083e-01	ci left: 1.265918e-04	ci right 1.504966e-04	k: 525	n:3800000
C2CD3   3800000 perm   7213 sec   (527 perm/sec)   p_kst 1.381579e-04   p_cons 3.270821e-01   p_joint 8.763158e-05

Joint ci ratio: 2.141630e-01	ci left: 7.851392e-05	ci right 9.758765e-05	k: 334	n:3810000
Cons ci ratio: 2.880595e-03	ci left: 3.266048e-01	ci right 3.275472e-01	k: 1246159	n:3810000
KS ci ratio: 1.707460e-01	ci left: 1.265108e-04	ci right 1.503753e-04	k: 526	n:3810000
C2CD3   3810000 perm   7248 sec   (526 perm/sec)   p_kst 1.380577e-04   p_cons 3.270759e-01   p_joint 8.766404e-05

Joint ci ratio: 2.141631e-01	ci left: 7.830838e-05	ci right 9.733219e-05	k: 334	n:3820000
Cons ci ratio: 2.876910e-03	ci left: 3.265918e-01	ci right 3.275330e-01	k: 1249378	n:3820000
KS ci ratio: 1.704230e-01	ci left: 1.266808e-04	ci right 1.505275e-04	k: 528	n:3820000
C2CD3   3820000 perm   7283 sec   (524 perm/sec)   p_kst 1.382199e-04   p_cons 3.270623e-01   p_joint 8.743455e-05

Joint ci ratio: 2.141631e-01	ci left: 7.810392e-05	ci right 9.707806e-05	k: 334	n:3830000
Cons ci ratio: 2.873145e-03	ci left: 3.265936e-01	ci right 3.275335e-01	k: 1252653	n:3830000
KS ci ratio: 1.702621e-01	ci left: 1.266000e-04	ci right 1.504067e-04	k: 529	n:3830000
C2CD3   3830000 perm   7319 sec   (523 perm/sec)   p_kst 1.381201e-04   p_cons 3.270634e-01   p_joint 8.720627e-05

Joint ci ratio: 2.138441e-01	ci left: 7.814699e-05	ci right 9.709960e-05	k: 335	n:3840000
Cons ci ratio: 2.869361e-03	ci left: 3.266003e-01	ci right 3.275390e-01	k: 1255947	n:3840000
KS ci ratio: 1.699418e-01	ci left: 1.267690e-04	ci right 1.505580e-04	k: 531	n:3840000
C2CD3   3840000 perm   7354 sec   (522 perm/sec)   p_kst 1.382813e-04   p_cons 3.270695e-01   p_joint 8.723958e-05

Joint ci ratio: 1.696232e-01	ci left: 1.269371e-04	ci right 1.507085e-04	k: 533	n:3850000
Cons ci ratio: 2.865644e-03	ci left: 3.265992e-01	ci right 3.275367e-01	k: 1259211	n:3850000
KS ci ratio: 1.696232e-01	ci left: 1.269371e-04	ci right 1.507085e-04	k: 533	n:3850000
C2CD3   3850000 perm   7389 sec   (521 perm/sec)   p_kst 1.384416e-04   p_cons 3.270678e-01   p_joint 1.384416e-04

Joint ci ratio: 1.693064e-01	ci left: 1.271044e-04	ci right 1.508582e-04	k: 535	n:3860000
Cons ci ratio: 2.862043e-03	ci left: 3.265823e-01	ci right 3.275185e-01	k: 1262414	n:3860000
KS ci ratio: 1.693064e-01	ci left: 1.271044e-04	ci right 1.508582e-04	k: 535	n:3860000
C2CD3   3860000 perm   7425 sec   (520 perm/sec)   p_kst 1.386010e-04   p_cons 3.270503e-01   p_joint 1.386010e-04

Joint ci ratio: 1.693065e-01	ci left: 1.267760e-04	ci right 1.504683e-04	k: 535	n:3870000
Cons ci ratio: 2.858311e-03	ci left: 3.265879e-01	ci right 3.275230e-01	k: 1265704	n:3870000
KS ci ratio: 1.693065e-01	ci left: 1.267760e-04	ci right 1.504683e-04	k: 535	n:3870000
C2CD3   3870000 perm   7460 sec   (519 perm/sec)   p_kst 1.382429e-04   p_cons 3.270553e-01   p_joint 1.382429e-04

Joint ci ratio: 1.693065e-01	ci left: 1.264493e-04	ci right 1.500805e-04	k: 535	n:3880000
Cons ci ratio: 2.854706e-03	ci left: 3.265760e-01	ci right 3.275098e-01	k: 1268926	n:3880000
KS ci ratio: 1.693065e-01	ci left: 1.264493e-04	ci right 1.500805e-04	k: 535	n:3880000
C2CD3   3880000 perm   7495 sec   (518 perm/sec)   p_kst 1.378866e-04   p_cons 3.270428e-01   p_joint 1.378866e-04

Joint ci ratio: 1.691488e-01	ci left: 1.263704e-04	ci right 1.499627e-04	k: 536	n:3890000
Cons ci ratio: 2.851067e-03	ci left: 3.265716e-01	ci right 3.275042e-01	k: 1272177	n:3890000
KS ci ratio: 1.691488e-01	ci left: 1.263704e-04	ci right 1.499627e-04	k: 536	n:3890000
C2CD3   3890000 perm   7531 sec   (517 perm/sec)   p_kst 1.377892e-04   p_cons 3.270378e-01   p_joint 1.377892e-04

Joint ci ratio: 1.691488e-01	ci left: 1.260463e-04	ci right 1.495782e-04	k: 536	n:3900000
Cons ci ratio: 2.847513e-03	ci left: 3.265562e-01	ci right 3.274876e-01	k: 1275385	n:3900000
KS ci ratio: 1.691488e-01	ci left: 1.260463e-04	ci right 1.495782e-04	k: 536	n:3900000
C2CD3   3900000 perm   7566 sec   (515 perm/sec)   p_kst 1.374359e-04   p_cons 3.270218e-01   p_joint 1.374359e-04

Joint ci ratio: 1.689916e-01	ci left: 1.259689e-04	ci right 1.494622e-04	k: 537	n:3910000
Cons ci ratio: 2.843871e-03	ci left: 3.265565e-01	ci right 3.274867e-01	k: 1278654	n:3910000
KS ci ratio: 1.689916e-01	ci left: 1.259689e-04	ci right 1.494622e-04	k: 537	n:3910000
C2CD3   3910000 perm   7602 sec   (514 perm/sec)   p_kst 1.373402e-04   p_cons 3.270215e-01   p_joint 1.373402e-04

Joint ci ratio: 1.689916e-01	ci left: 1.256476e-04	ci right 1.490809e-04	k: 537	n:3920000
Cons ci ratio: 2.840100e-03	ci left: 3.265790e-01	ci right 3.275080e-01	k: 1282010	n:3920000
KS ci ratio: 1.689916e-01	ci left: 1.256476e-04	ci right 1.490809e-04	k: 537	n:3920000
C2CD3   3920000 perm   7638 sec   (513 perm/sec)   p_kst 1.369898e-04   p_cons 3.270434e-01   p_joint 1.369898e-04

Joint ci ratio: 1.685223e-01	ci left: 1.260590e-04	ci right 1.494971e-04	k: 540	n:3930000
Cons ci ratio: 2.836531e-03	ci left: 3.265723e-01	ci right 3.275002e-01	k: 1285252	n:3930000
KS ci ratio: 1.685223e-01	ci left: 1.260590e-04	ci right 1.494971e-04	k: 540	n:3930000
C2CD3   3930000 perm   7675 sec   (512 perm/sec)   p_kst 1.374046e-04   p_cons 3.270361e-01   p_joint 1.374046e-04

Joint ci ratio: 1.683668e-01	ci left: 1.259821e-04	ci right 1.493822e-04	k: 541	n:3940000
Cons ci ratio: 2.832954e-03	ci left: 3.265690e-01	ci right 3.274957e-01	k: 1288507	n:3940000
KS ci ratio: 1.683668e-01	ci left: 1.259821e-04	ci right 1.493822e-04	k: 541	n:3940000
C2CD3   3940000 perm   7710 sec   (511 perm/sec)   p_kst 1.373096e-04   p_cons 3.270322e-01   p_joint 1.373096e-04

Joint ci ratio: 1.682117e-01	ci left: 1.259057e-04	ci right 1.492678e-04	k: 542	n:3950000
Cons ci ratio: 2.829432e-03	ci left: 3.265594e-01	ci right 3.274849e-01	k: 1291737	n:3950000
KS ci ratio: 1.682117e-01	ci left: 1.259057e-04	ci right 1.492678e-04	k: 542	n:3950000
C2CD3   3950000 perm   7746 sec   (510 perm/sec)   p_kst 1.372152e-04   p_cons 3.270220e-01   p_joint 1.372152e-04

Joint ci ratio: 1.677489e-01	ci left: 1.263135e-04	ci right 1.496803e-04	k: 545	n:3960000
Cons ci ratio: 2.825789e-03	ci left: 3.265705e-01	ci right 3.274949e-01	k: 1295049	n:3960000
KS ci ratio: 1.677489e-01	ci left: 1.263135e-04	ci right 1.496803e-04	k: 545	n:3960000
C2CD3   3960000 perm   7782 sec   (509 perm/sec)   p_kst 1.376263e-04   p_cons 3.270326e-01   p_joint 1.376263e-04

Joint ci ratio: 1.672899e-01	ci left: 1.267193e-04	ci right 1.500906e-04	k: 548	n:3970000
Cons ci ratio: 2.822207e-03	ci left: 3.265743e-01	ci right 3.274975e-01	k: 1298332	n:3970000
KS ci ratio: 1.672899e-01	ci left: 1.267193e-04	ci right 1.500906e-04	k: 548	n:3970000
C2CD3   3970000 perm   7818 sec   (508 perm/sec)   p_kst 1.380353e-04   p_cons 3.270358e-01   p_joint 1.380353e-04

Joint ci ratio: 1.668347e-01	ci left: 1.271232e-04	ci right 1.504987e-04	k: 551	n:3980000
Cons ci ratio: 2.818741e-03	ci left: 3.265622e-01	ci right 3.274843e-01	k: 1301552	n:3980000
KS ci ratio: 1.668347e-01	ci left: 1.271232e-04	ci right 1.504987e-04	k: 551	n:3980000
C2CD3   3980000 perm   7854 sec   (507 perm/sec)   p_kst 1.384422e-04   p_cons 3.270231e-01   p_joint 1.384422e-04

Joint ci ratio: 1.663831e-01	ci left: 1.275251e-04	ci right 1.509047e-04	k: 554	n:3990000
Cons ci ratio: 2.815264e-03	ci left: 3.265537e-01	ci right 3.274746e-01	k: 1304786	n:3990000
KS ci ratio: 1.663831e-01	ci left: 1.275251e-04	ci right 1.509047e-04	k: 554	n:3990000
C2CD3   3990000 perm   7891 sec   (506 perm/sec)   p_kst 1.388471e-04   p_cons 3.270140e-01   p_joint 1.388471e-04

Joint ci ratio: 1.663832e-01	ci left: 1.272063e-04	ci right 1.505275e-04	k: 554	n:4000000
Cons ci ratio: 2.811708e-03	ci left: 3.265598e-01	ci right 3.274795e-01	k: 1308078	n:4000000
KS ci ratio: 1.663832e-01	ci left: 1.272063e-04	ci right 1.505275e-04	k: 554	n:4000000
C2CD3   4000000 perm   7927 sec   (505 perm/sec)   p_kst 1.385000e-04   p_cons 3.270195e-01   p_joint 1.385000e-04

Joint ci ratio: 1.660842e-01	ci left: 1.273670e-04	ci right 1.506716e-04	k: 556	n:4010000
Cons ci ratio: 2.808145e-03	ci left: 3.265690e-01	ci right 3.274876e-01	k: 1311383	n:4010000
KS ci ratio: 1.660842e-01	ci left: 1.273670e-04	ci right 1.506716e-04	k: 556	n:4010000
C2CD3   4010000 perm   7963 sec   (504 perm/sec)   p_kst 1.386534e-04   p_cons 3.270282e-01   p_joint 1.386534e-04

Joint ci ratio: 1.659353e-01	ci left: 1.272886e-04	ci right 1.505558e-04	k: 557	n:4020000
Cons ci ratio: 2.804536e-03	ci left: 3.265874e-01	ci right 3.275049e-01	k: 1314725	n:4020000
KS ci ratio: 1.659353e-01	ci left: 1.272886e-04	ci right 1.505558e-04	k: 557	n:4020000
C2CD3   4020000 perm   8000 sec   (503 perm/sec)   p_kst 1.385572e-04   p_cons 3.270460e-01   p_joint 1.385572e-04

Joint ci ratio: 1.659353e-01	ci left: 1.269728e-04	ci right 1.501822e-04	k: 557	n:4030000
Cons ci ratio: 2.801041e-03	ci left: 3.265901e-01	ci right 3.275064e-01	k: 1318004	n:4030000
KS ci ratio: 1.659353e-01	ci left: 1.269728e-04	ci right 1.501822e-04	k: 557	n:4030000
C2CD3   4030000 perm   8037 sec   (501 perm/sec)   p_kst 1.382134e-04   p_cons 3.270481e-01   p_joint 1.382134e-04

Joint ci ratio: 1.659354e-01	ci left: 1.266585e-04	ci right 1.498105e-04	k: 557	n:4040000
Cons ci ratio: 2.797589e-03	ci left: 3.265881e-01	ci right 3.275033e-01	k: 1321264	n:4040000
KS ci ratio: 1.659354e-01	ci left: 1.266585e-04	ci right 1.498105e-04	k: 557	n:4040000
C2CD3   4040000 perm   8074 sec   (500 perm/sec)   p_kst 1.378713e-04   p_cons 3.270455e-01   p_joint 1.378713e-04

Joint ci ratio: 1.659354e-01	ci left: 1.263458e-04	ci right 1.494406e-04	k: 557	n:4050000
Cons ci ratio: 2.794235e-03	ci left: 3.265725e-01	ci right 3.274865e-01	k: 1324469	n:4050000
KS ci ratio: 1.659354e-01	ci left: 1.263458e-04	ci right 1.494406e-04	k: 557	n:4050000
C2CD3   4050000 perm   8111 sec   (499 perm/sec)   p_kst 1.375309e-04   p_cons 3.270294e-01   p_joint 1.375309e-04

Joint ci ratio: 1.768964e-01	ci left: 1.102393e-04	ci right 1.318636e-04	k: 490	n:4060000
Cons ci ratio: 2.790808e-03	ci left: 3.265705e-01	ci right 3.274834e-01	k: 1327729	n:4060000
KS ci ratio: 1.656388e-01	ci left: 1.265067e-04	ci right 1.495856e-04	k: 559	n:4060000
C2CD3   4060000 perm   8148 sec   (498 perm/sec)   p_kst 1.376847e-04   p_cons 3.270268e-01   p_joint 1.206897e-04

Joint ci ratio: 1.768964e-01	ci left: 1.099684e-04	ci right 1.315396e-04	k: 490	n:4070000
Cons ci ratio: 2.787476e-03	ci left: 3.265555e-01	ci right 3.274673e-01	k: 1330936	n:4070000
KS ci ratio: 1.654911e-01	ci left: 1.264314e-04	ci right 1.494739e-04	k: 560	n:4070000
C2CD3   4070000 perm   8185 sec   (497 perm/sec)   p_kst 1.375921e-04   p_cons 3.270113e-01   p_joint 1.203931e-04

Joint ci ratio: 1.767166e-01	ci left: 1.099331e-04	ci right 1.314731e-04	k: 491	n:4080000
Cons ci ratio: 2.783987e-03	ci left: 3.265673e-01	ci right 3.274780e-01	k: 1334252	n:4080000
KS ci ratio: 1.653438e-01	ci left: 1.263565e-04	ci right 1.493628e-04	k: 561	n:4080000
C2CD3   4080000 perm   8222 sec   (496 perm/sec)   p_kst 1.375000e-04   p_cons 3.270225e-01   p_joint 1.203431e-04

Joint ci ratio: 1.760025e-01	ci left: 1.105992e-04	ci right 1.321728e-04	k: 495	n:4090000
Cons ci ratio: 2.780645e-03	ci left: 3.265578e-01	ci right 3.274674e-01	k: 1337481	n:4090000
KS ci ratio: 1.646131e-01	ci left: 1.272196e-04	ci right 1.502705e-04	k: 566	n:4090000
C2CD3   4090000 perm   8259 sec   (495 perm/sec)   p_kst 1.383863e-04   p_cons 3.270125e-01   p_joint 1.210269e-04

Joint ci ratio: 1.758254e-01	ci left: 1.105626e-04	ci right 1.321051e-04	k: 496	n:4100000
Cons ci ratio: 2.777241e-03	ci left: 3.265601e-01	ci right 3.274685e-01	k: 1340758	n:4100000
KS ci ratio: 1.644681e-01	ci left: 1.271431e-04	ci right 1.501579e-04	k: 567	n:4100000
C2CD3   4100000 perm   8297 sec   (494 perm/sec)   p_kst 1.382927e-04   p_cons 3.270141e-01   p_joint 1.209756e-04

Joint ci ratio: 1.756487e-01	ci left: 1.105262e-04	ci right 1.320376e-04	k: 497	n:4110000
Cons ci ratio: 2.773824e-03	ci left: 3.265664e-01	ci right 3.274737e-01	k: 1344052	n:4110000
KS ci ratio: 1.643236e-01	ci left: 1.270671e-04	ci right 1.500459e-04	k: 568	n:4110000
C2CD3   4110000 perm   8335 sec   (493 perm/sec)   p_kst 1.381995e-04   p_cons 3.270200e-01   p_joint 1.209246e-04

Joint ci ratio: 1.754727e-01	ci left: 1.104900e-04	ci right 1.319705e-04	k: 498	n:4120000
Cons ci ratio: 2.770470e-03	ci left: 3.265647e-01	ci right 3.274709e-01	k: 1347313	n:4120000
KS ci ratio: 1.641794e-01	ci left: 1.269914e-04	ci right 1.499344e-04	k: 569	n:4120000
C2CD3   4120000 perm   8372 sec   (492 perm/sec)   p_kst 1.381068e-04   p_cons 3.270177e-01   p_joint 1.208738e-04

Joint ci ratio: 1.754727e-01	ci left: 1.102224e-04	ci right 1.316510e-04	k: 498	n:4130000
Cons ci ratio: 2.767210e-03	ci left: 3.265500e-01	ci right 3.274551e-01	k: 1350520	n:4130000
KS ci ratio: 1.641794e-01	ci left: 1.266839e-04	ci right 1.495714e-04	k: 569	n:4130000
C2CD3   4130000 perm   8409 sec   (491 perm/sec)   p_kst 1.377724e-04   p_cons 3.270024e-01   p_joint 1.205811e-04

Joint ci ratio: 1.751221e-01	ci left: 1.104181e-04	ci right 1.318373e-04	k: 500	n:4140000
Cons ci ratio: 2.763873e-03	ci left: 3.265493e-01	ci right 3.274533e-01	k: 1353785	n:4140000
KS ci ratio: 1.638921e-01	ci left: 1.268412e-04	ci right 1.497130e-04	k: 571	n:4140000
C2CD3   4140000 perm   8447 sec   (490 perm/sec)   p_kst 1.379227e-04   p_cons 3.270012e-01   p_joint 1.207729e-04

Joint ci ratio: 1.747735e-01	ci left: 1.106128e-04	ci right 1.320226e-04	k: 502	n:4150000
Cons ci ratio: 2.760590e-03	ci left: 3.265422e-01	ci right 3.274451e-01	k: 1357023	n:4150000
KS ci ratio: 1.636063e-01	ci left: 1.269977e-04	ci right 1.498539e-04	k: 573	n:4150000
C2CD3   4150000 perm   8485 sec   (489 perm/sec)   p_kst 1.380723e-04   p_cons 3.269935e-01   p_joint 1.209639e-04

Joint ci ratio: 1.631804e-01	ci left: 1.273841e-04	ci right 1.502443e-04	k: 576	n:4160000
Cons ci ratio: 2.757357e-03	ci left: 3.265288e-01	ci right 3.274306e-01	k: 1360235	n:4160000
KS ci ratio: 1.631804e-01	ci left: 1.273841e-04	ci right 1.502443e-04	k: 576	n:4160000
C2CD3   4160000 perm   8522 sec   (488 perm/sec)   p_kst 1.384615e-04   p_cons 3.269796e-01   p_joint 1.384615e-04

Joint ci ratio: 1.630392e-01	ci left: 1.273087e-04	ci right 1.501336e-04	k: 577	n:4170000
Cons ci ratio: 2.754159e-03	ci left: 3.265116e-01	ci right 3.274124e-01	k: 1363431	n:4170000
KS ci ratio: 1.630392e-01	ci left: 1.273087e-04	ci right 1.501336e-04	k: 577	n:4170000
C2CD3   4170000 perm   8560 sec   (487 perm/sec)   p_kst 1.383693e-04   p_cons 3.269619e-01   p_joint 1.383693e-04

Joint ci ratio: 1.628983e-01	ci left: 1.272336e-04	ci right 1.500234e-04	k: 578	n:4180000
Cons ci ratio: 2.750871e-03	ci left: 3.265108e-01	ci right 3.274105e-01	k: 1366695	n:4180000
KS ci ratio: 1.628983e-01	ci left: 1.272336e-04	ci right 1.500234e-04	k: 578	n:4180000
C2CD3   4180000 perm   8598 sec   (486 perm/sec)   p_kst 1.382775e-04   p_cons 3.269605e-01   p_joint 1.382775e-04

Joint ci ratio: 1.626177e-01	ci left: 1.273878e-04	ci right 1.501621e-04	k: 580	n:4190000
Cons ci ratio: 2.747616e-03	ci left: 3.265067e-01	ci right 3.274053e-01	k: 1369945	n:4190000
KS ci ratio: 1.626177e-01	ci left: 1.273878e-04	ci right 1.501621e-04	k: 580	n:4190000
C2CD3   4190000 perm   8636 sec   (485 perm/sec)   p_kst 1.384248e-04   p_cons 3.269558e-01   p_joint 1.384248e-04

Joint ci ratio: 1.623385e-01	ci left: 1.275413e-04	ci right 1.503001e-04	k: 582	n:4200000
Cons ci ratio: 2.744316e-03	ci left: 3.265116e-01	ci right 3.274091e-01	k: 1373233	n:4200000
KS ci ratio: 1.623385e-01	ci left: 1.275413e-04	ci right 1.503001e-04	k: 582	n:4200000
C2CD3   4200000 perm   8674 sec   (484 perm/sec)   p_kst 1.385714e-04   p_cons 3.269602e-01   p_joint 1.385714e-04

Joint ci ratio: 1.621995e-01	ci left: 1.274663e-04	ci right 1.501902e-04	k: 583	n:4210000
Cons ci ratio: 2.741026e-03	ci left: 3.265167e-01	ci right 3.274132e-01	k: 1376522	n:4210000
KS ci ratio: 1.621995e-01	ci left: 1.274663e-04	ci right 1.501902e-04	k: 583	n:4210000
C2CD3   4210000 perm   8712 sec   (483 perm/sec)   p_kst 1.384798e-04   p_cons 3.269648e-01   p_joint 1.384798e-04

Joint ci ratio: 1.621995e-01	ci left: 1.271642e-04	ci right 1.498343e-04	k: 583	n:4220000
Cons ci ratio: 2.737900e-03	ci left: 3.264975e-01	ci right 3.273928e-01	k: 1379708	n:4220000
KS ci ratio: 1.621995e-01	ci left: 1.271642e-04	ci right 1.498343e-04	k: 583	n:4220000
C2CD3   4220000 perm   8751 sec   (482 perm/sec)   p_kst 1.381517e-04   p_cons 3.269450e-01   p_joint 1.381517e-04

Joint ci ratio: 1.621995e-01	ci left: 1.268636e-04	ci right 1.494801e-04	k: 583	n:4230000
Cons ci ratio: 2.734702e-03	ci left: 3.264915e-01	ci right 3.273858e-01	k: 1382950	n:4230000
KS ci ratio: 1.621995e-01	ci left: 1.268636e-04	ci right 1.494801e-04	k: 583	n:4230000
C2CD3   4230000 perm   8789 sec   (481 perm/sec)   p_kst 1.378251e-04   p_cons 3.269385e-01   p_joint 1.378251e-04

Joint ci ratio: 1.620609e-01	ci left: 1.267907e-04	ci right 1.493730e-04	k: 584	n:4240000
Cons ci ratio: 2.731477e-03	ci left: 3.264917e-01	ci right 3.273849e-01	k: 1386218	n:4240000
KS ci ratio: 1.620609e-01	ci left: 1.267907e-04	ci right 1.493730e-04	k: 584	n:4240000
C2CD3   4240000 perm   8827 sec   (480 perm/sec)   p_kst 1.377358e-04   p_cons 3.269382e-01   p_joint 1.377358e-04

Joint ci ratio: 1.617845e-01	ci left: 1.269438e-04	ci right 1.495112e-04	k: 586	n:4250000
Cons ci ratio: 2.728247e-03	ci left: 3.264945e-01	ci right 3.273867e-01	k: 1389497	n:4250000
KS ci ratio: 1.617845e-01	ci left: 1.269438e-04	ci right 1.495112e-04	k: 586	n:4250000
C2CD3   4250000 perm   8867 sec   (479 perm/sec)   p_kst 1.378824e-04   p_cons 3.269405e-01   p_joint 1.378824e-04

Joint ci ratio: 1.615096e-01	ci left: 1.270963e-04	ci right 1.496486e-04	k: 588	n:4260000
Cons ci ratio: 2.725080e-03	ci left: 3.264891e-01	ci right 3.273802e-01	k: 1392741	n:4260000
KS ci ratio: 1.615096e-01	ci left: 1.270963e-04	ci right 1.496486e-04	k: 588	n:4260000
C2CD3   4260000 perm   8906 sec   (478 perm/sec)   p_kst 1.380282e-04   p_cons 3.269345e-01   p_joint 1.380282e-04

Joint ci ratio: 1.615096e-01	ci left: 1.267987e-04	ci right 1.492982e-04	k: 588	n:4270000
Cons ci ratio: 2.721869e-03	ci left: 3.264925e-01	ci right 3.273826e-01	k: 1396023	n:4270000
KS ci ratio: 1.615096e-01	ci left: 1.267987e-04	ci right 1.492982e-04	k: 588	n:4270000
C2CD3   4270000 perm   8945 sec   (477 perm/sec)   p_kst 1.377049e-04   p_cons 3.269375e-01   p_joint 1.377049e-04

Joint ci ratio: 1.615097e-01	ci left: 1.265024e-04	ci right 1.489494e-04	k: 588	n:4280000
Cons ci ratio: 2.718528e-03	ci left: 3.265189e-01	ci right 3.274080e-01	k: 1399403	n:4280000
KS ci ratio: 1.615097e-01	ci left: 1.265024e-04	ci right 1.489494e-04	k: 588	n:4280000
C2CD3   4280000 perm   8984 sec   (476 perm/sec)   p_kst 1.373832e-04   p_cons 3.269633e-01   p_joint 1.373832e-04

Joint ci ratio: 1.613727e-01	ci left: 1.264312e-04	ci right 1.488447e-04	k: 589	n:4290000
Cons ci ratio: 2.715307e-03	ci left: 3.265277e-01	ci right 3.274157e-01	k: 1402708	n:4290000
KS ci ratio: 1.613727e-01	ci left: 1.264312e-04	ci right 1.488447e-04	k: 589	n:4290000
C2CD3   4290000 perm   9022 sec   (475 perm/sec)   p_kst 1.372960e-04   p_cons 3.269716e-01   p_joint 1.372960e-04

Joint ci ratio: 1.612362e-01	ci left: 1.263604e-04	ci right 1.487405e-04	k: 590	n:4300000
Cons ci ratio: 2.712189e-03	ci left: 3.265215e-01	ci right 3.274085e-01	k: 1405949	n:4300000
KS ci ratio: 1.612362e-01	ci left: 1.263604e-04	ci right 1.487405e-04	k: 590	n:4300000
C2CD3   4300000 perm   9062 sec   (475 perm/sec)   p_kst 1.372093e-04   p_cons 3.269649e-01   p_joint 1.372093e-04

Joint ci ratio: 1.610999e-01	ci left: 1.262899e-04	ci right 1.486367e-04	k: 591	n:4310000
Cons ci ratio: 2.709129e-03	ci left: 3.265077e-01	ci right 3.273937e-01	k: 1409157	n:4310000
KS ci ratio: 1.610999e-01	ci left: 1.262899e-04	ci right 1.486367e-04	k: 591	n:4310000
C2CD3   4310000 perm   9101 sec   (474 perm/sec)   p_kst 1.371230e-04   p_cons 3.269506e-01   p_joint 1.371230e-04

Joint ci ratio: 1.609640e-01	ci left: 1.262197e-04	ci right 1.485335e-04	k: 592	n:4320000
Cons ci ratio: 2.705899e-03	ci left: 3.265231e-01	ci right 3.274081e-01	k: 1412491	n:4320000
KS ci ratio: 1.609640e-01	ci left: 1.262197e-04	ci right 1.485335e-04	k: 592	n:4320000
C2CD3   4320000 perm   9141 sec   (473 perm/sec)   p_kst 1.370370e-04   p_cons 3.269655e-01   p_joint 1.370370e-04

Joint ci ratio: 1.609641e-01	ci left: 1.259282e-04	ci right 1.481904e-04	k: 592	n:4330000
Cons ci ratio: 2.702828e-03	ci left: 3.265147e-01	ci right 3.273987e-01	k: 1415722	n:4330000
KS ci ratio: 1.609641e-01	ci left: 1.259282e-04	ci right 1.481904e-04	k: 592	n:4330000
C2CD3   4330000 perm   9180 sec   (472 perm/sec)   p_kst 1.367206e-04   p_cons 3.269566e-01   p_joint 1.367206e-04

Joint ci ratio: 1.608285e-01	ci left: 1.258592e-04	ci right 1.480887e-04	k: 593	n:4340000
Cons ci ratio: 2.699597e-03	ci left: 3.265340e-01	ci right 3.274169e-01	k: 1419073	n:4340000
KS ci ratio: 1.608285e-01	ci left: 1.258592e-04	ci right 1.480887e-04	k: 593	n:4340000
C2CD3   4340000 perm   9220 sec   (471 perm/sec)   p_kst 1.366359e-04   p_cons 3.269753e-01   p_joint 1.366359e-04

Joint ci ratio: 1.606933e-01	ci left: 1.257905e-04	ci right 1.479873e-04	k: 594	n:4350000
Cons ci ratio: 2.696502e-03	ci left: 3.265330e-01	ci right 3.274149e-01	k: 1422336	n:4350000
KS ci ratio: 1.606933e-01	ci left: 1.257905e-04	ci right 1.479873e-04	k: 594	n:4350000
C2CD3   4350000 perm   9260 sec   (470 perm/sec)   p_kst 1.365517e-04   p_cons 3.269738e-01   p_joint 1.365517e-04

Joint ci ratio: 1.602897e-01	ci left: 1.261624e-04	ci right 1.483636e-04	k: 597	n:4360000
Cons ci ratio: 2.693486e-03	ci left: 3.265207e-01	ci right 3.274016e-01	k: 1425550	n:4360000
KS ci ratio: 1.602897e-01	ci left: 1.261624e-04	ci right 1.483636e-04	k: 597	n:4360000
C2CD3   4360000 perm   9300 sec   (469 perm/sec)   p_kst 1.369266e-04   p_cons 3.269610e-01   p_joint 1.369266e-04

Joint ci ratio: 1.601559e-01	ci left: 1.260933e-04	ci right 1.482621e-04	k: 598	n:4370000
Cons ci ratio: 2.690333e-03	ci left: 3.265325e-01	ci right 3.274124e-01	k: 1428869	n:4370000
KS ci ratio: 1.601559e-01	ci left: 1.260933e-04	ci right 1.482621e-04	k: 598	n:4370000
C2CD3   4370000 perm   9339 sec   (468 perm/sec)   p_kst 1.368421e-04   p_cons 3.269723e-01   p_joint 1.368421e-04

Joint ci ratio: 1.594915e-01	ci left: 1.269014e-04	ci right 1.491108e-04	k: 603	n:4380000
Cons ci ratio: 2.687274e-03	ci left: 3.265308e-01	ci right 3.274096e-01	k: 1432129	n:4380000
KS ci ratio: 1.594915e-01	ci left: 1.269014e-04	ci right 1.491108e-04	k: 603	n:4380000
C2CD3   4380000 perm   9380 sec   (467 perm/sec)   p_kst 1.376712e-04   p_cons 3.269701e-01   p_joint 1.376712e-04

Joint ci ratio: 1.594915e-01	ci left: 1.266123e-04	ci right 1.487711e-04	k: 603	n:4390000
Cons ci ratio: 2.684213e-03	ci left: 3.265311e-01	ci right 3.274090e-01	k: 1435398	n:4390000
KS ci ratio: 1.594915e-01	ci left: 1.266123e-04	ci right 1.487711e-04	k: 603	n:4390000
C2CD3   4390000 perm   9419 sec   (466 perm/sec)   p_kst 1.373576e-04   p_cons 3.269699e-01   p_joint 1.373576e-04

Joint ci ratio: 1.592281e-01	ci left: 1.267610e-04	ci right 1.489057e-04	k: 605	n:4400000
Cons ci ratio: 2.681213e-03	ci left: 3.265230e-01	ci right 3.273999e-01	k: 1438630	n:4400000
KS ci ratio: 1.592281e-01	ci left: 1.267610e-04	ci right 1.489057e-04	k: 605	n:4400000
C2CD3   4400000 perm   9459 sec   (465 perm/sec)   p_kst 1.375000e-04   p_cons 3.269614e-01   p_joint 1.375000e-04

Joint ci ratio: 1.589660e-01	ci left: 1.269090e-04	ci right 1.490396e-04	k: 607	n:4410000
Cons ci ratio: 2.678223e-03	ci left: 3.265150e-01	ci right 3.273909e-01	k: 1441862	n:4410000
KS ci ratio: 1.589660e-01	ci left: 1.269090e-04	ci right 1.490396e-04	k: 607	n:4410000
C2CD3   4410000 perm   9498 sec   (464 perm/sec)   p_kst 1.376417e-04   p_cons 3.269528e-01   p_joint 1.376417e-04

Joint ci ratio: 1.589660e-01	ci left: 1.266219e-04	ci right 1.487024e-04	k: 607	n:4420000
Cons ci ratio: 2.675197e-03	ci left: 3.265147e-01	ci right 3.273896e-01	k: 1445128	n:4420000
KS ci ratio: 1.589660e-01	ci left: 1.266219e-04	ci right 1.487024e-04	k: 607	n:4420000
C2CD3   4420000 perm   9539 sec   (463 perm/sec)   p_kst 1.373303e-04   p_cons 3.269520e-01   p_joint 1.373303e-04

Joint ci ratio: 1.588355e-01	ci left: 1.265528e-04	ci right 1.486014e-04	k: 608	n:4430000
Cons ci ratio: 2.672047e-03	ci left: 3.265363e-01	ci right 3.274102e-01	k: 1448491	n:4430000
KS ci ratio: 1.588355e-01	ci left: 1.265528e-04	ci right 1.486014e-04	k: 608	n:4430000
C2CD3   4430000 perm   9580 sec   (462 perm/sec)   p_kst 1.372460e-04   p_cons 3.269731e-01   p_joint 1.372460e-04

Joint ci ratio: 1.588355e-01	ci left: 1.262678e-04	ci right 1.482667e-04	k: 608	n:4440000
Cons ci ratio: 2.669061e-03	ci left: 3.265328e-01	ci right 3.274057e-01	k: 1451743	n:4440000
KS ci ratio: 1.588355e-01	ci left: 1.262678e-04	ci right 1.482667e-04	k: 608	n:4440000
C2CD3   4440000 perm   9620 sec   (462 perm/sec)   p_kst 1.369369e-04   p_cons 3.269691e-01   p_joint 1.369369e-04

Joint ci ratio: 1.588355e-01	ci left: 1.259840e-04	ci right 1.479335e-04	k: 608	n:4450000
Cons ci ratio: 2.666018e-03	ci left: 3.265403e-01	ci right 3.274123e-01	k: 1455044	n:4450000
KS ci ratio: 1.588355e-01	ci left: 1.259840e-04	ci right 1.479335e-04	k: 608	n:4450000
C2CD3   4450000 perm   9661 sec   (461 perm/sec)   p_kst 1.366292e-04   p_cons 3.269762e-01   p_joint 1.366292e-04

Joint ci ratio: 1.587053e-01	ci left: 1.259168e-04	ci right 1.478350e-04	k: 609	n:4460000
Cons ci ratio: 2.663038e-03	ci left: 3.265391e-01	ci right 3.274100e-01	k: 1458306	n:4460000
KS ci ratio: 1.587053e-01	ci left: 1.259168e-04	ci right 1.478350e-04	k: 609	n:4460000
C2CD3   4460000 perm   9701 sec   (460 perm/sec)   p_kst 1.365471e-04   p_cons 3.269744e-01   p_joint 1.365471e-04

Joint ci ratio: 1.585754e-01	ci left: 1.258500e-04	ci right 1.477368e-04	k: 610	n:4470000
Cons ci ratio: 2.659978e-03	ci left: 3.265526e-01	ci right 3.274226e-01	k: 1461634	n:4470000
KS ci ratio: 1.585754e-01	ci left: 1.258500e-04	ci right 1.477368e-04	k: 610	n:4470000
C2CD3   4470000 perm   9742 sec   (459 perm/sec)   p_kst 1.364653e-04   p_cons 3.269875e-01   p_joint 1.364653e-04

Joint ci ratio: 1.583165e-01	ci left: 1.259978e-04	ci right 1.478712e-04	k: 612	n:4480000
Cons ci ratio: 2.657052e-03	ci left: 3.265457e-01	ci right 3.274148e-01	k: 1464871	n:4480000
KS ci ratio: 1.583165e-01	ci left: 1.259978e-04	ci right 1.478712e-04	k: 612	n:4480000
C2CD3   4480000 perm   9783 sec   (458 perm/sec)   p_kst 1.366071e-04   p_cons 3.269801e-01   p_joint 1.366071e-04

Joint ci ratio: 1.580588e-01	ci left: 1.261450e-04	ci right 1.480049e-04	k: 614	n:4490000
Cons ci ratio: 2.654044e-03	ci left: 3.265541e-01	ci right 3.274221e-01	k: 1468176	n:4490000
KS ci ratio: 1.580588e-01	ci left: 1.261450e-04	ci right 1.480049e-04	k: 614	n:4490000
C2CD3   4490000 perm   9825 sec   (457 perm/sec)   p_kst 1.367483e-04   p_cons 3.269880e-01   p_joint 1.367483e-04

Joint ci ratio: 1.575472e-01	ci left: 1.267184e-04	ci right 1.485999e-04	k: 618	n:4500000
Cons ci ratio: 2.651098e-03	ci left: 3.265539e-01	ci right 3.274210e-01	k: 1471443	n:4500000
KS ci ratio: 1.575472e-01	ci left: 1.267184e-04	ci right 1.485999e-04	k: 618	n:4500000
C2CD3   4500000 perm   9866 sec   (456 perm/sec)   p_kst 1.373333e-04   p_cons 3.269873e-01   p_joint 1.373333e-04

Joint ci ratio: 1.574201e-01	ci left: 1.266505e-04	ci right 1.485009e-04	k: 619	n:4510000
Cons ci ratio: 2.648208e-03	ci left: 3.265460e-01	ci right 3.274121e-01	k: 1474675	n:4510000
KS ci ratio: 1.574201e-01	ci left: 1.266505e-04	ci right 1.485009e-04	k: 619	n:4510000
C2CD3   4510000 perm   9907 sec   (455 perm/sec)   p_kst 1.372506e-04   p_cons 3.269789e-01   p_joint 1.372506e-04

Joint ci ratio: 1.569147e-01	ci left: 1.272204e-04	ci right 1.490921e-04	k: 623	n:4520000
Cons ci ratio: 2.645218e-03	ci left: 3.265562e-01	ci right 3.274214e-01	k: 1477989	n:4520000
KS ci ratio: 1.569147e-01	ci left: 1.272204e-04	ci right 1.490921e-04	k: 623	n:4520000
C2CD3   4520000 perm   9949 sec   (454 perm/sec)   p_kst 1.378319e-04   p_cons 3.269887e-01   p_joint 1.378319e-04

Joint ci ratio: 1.569148e-01	ci left: 1.269396e-04	ci right 1.487630e-04	k: 623	n:4530000
Cons ci ratio: 2.642200e-03	ci left: 3.265729e-01	ci right 3.274371e-01	k: 1481332	n:4530000
KS ci ratio: 1.569148e-01	ci left: 1.269396e-04	ci right 1.487630e-04	k: 623	n:4530000
C2CD3   4530000 perm   9990 sec   (453 perm/sec)   p_kst 1.375276e-04   p_cons 3.270049e-01   p_joint 1.375276e-04

Joint ci ratio: 1.569148e-01	ci left: 1.266600e-04	ci right 1.484353e-04	k: 623	n:4540000
Cons ci ratio: 2.639309e-03	ci left: 3.265698e-01	ci right 3.274331e-01	k: 1484586	n:4540000
KS ci ratio: 1.569148e-01	ci left: 1.266600e-04	ci right 1.484353e-04	k: 623	n:4540000
C2CD3   4540000 perm   10032 sec   (453 perm/sec)   p_kst 1.372247e-04   p_cons 3.270013e-01   p_joint 1.372247e-04

Joint ci ratio: 1.567892e-01	ci left: 1.265928e-04	ci right 1.483375e-04	k: 624	n:4550000
Cons ci ratio: 2.636306e-03	ci left: 3.265872e-01	ci right 3.274495e-01	k: 1487933	n:4550000
KS ci ratio: 1.567892e-01	ci left: 1.265928e-04	ci right 1.483375e-04	k: 624	n:4550000
C2CD3   4550000 perm   10073 sec   (452 perm/sec)   p_kst 1.371429e-04   p_cons 3.270182e-01   p_joint 1.371429e-04

Joint ci ratio: 1.566639e-01	ci left: 1.265258e-04	ci right 1.482401e-04	k: 625	n:4560000
Cons ci ratio: 2.633476e-03	ci left: 3.265773e-01	ci right 3.274387e-01	k: 1491156	n:4560000
KS ci ratio: 1.566639e-01	ci left: 1.265258e-04	ci right 1.482401e-04	k: 625	n:4560000
C2CD3   4560000 perm   10116 sec   (451 perm/sec)   p_kst 1.370614e-04   p_cons 3.270079e-01   p_joint 1.370614e-04

Joint ci ratio: 1.564143e-01	ci left: 1.266695e-04	ci right 1.483704e-04	k: 627	n:4570000
Cons ci ratio: 2.630544e-03	ci left: 3.265859e-01	ci right 3.274463e-01	k: 1494463	n:4570000
KS ci ratio: 1.564143e-01	ci left: 1.266695e-04	ci right 1.483704e-04	k: 627	n:4570000
C2CD3   4570000 perm   10159 sec   (450 perm/sec)   p_kst 1.371991e-04   p_cons 3.270160e-01   p_joint 1.371991e-04

Joint ci ratio: 1.564143e-01	ci left: 1.263929e-04	ci right 1.480465e-04	k: 627	n:4580000
Cons ci ratio: 2.627730e-03	ci left: 3.265765e-01	ci right 3.274360e-01	k: 1497688	n:4580000
KS ci ratio: 1.564143e-01	ci left: 1.263929e-04	ci right 1.480465e-04	k: 627	n:4580000
C2CD3   4580000 perm   10201 sec   (449 perm/sec)   p_kst 1.368996e-04   p_cons 3.270061e-01   p_joint 1.368996e-04

Joint ci ratio: 1.561658e-01	ci left: 1.265362e-04	ci right 1.481767e-04	k: 629	n:4590000
Cons ci ratio: 2.624767e-03	ci left: 3.265935e-01	ci right 3.274520e-01	k: 1501034	n:4590000
KS ci ratio: 1.561658e-01	ci left: 1.265362e-04	ci right 1.481767e-04	k: 629	n:4590000
C2CD3   4590000 perm   10242 sec   (448 perm/sec)   p_kst 1.370370e-04   p_cons 3.270227e-01   p_joint 1.370370e-04

Joint ci ratio: 1.561658e-01	ci left: 1.262611e-04	ci right 1.478546e-04	k: 629	n:4600000
Cons ci ratio: 2.621947e-03	ci left: 3.265883e-01	ci right 3.274459e-01	k: 1504278	n:4600000
KS ci ratio: 1.561658e-01	ci left: 1.262611e-04	ci right 1.478546e-04	k: 629	n:4600000
C2CD3   4600000 perm   10284 sec   (447 perm/sec)   p_kst 1.367391e-04   p_cons 3.270170e-01   p_joint 1.367391e-04

Joint ci ratio: 1.560420e-01	ci left: 1.261957e-04	ci right 1.477593e-04	k: 630	n:4610000
Cons ci ratio: 2.619049e-03	ci left: 3.265976e-01	ci right 3.274543e-01	k: 1507589	n:4610000
KS ci ratio: 1.560420e-01	ci left: 1.261957e-04	ci right 1.477593e-04	k: 630	n:4610000
C2CD3   4610000 perm   10325 sec   (446 perm/sec)   p_kst 1.366594e-04   p_cons 3.270258e-01   p_joint 1.366594e-04

Joint ci ratio: 1.560421e-01	ci left: 1.259225e-04	ci right 1.474394e-04	k: 630	n:4620000
Cons ci ratio: 2.616171e-03	ci left: 3.266051e-01	ci right 3.274609e-01	k: 1510892	n:4620000
KS ci ratio: 1.560421e-01	ci left: 1.259225e-04	ci right 1.474394e-04	k: 630	n:4620000
C2CD3   4620000 perm   10368 sec   (446 perm/sec)   p_kst 1.363636e-04   p_cons 3.270329e-01   p_joint 1.363636e-04

Joint ci ratio: 1.560421e-01	ci left: 1.256506e-04	ci right 1.471210e-04	k: 630	n:4630000
Cons ci ratio: 2.613321e-03	ci left: 3.266094e-01	ci right 3.274643e-01	k: 1514180	n:4630000
KS ci ratio: 1.560421e-01	ci left: 1.256506e-04	ci right 1.471210e-04	k: 630	n:4630000
C2CD3   4630000 perm   10410 sec   (445 perm/sec)   p_kst 1.360691e-04   p_cons 3.270367e-01   p_joint 1.360691e-04

Joint ci ratio: 1.559186e-01	ci left: 1.255869e-04	ci right 1.470278e-04	k: 631	n:4640000
Cons ci ratio: 2.610498e-03	ci left: 3.266109e-01	ci right 3.274648e-01	k: 1517455	n:4640000
KS ci ratio: 1.559186e-01	ci left: 1.255869e-04	ci right 1.470278e-04	k: 631	n:4640000
C2CD3   4640000 perm   10452 sec   (444 perm/sec)   p_kst 1.359914e-04   p_cons 3.270377e-01   p_joint 1.359914e-04

Joint ci ratio: 1.556725e-01	ci left: 1.257301e-04	ci right 1.471585e-04	k: 633	n:4650000
Cons ci ratio: 2.607721e-03	ci left: 3.266059e-01	ci right 3.274589e-01	k: 1520700	n:4650000
KS ci ratio: 1.556725e-01	ci left: 1.257301e-04	ci right 1.471585e-04	k: 633	n:4650000
C2CD3   4650000 perm   10495 sec   (443 perm/sec)   p_kst 1.361290e-04   p_cons 3.270323e-01   p_joint 1.361290e-04

Joint ci ratio: 1.967308e-01	ci left: 7.681422e-05	ci right 9.377434e-05	k: 396	n:4660000
Cons ci ratio: 2.605000e-03	ci left: 3.265932e-01	ci right 3.274452e-01	k: 1523909	n:4660000
KS ci ratio: 1.555498e-01	ci left: 1.256666e-04	ci right 1.470657e-04	k: 634	n:4660000
C2CD3   4660000 perm   10537 sec   (442 perm/sec)   p_kst 1.360515e-04   p_cons 3.270191e-01   p_joint 8.497854e-05

Joint ci ratio: 1.551837e-01	ci left: 1.260149e-04	ci right 1.474181e-04	k: 637	n:4670000
Cons ci ratio: 2.602199e-03	ci left: 3.265953e-01	ci right 3.274465e-01	k: 1527187	n:4670000
KS ci ratio: 1.551837e-01	ci left: 1.260149e-04	ci right 1.474181e-04	k: 637	n:4670000
C2CD3   4670000 perm   10579 sec   (441 perm/sec)   p_kst 1.364026e-04   p_cons 3.270208e-01   p_joint 1.364026e-04

Joint ci ratio: 1.550622e-01	ci left: 1.259510e-04	ci right 1.473251e-04	k: 638	n:4680000
Cons ci ratio: 2.599418e-03	ci left: 3.265957e-01	ci right 3.274460e-01	k: 1530457	n:4680000
KS ci ratio: 1.550622e-01	ci left: 1.259510e-04	ci right 1.473251e-04	k: 638	n:4680000
C2CD3   4680000 perm   10622 sec   (441 perm/sec)   p_kst 1.363248e-04   p_cons 3.270207e-01   p_joint 1.363248e-04

Joint ci ratio: 1.656403e-01	ci left: 1.095132e-04	ci right 1.294921e-04	k: 559	n:4690000
Cons ci ratio: 2.596649e-03	ci left: 3.265955e-01	ci right 3.274448e-01	k: 1533724	n:4690000
KS ci ratio: 1.546995e-01	ci left: 1.262973e-04	ci right 1.476754e-04	k: 641	n:4690000
C2CD3   4690000 perm   10664 sec   (440 perm/sec)   p_kst 1.366738e-04   p_cons 3.270200e-01   p_joint 1.191898e-04

Joint ci ratio: 1.656403e-01	ci left: 1.092802e-04	ci right 1.292166e-04	k: 559	n:4700000
Cons ci ratio: 2.593792e-03	ci left: 3.266118e-01	ci right 3.274603e-01	k: 1537069	n:4700000
KS ci ratio: 1.546995e-01	ci left: 1.260286e-04	ci right 1.473612e-04	k: 641	n:4700000
C2CD3   4700000 perm   10707 sec   (439 perm/sec)   p_kst 1.363830e-04   p_cons 3.270360e-01   p_joint 1.189362e-04

Joint ci ratio: 1.656404e-01	ci left: 1.090482e-04	ci right 1.289422e-04	k: 559	n:4710000
Cons ci ratio: 2.591018e-03	ci left: 3.266154e-01	ci right 3.274630e-01	k: 1540354	n:4710000
KS ci ratio: 1.546995e-01	ci left: 1.257610e-04	ci right 1.470483e-04	k: 641	n:4710000
C2CD3   4710000 perm   10750 sec   (438 perm/sec)   p_kst 1.360934e-04   p_cons 3.270391e-01   p_joint 1.186837e-04

Joint ci ratio: 1.654927e-01	ci left: 1.090202e-04	ci right 1.288897e-04	k: 560	n:4720000
Cons ci ratio: 2.588361e-03	ci left: 3.266007e-01	ci right 3.274474e-01	k: 1543553	n:4720000
KS ci ratio: 1.545792e-01	ci left: 1.256983e-04	ci right 1.469568e-04	k: 642	n:4720000
C2CD3   4720000 perm   10793 sec   (437 perm/sec)   p_kst 1.360169e-04   p_cons 3.270239e-01   p_joint 1.186441e-04

Joint ci ratio: 1.654927e-01	ci left: 1.087897e-04	ci right 1.286172e-04	k: 560	n:4730000
Cons ci ratio: 2.585603e-03	ci left: 3.266047e-01	ci right 3.274505e-01	k: 1546840	n:4730000
KS ci ratio: 1.545792e-01	ci left: 1.254325e-04	ci right 1.466461e-04	k: 642	n:4730000
C2CD3   4730000 perm   10836 sec   (437 perm/sec)   p_kst 1.357294e-04   p_cons 3.270275e-01   p_joint 1.183932e-04

Joint ci ratio: 1.653454e-01	ci left: 1.087625e-04	ci right 1.285655e-04	k: 561	n:4740000
Cons ci ratio: 2.582850e-03	ci left: 3.266093e-01	ci right 3.274542e-01	k: 1550130	n:4740000
KS ci ratio: 1.544591e-01	ci left: 1.253707e-04	ci right 1.465559e-04	k: 643	n:4740000
C2CD3   4740000 perm   10878 sec   (436 perm/sec)   p_kst 1.356540e-04   p_cons 3.270316e-01   p_joint 1.183544e-04

Joint ci ratio: 1.653454e-01	ci left: 1.085335e-04	ci right 1.282949e-04	k: 561	n:4750000
Cons ci ratio: 2.580153e-03	ci left: 3.266057e-01	ci right 3.274497e-01	k: 1553381	n:4750000
KS ci ratio: 1.544592e-01	ci left: 1.251068e-04	ci right 1.462473e-04	k: 643	n:4750000
C2CD3   4750000 perm   10922 sec   (435 perm/sec)   p_kst 1.353684e-04   p_cons 3.270276e-01   p_joint 1.181053e-04

Joint ci ratio: 1.543394e-01	ci left: 1.250459e-04	ci right 1.461583e-04	k: 644	n:4760000
Cons ci ratio: 2.577417e-03	ci left: 3.266103e-01	ci right 3.274534e-01	k: 1556671	n:4760000
KS ci ratio: 1.543394e-01	ci left: 1.250459e-04	ci right 1.461583e-04	k: 644	n:4760000
C2CD3   4760000 perm   10964 sec   (434 perm/sec)   p_kst 1.352941e-04   p_cons 3.270317e-01   p_joint 1.352941e-04

Joint ci ratio: 1.542199e-01	ci left: 1.249853e-04	ci right 1.460696e-04	k: 645	n:4770000
Cons ci ratio: 2.574706e-03	ci left: 3.266121e-01	ci right 3.274543e-01	k: 1559948	n:4770000
KS ci ratio: 1.542199e-01	ci left: 1.249853e-04	ci right 1.460696e-04	k: 645	n:4770000
C2CD3   4770000 perm   11007 sec   (433 perm/sec)   p_kst 1.352201e-04   p_cons 3.270331e-01   p_joint 1.352201e-04

Joint ci ratio: 1.542199e-01	ci left: 1.247238e-04	ci right 1.457640e-04	k: 645	n:4780000
Cons ci ratio: 2.572018e-03	ci left: 3.266115e-01	ci right 3.274528e-01	k: 1563213	n:4780000
KS ci ratio: 1.542199e-01	ci left: 1.247238e-04	ci right 1.457640e-04	k: 645	n:4780000
C2CD3   4780000 perm   11051 sec   (433 perm/sec)   p_kst 1.349372e-04   p_cons 3.270320e-01   p_joint 1.349372e-04

Joint ci ratio: 1.542199e-01	ci left: 1.244634e-04	ci right 1.454597e-04	k: 645	n:4790000
Cons ci ratio: 2.569274e-03	ci left: 3.266218e-01	ci right 3.274623e-01	k: 1566531	n:4790000
KS ci ratio: 1.542199e-01	ci left: 1.244634e-04	ci right 1.454597e-04	k: 645	n:4790000
C2CD3   4790000 perm   11094 sec   (432 perm/sec)   p_kst 1.346555e-04   p_cons 3.270420e-01   p_joint 1.346555e-04

Joint ci ratio: 1.539817e-01	ci left: 1.246047e-04	ci right 1.455894e-04	k: 647	n:4800000
Cons ci ratio: 2.566538e-03	ci left: 3.266322e-01	ci right 3.274718e-01	k: 1569849	n:4800000
KS ci ratio: 1.539817e-01	ci left: 1.246047e-04	ci right 1.455894e-04	k: 647	n:4800000
C2CD3   4800000 perm   11137 sec   (431 perm/sec)   p_kst 1.347917e-04   p_cons 3.270519e-01   p_joint 1.347917e-04

Joint ci ratio: 1.536265e-01	ci left: 1.249454e-04	ci right 1.459344e-04	k: 650	n:4810000
Cons ci ratio: 2.563855e-03	ci left: 3.266350e-01	ci right 3.274737e-01	k: 1573131	n:4810000
KS ci ratio: 1.536265e-01	ci left: 1.249454e-04	ci right 1.459344e-04	k: 650	n:4810000
C2CD3   4810000 perm   11180 sec   (430 perm/sec)   p_kst 1.351351e-04   p_cons 3.270543e-01   p_joint 1.351351e-04

Joint ci ratio: 1.536265e-01	ci left: 1.246862e-04	ci right 1.456316e-04	k: 650	n:4820000
Cons ci ratio: 2.561172e-03	ci left: 3.266393e-01	ci right 3.274771e-01	k: 1576420	n:4820000
KS ci ratio: 1.536265e-01	ci left: 1.246862e-04	ci right 1.456316e-04	k: 650	n:4820000
C2CD3   4820000 perm   11223 sec   (429 perm/sec)   p_kst 1.348548e-04   p_cons 3.270581e-01   p_joint 1.348548e-04

Joint ci ratio: 1.536265e-01	ci left: 1.244280e-04	ci right 1.453301e-04	k: 650	n:4830000
Cons ci ratio: 2.558425e-03	ci left: 3.266559e-01	ci right 3.274929e-01	k: 1579769	n:4830000
KS ci ratio: 1.536265e-01	ci left: 1.244280e-04	ci right 1.453301e-04	k: 650	n:4830000
C2CD3   4830000 perm   11267 sec   (429 perm/sec)   p_kst 1.345756e-04   p_cons 3.270743e-01   p_joint 1.345756e-04

Joint ci ratio: 1.533911e-01	ci left: 1.245683e-04	ci right 1.454589e-04	k: 652	n:4840000
Cons ci ratio: 2.555701e-03	ci left: 3.266701e-01	ci right 3.275062e-01	k: 1583106	n:4840000
KS ci ratio: 1.533911e-01	ci left: 1.245683e-04	ci right 1.454589e-04	k: 652	n:4840000
C2CD3   4840000 perm   11311 sec   (428 perm/sec)   p_kst 1.347107e-04   p_cons 3.270880e-01   p_joint 1.347107e-04

Joint ci ratio: 1.529234e-01	ci left: 1.251046e-04	ci right 1.460153e-04	k: 656	n:4850000
Cons ci ratio: 2.553051e-03	ci left: 3.266728e-01	ci right 3.275080e-01	k: 1586388	n:4850000
KS ci ratio: 1.529234e-01	ci left: 1.251046e-04	ci right 1.460153e-04	k: 656	n:4850000
C2CD3   4850000 perm   11355 sec   (427 perm/sec)   p_kst 1.352577e-04   p_cons 3.270903e-01   p_joint 1.352577e-04

Joint ci ratio: 1.526912e-01	ci left: 1.252430e-04	ci right 1.461421e-04	k: 658	n:4860000
Cons ci ratio: 2.550466e-03	ci left: 3.266658e-01	ci right 3.275002e-01	k: 1589623	n:4860000
KS ci ratio: 1.526912e-01	ci left: 1.252430e-04	ci right 1.461421e-04	k: 658	n:4860000
C2CD3   4860000 perm   11399 sec   (426 perm/sec)   p_kst 1.353909e-04   p_cons 3.270829e-01   p_joint 1.353909e-04

Joint ci ratio: 1.524600e-01	ci left: 1.253808e-04	ci right 1.462684e-04	k: 660	n:4870000
Cons ci ratio: 2.547821e-03	ci left: 3.266706e-01	ci right 3.275041e-01	k: 1592915	n:4870000
KS ci ratio: 1.524600e-01	ci left: 1.253808e-04	ci right 1.462684e-04	k: 660	n:4870000
C2CD3   4870000 perm   11443 sec   (426 perm/sec)   p_kst 1.355236e-04   p_cons 3.270873e-01   p_joint 1.355236e-04

Joint ci ratio: 1.522298e-01	ci left: 1.255181e-04	ci right 1.463941e-04	k: 662	n:4880000
Cons ci ratio: 2.545181e-03	ci left: 3.266760e-01	ci right 3.275087e-01	k: 1596210	n:4880000
KS ci ratio: 1.522298e-01	ci left: 1.255181e-04	ci right 1.463941e-04	k: 662	n:4880000
C2CD3   4880000 perm   11487 sec   (425 perm/sec)   p_kst 1.356557e-04   p_cons 3.270922e-01   p_joint 1.356557e-04

Joint ci ratio: 1.521152e-01	ci left: 1.254581e-04	ci right 1.463070e-04	k: 663	n:4890000
Cons ci ratio: 2.542570e-03	ci left: 3.266776e-01	ci right 3.275095e-01	k: 1599487	n:4890000
KS ci ratio: 1.521152e-01	ci left: 1.254581e-04	ci right 1.463070e-04	k: 663	n:4890000
C2CD3   4890000 perm   11532 sec   (424 perm/sec)   p_kst 1.355828e-04   p_cons 3.270935e-01   p_joint 1.355828e-04

Joint ci ratio: 1.516590e-01	ci left: 1.259874e-04	ci right 1.468557e-04	k: 667	n:4900000
Cons ci ratio: 2.539989e-03	ci left: 3.266754e-01	ci right 3.275064e-01	k: 1602745	n:4900000
KS ci ratio: 1.516590e-01	ci left: 1.259874e-04	ci right 1.468557e-04	k: 667	n:4900000
C2CD3   4900000 perm   11576 sec   (423 perm/sec)   p_kst 1.361224e-04   p_cons 3.270908e-01   p_joint 1.361224e-04

Joint ci ratio: 1.516590e-01	ci left: 1.257308e-04	ci right 1.465567e-04	k: 667	n:4910000
Cons ci ratio: 2.537304e-03	ci left: 3.266928e-01	ci right 3.275229e-01	k: 1606099	n:4910000
KS ci ratio: 1.516590e-01	ci left: 1.257308e-04	ci right 1.465567e-04	k: 667	n:4910000
C2CD3   4910000 perm   11620 sec   (423 perm/sec)   p_kst 1.358452e-04   p_cons 3.271077e-01   p_joint 1.358452e-04

Joint ci ratio: 1.516590e-01	ci left: 1.254752e-04	ci right 1.462588e-04	k: 667	n:4920000
Cons ci ratio: 2.534759e-03	ci left: 3.266871e-01	ci right 3.275164e-01	k: 1609340	n:4920000
KS ci ratio: 1.516590e-01	ci left: 1.254752e-04	ci right 1.462588e-04	k: 667	n:4920000
C2CD3   4920000 perm   11665 sec   (422 perm/sec)   p_kst 1.355691e-04   p_cons 3.271016e-01   p_joint 1.355691e-04

Joint ci ratio: 1.515457e-01	ci left: 1.254158e-04	ci right 1.461726e-04	k: 668	n:4930000
Cons ci ratio: 2.532133e-03	ci left: 3.266968e-01	ci right 3.275253e-01	k: 1612657	n:4930000
KS ci ratio: 1.515457e-01	ci left: 1.254158e-04	ci right 1.461726e-04	k: 668	n:4930000
C2CD3   4930000 perm   11710 sec   (421 perm/sec)   p_kst 1.354970e-04   p_cons 3.271110e-01   p_joint 1.354970e-04

Joint ci ratio: 1.515457e-01	ci left: 1.251620e-04	ci right 1.458767e-04	k: 668	n:4940000
Cons ci ratio: 2.529569e-03	ci left: 3.266972e-01	ci right 3.275249e-01	k: 1615928	n:4940000
KS ci ratio: 1.515457e-01	ci left: 1.251620e-04	ci right 1.458767e-04	k: 668	n:4940000
C2CD3   4940000 perm   11754 sec   (420 perm/sec)   p_kst 1.352227e-04   p_cons 3.271109e-01   p_joint 1.352227e-04

Joint ci ratio: 1.515457e-01	ci left: 1.249091e-04	ci right 1.455820e-04	k: 668	n:4950000
Cons ci ratio: 2.527055e-03	ci left: 3.266903e-01	ci right 3.275171e-01	k: 1619163	n:4950000
KS ci ratio: 1.515457e-01	ci left: 1.249091e-04	ci right 1.455820e-04	k: 668	n:4950000
C2CD3   4950000 perm   11800 sec   (420 perm/sec)   p_kst 1.349495e-04   p_cons 3.271036e-01   p_joint 1.349495e-04

Joint ci ratio: 1.510946e-01	ci left: 1.254332e-04	ci right 1.461255e-04	k: 672	n:4960000
Cons ci ratio: 2.524466e-03	ci left: 3.266978e-01	ci right 3.275238e-01	k: 1622469	n:4960000
KS ci ratio: 1.510946e-01	ci left: 1.254332e-04	ci right 1.461255e-04	k: 672	n:4960000
C2CD3   4960000 perm   11844 sec   (419 perm/sec)   p_kst 1.354839e-04   p_cons 3.271107e-01   p_joint 1.354839e-04

Joint ci ratio: 1.510946e-01	ci left: 1.251808e-04	ci right 1.458315e-04	k: 672	n:4970000
Cons ci ratio: 2.521885e-03	ci left: 3.267052e-01	ci right 3.275304e-01	k: 1625775	n:4970000
KS ci ratio: 1.510946e-01	ci left: 1.251808e-04	ci right 1.458315e-04	k: 672	n:4970000
C2CD3   4970000 perm   11888 sec   (418 perm/sec)   p_kst 1.352113e-04   p_cons 3.271177e-01   p_joint 1.352113e-04

Joint ci ratio: 1.507590e-01	ci left: 1.255091e-04	ci right 1.461638e-04	k: 675	n:4980000
Cons ci ratio: 2.519281e-03	ci left: 3.267179e-01	ci right 3.275422e-01	k: 1629107	n:4980000
KS ci ratio: 1.507590e-01	ci left: 1.255091e-04	ci right 1.461638e-04	k: 675	n:4980000
C2CD3   4980000 perm   11934 sec   (417 perm/sec)   p_kst 1.355422e-04   p_cons 3.271299e-01   p_joint 1.355422e-04

Joint ci ratio: 1.507590e-01	ci left: 1.252576e-04	ci right 1.458709e-04	k: 675	n:4990000
Cons ci ratio: 2.516698e-03	ci left: 3.267284e-01	ci right 3.275519e-01	k: 1632429	n:4990000
KS ci ratio: 1.507590e-01	ci left: 1.252576e-04	ci right 1.458709e-04	k: 675	n:4990000
C2CD3   4990000 perm   11979 sec   (417 perm/sec)   p_kst 1.352705e-04   p_cons 3.271401e-01   p_joint 1.352705e-04

Joint ci ratio: 1.507590e-01	ci left: 1.250071e-04	ci right 1.455791e-04	k: 675	n:5000000
Cons ci ratio: 2.514254e-03	ci left: 3.267158e-01	ci right 3.275384e-01	k: 1635635	n:5000000
KS ci ratio: 1.507590e-01	ci left: 1.250071e-04	ci right 1.455791e-04	k: 675	n:5000000
C2CD3   5000000 perm   12024 sec   (416 perm/sec)   p_kst 1.350000e-04   p_cons 3.271270e-01   p_joint 1.350000e-04

Outputting figure to mutsig2_images.part000000000024/C2CD3.2_6016_5000000_0.000135_0.32713_0.000135.png
                gene_name: C2CD3
               theta_stop: 0.15 
                    nperm: 5000000 
                     p_ks: 0.00014 
        ci_ks_bounds_left: 0.00013 
       ci_ks_bounds_right: 0.00015 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.00014 
     ci_joint_bounds_left: 0.00013 
    ci_joint_bounds_right: 0.00015 

Current progress: 33 percent done.
C2orf16
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.470375e-02	ci left: 8.700961e-01	ci right 8.830836e-01	k: 8767	n:10000
KS ci ratio: 2.992891e-02	ci left: 6.221590e-01	ci right 6.411643e-01	k: 6317	n:10000
C2orf16   10000 perm   2 sec   (4206 perm/sec)   p_kst 6.317000e-01   p_cons 8.767000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000024/C2orf16.2_5959_10000_0.6317_0.8767_1.png
                gene_name: C2orf16
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.88 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
C2orf78
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.192190e-02	ci left: 1.786127e-01	ci right 1.939705e-01	k: 1862	n:10000
Cons ci ratio: 1.091704e-01	ci left: 1.079317e-01	ci right 1.204941e-01	k: 1141	n:10000
KS ci ratio: 3.318984e-02	ci left: 5.726613e-01	ci right 5.920907e-01	k: 5824	n:10000
C2orf78   10000 perm   2 sec   (5565 perm/sec)   p_kst 5.824000e-01   p_cons 1.141000e-01   p_joint 1.862000e-01

Joint ci ratio: 7.325148e-02	ci left: 1.206431e-01	ci right 1.298661e-01	k: 2504	n:20000
Cons ci ratio: 7.787170e-02	ci left: 1.080541e-01	ci right 1.168589e-01	k: 2248	n:20000
KS ci ratio: 2.336896e-02	ci left: 5.776333e-01	ci right 5.913421e-01	k: 11690	n:20000
C2orf78   20000 perm   4 sec   (4886 perm/sec)   p_kst 5.845000e-01   p_cons 1.124000e-01   p_joint 1.252000e-01

Outputting figure to mutsig2_images.part000000000024/C2orf78.2_2781_20000_0.5845_0.1124_0.1252.png
                gene_name: C2orf78
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000024
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 24 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4397833: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000025> was used as the working directory.
Started at Wed Oct 24 16:08:57 2012
Results reported at Wed Oct 24 16:10:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000025.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000025.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 25  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000025.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    129.52 sec.
    Max Memory :      1011 MB
    Max Swap   :      3810 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
25
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 25
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 25: processing genes 2154 - 2243
Calculating significance of each gene.
Using projection method.
2154	C2orf86	1.122823e-01
2155	C2orf88	1
2156	C2orf89	1
2157	C3	1
2158	C3AR1	1
2159	C3orf1	1
2160	C3orf10	1
2161	C3orf14	5.086185e-02
2162	C3orf15	9.583297e-03
2163	C3orf17	1
2164	C3orf18	1
2165	C3orf19	1
2166	C3orf20	1.177637e-01
2167	C3orf21	1
2168	C3orf22	1
2169	C3orf23	1
2170	C3orf24	1
2171	C3orf26	3.393195e-02
2172	C3orf27	1
2173	C3orf30	1.086349e-01
2174	C3orf31	1
2175	C3orf32	1
2176	C3orf33	1
2177	C3orf34	1
2178	C3orf35	1
2179	C3orf36	1
2180	C3orf37	1
2181	C3orf38	1
2182	C3orf39	2.673631e-01
2183	C3orf43	8.791499e-02
2184	C3orf45	1
2185	C3orf52	1
2186	C3orf54	1
2187	C3orf55	1
2188	C3orf57	1
2189	C3orf58	1
2190	C3orf59	1
2191	C3orf62	1
2192	C3orf63	1
2193	C3orf64	1
2194	C3orf67	1
2195	C3orf70	1
2196	C3orf71	1
2197	C3orf72	1
2198	C3orf75	1
2199	C3orf79	3.211052e-02
2200	C4BPA	1
2201	C4BPB	1
2202	C4orf14	1
2203	C4orf17	1
2204	C4orf19	1
2205	C4orf21	1
2206	C4orf22	1
2207	C4orf23	1
2208	C4orf26	1
2209	C4orf27	1
2210	C4orf29	1
2211	C4orf3	1
2212	C4orf31	1
2213	C4orf32	1
2214	C4orf33	1
2215	C4orf34	1
2216	C4orf35	1
2217	C4orf36	1
2218	C4orf37	1
2219	C4orf39	1
2220	C4orf40	1
2221	C4orf41	3.934807e-01
2222	C4orf43	1
2223	C4orf44	1
2224	C4orf45	1
2225	C4orf46	1
2226	C4orf49	1
2227	C4orf50	1
2228	C4orf51	1
2229	C4orf6	1
2230	C4orf7	1
2231	C5	1
2232	C5AR1	1.035131e-01
2233	C5orf13	1
2234	C5orf15	1
2235	C5orf20	1
2236	C5orf22	1
2237	C5orf23	1
2238	C5orf24	1
2239	C5orf25	1
2240	C5orf28	1
2241	C5orf30	1
2242	C5orf32	1
2243	C5orf33	1
Done

Running MutSig 2:
Scatter job 25: processing genes 2154 - 2243
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C3orf15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.458791e-02	ci left: 5.524094e-01	ci right 5.719544e-01	k: 5622	n:10000
KS ci ratio: 1.854737e-02	ci left: 8.093811e-01	ci right 8.246338e-01	k: 8171	n:10000
C3orf15   10000 perm   2 sec   (5951 perm/sec)   p_kst 8.171000e-01   p_cons 5.622000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000025/C3orf15.2_2372_10000_0.8171_0.5622_1.png
                gene_name: C3orf15
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000025
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 25 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1428>
Subject: Job 4397836: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000026> was used as the working directory.
Started at Wed Oct 24 16:09:02 2012
Results reported at Wed Oct 24 16:11:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000026.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000026.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 26  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000026.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    165.35 sec.
    Max Memory :       688 MB
    Max Swap   :      3474 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
26
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 26
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 26: processing genes 2244 - 2332
Calculating significance of each gene.
Using projection method.
2244	C5orf34	1.688174e-01
2245	C5orf35	1
2246	C5orf38	1
2247	C5orf39	1
2248	C5orf4	1
2249	C5orf40	1
2250	C5orf41	1
2251	C5orf42	1
2252	C5orf43	1
2253	C5orf44	1
2254	C5orf45	1
2255	C5orf46	1
2256	C5orf48	1
2257	C5orf49	1
2258	C5orf51	1
2259	C5orf53	1
2260	C5orf54	4.686430e-02
2261	C5orf55	1
2262	C5orf56	1
2263	C5orf58	1
2264	C6	7.969780e-02
2265	C6orf1	1
2266	C6orf10	1
2267	C6orf105	1
2268	C6orf106	1
2269	C6orf108	1.559984e-02
2270	C6orf114	1
2271	C6orf115	1
2272	C6orf118	1.234960e-01
2273	C6orf120	1
2274	C6orf125	1
2275	C6orf126	1
2276	C6orf127	1
2277	C6orf129	1
2278	C6orf130	5.191209e-02
2279	C6orf134	1
2280	C6orf136	1
2281	C6orf138	3.465390e-01
2282	C6orf142	1
2283	C6orf145	1
2284	C6orf146	1
2285	C6orf15	1
2286	C6orf150	1
2287	C6orf153	1.013865e-02
2288	C6orf154	1
2289	C6orf162	1
2290	C6orf165	1
2291	C6orf167	1
2292	C6orf168	1
2293	C6orf170	1
2294	C6orf174	1
2295	C6orf182	1
2296	C6orf186	1
2297	C6orf191	1
2298	C6orf192	8.918325e-02
2299	C6orf195	1
2300	C6orf201	1
2301	C6orf203	1
2302	C6orf204	1
2303	C6orf211	2.097700e-01
2304	C6orf221	1
2305	C6orf222	1
2306	C6orf223	1.213691e-02
2307	C6orf225	1
2308	C6orf226	1
2309	C6orf25	1
2310	C6orf26	4.012590e-02
2311	C6orf27	1
2312	C6orf35	1
2313	C6orf47	1
2314	C6orf48	1
2315	C6orf57	1
2316	C6orf58	1
2317	C6orf62	1
2318	C6orf64	1
2319	C6orf70	1
2320	C6orf72	1
2321	C6orf81	1
2322	C6orf89	1
2323	C6orf97	1
2324	C7	1
2325	C7orf10	1.318045e-01
2326	C7orf11	1
2327	C7orf16	1
2328	C7orf23	1
2329	C7orf25	1
2330	C7orf26	1
2331	C7orf27	1
2332	C7orf28A	1
Done

Running MutSig 2:
Scatter job 26: processing genes 2244 - 2332
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000026
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 26 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4397838: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000027> was used as the working directory.
Started at Wed Oct 24 16:09:02 2012
Results reported at Wed Oct 24 16:10:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000027.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000027.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 27  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000027.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    116.77 sec.
    Max Memory :       685 MB
    Max Swap   :      3523 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
27
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 27
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 27: processing genes 2333 - 2422
Calculating significance of each gene.
Using projection method.
2333	C7orf28B	1
2334	C7orf29	1
2335	C7orf30	1
2336	C7orf31	1
2337	C7orf33	1
2338	C7orf34	1
2339	C7orf36	1
2340	C7orf41	1
2341	C7orf42	1
2342	C7orf43	1
2343	C7orf44	1
2344	C7orf45	1
2345	C7orf46	1
2346	C7orf47	1
2347	C7orf49	1
2348	C7orf50	1
2349	C7orf51	1
2350	C7orf52	1
2351	C7orf53	1
2352	C7orf55	1
2353	C7orf57	1
2354	C7orf58	3.597893e-01
2355	C7orf59	1
2356	C7orf60	1
2357	C7orf61	1
2358	C7orf63	1.869681e-01
2359	C7orf64	1
2360	C7orf65	1
2361	C7orf66	1
2362	C7orf68	1
2363	C7orf69	1
2364	C7orf70	1
2365	C8A	1
2366	C8B	1
2367	C8G	1
2368	C8orf22	1
2369	C8orf31	1
2370	C8orf33	1
2371	C8orf34	1
2372	C8orf37	1
2373	C8orf38	1
2374	C8orf4	1
2375	C8orf40	1
2376	C8orf41	1
2377	C8orf42	5.178292e-02
2378	C8orf44	1
2379	C8orf45	1
2380	C8orf46	1
2381	C8orf47	1
2382	C8orf58	1
2383	C8orf59	1
2384	C8orf73	1
2385	C8orf74	1
2386	C8orf76	1
2387	C8orf79	1
2388	C8orf80	1
2389	C8orf84	1
2390	C8orf85	1
2391	C8orf86	1
2392	C9	1
2393	C9orf100	1
2394	C9orf102	1
2395	C9orf103	1
2396	C9orf106	1
2397	C9orf11	8.076156e-02
2398	C9orf114	1
2399	C9orf116	1
2400	C9orf117	1
2401	C9orf119	1
2402	C9orf123	1
2403	C9orf125	1
2404	C9orf128	1
2405	C9orf129	1
2406	C9orf131	4.726302e-01
2407	C9orf135	1
2408	C9orf139	9.825788e-02
2409	C9orf142	1
2410	C9orf150	1
2411	C9orf152	1
2412	C9orf153	1
2413	C9orf156	1
2414	C9orf16	1
2415	C9orf163	1
2416	C9orf170	1
2417	C9orf171	1
2418	C9orf172	1
2419	C9orf173	1
2420	C9orf21	1
2421	C9orf23	1
2422	C9orf24	1
Done

Running MutSig 2:
Scatter job 27: processing genes 2333 - 2422
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000027
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 27 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 4397842: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000028> was used as the working directory.
Started at Wed Oct 24 16:09:02 2012
Results reported at Wed Oct 24 16:12:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000028.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000028.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 28  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000028.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    209.14 sec.
    Max Memory :      1365 MB
    Max Swap   :      3977 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
28
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 28
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 28: processing genes 2423 - 2512
Calculating significance of each gene.
Using projection method.
2423	C9orf25	1
2424	C9orf3	3.266006e-01
2425	C9orf30	1
2426	C9orf37	1
2427	C9orf4	1
2428	C9orf40	1
2429	C9orf41	1
2430	C9orf43	1
2431	C9orf46	1
2432	C9orf47	1
2433	C9orf5	1
2434	C9orf50	1
2435	C9orf6	1
2436	C9orf64	1
2437	C9orf66	1
2438	C9orf68	1
2439	C9orf69	1
2440	C9orf7	1
2441	C9orf71	1
2442	C9orf72	1
2443	C9orf78	1
2444	C9orf79	1
2445	C9orf80	1
2446	C9orf82	1
2447	C9orf84	1
2448	C9orf85	1
2449	C9orf86	1
2450	C9orf89	1
2451	C9orf9	2.637476e-02
2452	C9orf91	1
2453	C9orf93	1
2454	C9orf95	1
2455	C9orf96	1
2456	C9orf98	1
2457	CA1	1
2458	CA10	1.750681e-01
2459	CA11	1
2460	CA12	1
2461	CA13	1
2462	CA14	1.380572e-02
2463	CA2	6.399381e-02
2464	CA3	1
2465	CA4	1
2466	CA5A	1
2467	CA5B	1
2468	CA6	1
2469	CA7	1
2470	CA8	1
2471	CA9	1
2472	CAB39	1
2473	CAB39L	1
2474	CABC1	1
2475	CABIN1	1
2476	CABLES1	1
2477	CABLES2	1
2478	CABP1	2.687968e-02
2479	CABP2	6.986609e-02
2480	CABP4	8.237744e-02
2481	CABP5	6.972459e-02
2482	CABP7	1
2483	CABYR	1
2484	CACHD1	1
2485	CACNA1A	1
2486	CACNA1B	1.201014e-01
2487	CACNA1C	6.668996e-01
2488	CACNA1D	4.501837e-01
2489	CACNA1E	2.087702e-02
2490	CACNA1F	1
2491	CACNA1G	4.474922e-01
2492	CACNA1H	1
2493	CACNA1I	5.496405e-01
2494	CACNA1S	1
2495	CACNA2D1	4.108388e-01
2496	CACNA2D2	2.083315e-01
2497	CACNA2D3	1
2498	CACNA2D4	1
2499	CACNB1	1
2500	CACNB2	1
2501	CACNB3	1
2502	CACNB4	8.996501e-02
2503	CACNG1	1
2504	CACNG2	1
2505	CACNG3	2.466753e-02
2506	CACNG4	1
2507	CACNG5	1
2508	CACNG6	1
2509	CACNG7	5.933769e-02
2510	CACNG8	1
2511	CACYBP	1
2512	CAD	1.964057e-01
Done

Running MutSig 2:
Scatter job 28: processing genes 2423 - 2512
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CACNA1E
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.045244e-01	ci left: 4.494298e-03	ci right 7.604055e-03	k: 59	n:10000
Cons ci ratio: 4.208622e-01	ci left: 6.794980e-03	ci right 1.049980e-02	k: 85	n:10000
KS ci ratio: 9.743651e-02	ci left: 1.324713e-01	ci right 1.461396e-01	k: 1392	n:10000
CACNA1E   10000 perm   2 sec   (4002 perm/sec)   p_kst 1.392000e-01   p_cons 8.500000e-03   p_joint 5.900000e-03

Joint ci ratio: 3.613336e-01	ci left: 4.794950e-03	ci right 6.952521e-03	k: 116	n:20000
Cons ci ratio: 2.860817e-01	ci left: 7.969983e-03	ci right 1.067556e-02	k: 185	n:20000
KS ci ratio: 6.799445e-02	ci left: 1.376333e-01	ci right 1.473708e-01	k: 2849	n:20000
CACNA1E   20000 perm   7 sec   (2748 perm/sec)   p_kst 1.424500e-01   p_cons 9.250000e-03   p_joint 5.800000e-03

Joint ci ratio: 1.475034e-01	ci left: 2.130123e-02	ci right 2.472534e-02	k: 689	n:30000
Cons ci ratio: 2.483906e-01	ci left: 7.210699e-03	ci right 9.286228e-03	k: 246	n:30000
KS ci ratio: 5.560859e-02	ci left: 1.381342e-01	ci right 1.460686e-01	k: 4262	n:30000
CACNA1E   30000 perm   10 sec   (2952 perm/sec)   p_kst 1.420667e-01   p_cons 8.200000e-03   p_joint 2.296667e-02

Joint ci ratio: 1.265505e-01	ci left: 2.194073e-02	ci right 2.492900e-02	k: 936	n:40000
Cons ci ratio: 2.104389e-01	ci left: 7.694740e-03	ci right 9.527670e-03	k: 343	n:40000
KS ci ratio: 4.828739e-02	ci left: 1.380238e-01	ci right 1.448784e-01	k: 5657	n:40000
CACNA1E   40000 perm   13 sec   (3060 perm/sec)   p_kst 1.414250e-01   p_cons 8.575000e-03   p_joint 2.340000e-02

Joint ci ratio: 1.208769e-01	ci left: 1.935346e-02	ci right 2.186263e-02	k: 1029	n:50000
Cons ci ratio: 1.902412e-01	ci left: 7.618678e-03	ci right 9.239171e-03	k: 420	n:50000
KS ci ratio: 4.340610e-02	ci left: 1.371875e-01	ci right 1.432943e-01	k: 7011	n:50000
CACNA1E   50000 perm   16 sec   (3114 perm/sec)   p_kst 1.402200e-01   p_cons 8.400000e-03   p_joint 2.058000e-02

Joint ci ratio: 1.063301e-01	ci left: 2.097100e-02	ci right 2.334220e-02	k: 1328	n:60000
Cons ci ratio: 1.701679e-01	ci left: 8.020312e-03	ci right 9.527780e-03	k: 525	n:60000
KS ci ratio: 3.950797e-02	ci left: 1.381583e-01	ci right 1.437432e-01	k: 8456	n:60000
CACNA1E   60000 perm   19 sec   (3141 perm/sec)   p_kst 1.409333e-01   p_cons 8.750000e-03   p_joint 2.213333e-02

Joint ci ratio: 1.140368e-01	ci left: 1.565255e-02	ci right 1.755925e-02	k: 1161	n:70000
Cons ci ratio: 1.582840e-01	ci left: 7.997876e-03	ci right 9.386168e-03	k: 607	n:70000
KS ci ratio: 3.647301e-02	ci left: 1.390534e-01	ci right 1.442335e-01	k: 9914	n:70000
CACNA1E   70000 perm   22 sec   (3147 perm/sec)   p_kst 1.416286e-01   p_cons 8.671429e-03   p_joint 1.658571e-02

Joint ci ratio: 9.770211e-02	ci left: 1.876042e-02	ci right 2.069963e-02	k: 1577	n:80000
Cons ci ratio: 1.470882e-01	ci left: 8.152388e-03	ci right 9.458607e-03	k: 703	n:80000
KS ci ratio: 3.423970e-02	ci left: 1.383594e-01	ci right 1.431917e-01	k: 11261	n:80000
CACNA1E   80000 perm   25 sec   (3144 perm/sec)   p_kst 1.407625e-01   p_cons 8.787500e-03   p_joint 1.971250e-02

Joint ci ratio: 8.528861e-02	ci left: 2.195433e-02	ci right 2.392103e-02	k: 2063	n:90000
Cons ci ratio: 1.379748e-01	ci left: 8.275259e-03	ci right 9.512262e-03	k: 799	n:90000
KS ci ratio: 3.231677e-02	ci left: 1.382357e-01	ci right 1.427875e-01	k: 12645	n:90000
CACNA1E   90000 perm   29 sec   (3132 perm/sec)   p_kst 1.405000e-01   p_cons 8.877778e-03   p_joint 2.292222e-02

Joint ci ratio: 8.016966e-02	ci left: 2.241307e-02	ci right 2.429471e-02	k: 2334	n:100000
Cons ci ratio: 1.307379e-01	ci left: 8.327173e-03	ci right 9.501577e-03	k: 890	n:100000
KS ci ratio: 3.072089e-02	ci left: 1.378648e-01	ci right 1.421761e-01	k: 14001	n:100000
CACNA1E   100000 perm   32 sec   (3118 perm/sec)   p_kst 1.400100e-01   p_cons 8.900000e-03   p_joint 2.334000e-02

Joint ci ratio: 7.888694e-02	ci left: 2.108775e-02	ci right 2.282849e-02	k: 2414	n:110000
Cons ci ratio: 1.245321e-01	ci left: 8.371036e-03	ci right 9.491449e-03	k: 981	n:110000
KS ci ratio: 2.930251e-02	ci left: 1.378731e-01	ci right 1.419822e-01	k: 15391	n:110000
CACNA1E   110000 perm   35 sec   (3102 perm/sec)   p_kst 1.399182e-01   p_cons 8.918182e-03   p_joint 2.194545e-02

Joint ci ratio: 7.675192e-02	ci left: 2.045780e-02	ci right 2.209878e-02	k: 2552	n:120000
Cons ci ratio: 1.195842e-01	ci left: 8.343995e-03	ci right 9.413275e-03	k: 1064	n:120000
KS ci ratio: 2.807084e-02	ci left: 1.378259e-01	ci right 1.417582e-01	k: 16774	n:120000
CACNA1E   120000 perm   39 sec   (3079 perm/sec)   p_kst 1.397833e-01   p_cons 8.866667e-03   p_joint 2.126667e-02

Joint ci ratio: 7.754738e-02	ci left: 1.852884e-02	ci right 2.003117e-02	k: 2505	n:130000
Cons ci ratio: 1.144309e-01	ci left: 8.433960e-03	ci right 9.465046e-03	k: 1162	n:130000
KS ci ratio: 2.696607e-02	ci left: 1.379344e-01	ci right 1.417124e-01	k: 18176	n:130000
CACNA1E   130000 perm   43 sec   (3052 perm/sec)   p_kst 1.398154e-01   p_cons 8.938462e-03   p_joint 1.926923e-02

Joint ci ratio: 7.702484e-02	ci left: 1.746416e-02	ci right 1.887018e-02	k: 2542	n:140000
Cons ci ratio: 1.094974e-01	ci left: 8.574455e-03	ci right 9.574608e-03	k: 1269	n:140000
KS ci ratio: 2.591996e-02	ci left: 1.386054e-01	ci right 1.422523e-01	k: 19659	n:140000
CACNA1E   140000 perm   46 sec   (3027 perm/sec)   p_kst 1.404214e-01   p_cons 9.064286e-03   p_joint 1.815714e-02

Joint ci ratio: 7.174542e-02	ci left: 1.881276e-02	ci right 2.021923e-02	k: 2926	n:150000
Cons ci ratio: 1.056169e-01	ci left: 8.619132e-03	ci right 9.586652e-03	k: 1364	n:150000
KS ci ratio: 2.499503e-02	ci left: 1.391098e-01	ci right 1.426374e-01	k: 21130	n:150000
CACNA1E   150000 perm   50 sec   (3000 perm/sec)   p_kst 1.408667e-01   p_cons 9.093333e-03   p_joint 1.950667e-02

Joint ci ratio: 6.770915e-02	ci left: 1.982353e-02	ci right 2.121892e-02	k: 3282	n:160000
Cons ci ratio: 1.026552e-01	ci left: 8.567402e-03	ci right 9.500519e-03	k: 1444	n:160000
KS ci ratio: 2.418931e-02	ci left: 1.392857e-01	ci right 1.427023e-01	k: 22558	n:160000
CACNA1E   160000 perm   54 sec   (2971 perm/sec)   p_kst 1.409875e-01   p_cons 9.025000e-03   p_joint 2.051250e-02

Joint ci ratio: 5.992534e-02	ci left: 2.381666e-02	ci right 2.529373e-02	k: 4173	n:170000
Cons ci ratio: 9.950231e-02	ci left: 8.596674e-03	ci right 9.502541e-03	k: 1537	n:170000
KS ci ratio: 2.349443e-02	ci left: 1.390562e-01	ci right 1.423679e-01	k: 23920	n:170000
CACNA1E   170000 perm   58 sec   (2942 perm/sec)   p_kst 1.407059e-01   p_cons 9.041176e-03   p_joint 2.454706e-02

Outputting figure to mutsig2_images.part000000000028/CACNA1E.3_7001_170000_0.14071_0.0090412_0.024547.png
                gene_name: CACNA1E
               theta_stop: 0.100 
                    nperm: 170000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.0090 
      ci_cons_bounds_left: 0.0086 
     ci_cons_bounds_right: 0.0095 
                  p_joint: 0.025 
     ci_joint_bounds_left: 0.024 
    ci_joint_bounds_right: 0.025 

Current progress: 20 percent done.
CA14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.044806e-03	ci left: 9.923959e-01	ci right 9.955057e-01	k: 9941	n:10000
Cons ci ratio: 8.546586e-03	ci left: 9.504396e-01	ci right 9.586930e-01	k: 9547	n:10000
KS ci ratio: 2.218526e-02	ci left: 7.488743e-01	ci right 7.657756e-01	k: 7574	n:10000
CA14   10000 perm   1 sec   (6992 perm/sec)   p_kst 7.574000e-01   p_cons 9.547000e-01   p_joint 9.941000e-01

Outputting figure to mutsig2_images.part000000000028/CA14.2_1058_10000_0.7574_0.9547_0.9941.png
                gene_name: CA14
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 1.00 

Current progress: 40 percent done.
CACNA1B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.391178e-02	ci left: 7.199706e-01	ci right 7.374960e-01	k: 7288	n:10000
Cons ci ratio: 2.695714e-02	ci left: 6.696478e-01	ci right 6.880479e-01	k: 6789	n:10000
KS ci ratio: 1.214091e-01	ci left: 8.864084e-02	ci right 1.001967e-01	k: 943	n:10000
CACNA1B   10000 perm   2 sec   (4446 perm/sec)   p_kst 9.430000e-02   p_cons 6.789000e-01   p_joint 7.288000e-01

Joint ci ratio: 2.290059e-02	ci left: 5.874565e-01	ci right 6.011160e-01	k: 11886	n:20000
Cons ci ratio: 1.862643e-02	ci left: 6.824319e-01	ci right 6.953131e-01	k: 13778	n:20000
KS ci ratio: 8.565064e-02	ci left: 9.072523e-02	ci right 9.889301e-02	k: 1895	n:20000
CACNA1B   20000 perm   5 sec   (4058 perm/sec)   p_kst 9.475000e-02   p_cons 6.889000e-01   p_joint 5.943000e-01

Outputting figure to mutsig2_images.part000000000028/CACNA1B.2_7204_20000_0.09475_0.6889_0.5943.png
                gene_name: CACNA1B
               theta_stop: 0.086 
                    nperm: 20000 
                     p_ks: 0.095 
        ci_ks_bounds_left: 0.091 
       ci_ks_bounds_right: 0.099 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.60 

Current progress: 60 percent done.
CACNA1D
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.466872e-02	ci left: 2.599312e-01	ci right 2.774037e-01	k: 2686	n:10000
Cons ci ratio: 7.810253e-03	ci left: 9.579609e-01	ci right 9.655670e-01	k: 9619	n:10000
KS ci ratio: 6.964110e-02	ci left: 2.321499e-01	ci right 2.490015e-01	k: 2405	n:10000
CACNA1D   10000 perm   2 sec   (4671 perm/sec)   p_kst 2.405000e-01   p_cons 9.619000e-01   p_joint 2.686000e-01

Outputting figure to mutsig2_images.part000000000028/CACNA1D.2_6850_10000_0.2405_0.9619_0.2686.png
                gene_name: CACNA1D
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.28 

Current progress: 80 percent done.
CAD
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.658696e-02	ci left: 6.756920e-01	ci right 6.940002e-01	k: 6849	n:10000
KS ci ratio: 3.621153e-02	ci left: 5.296705e-01	ci right 5.493065e-01	k: 5395	n:10000
CAD   10000 perm   2 sec   (4435 perm/sec)   p_kst 5.395000e-01   p_cons 6.849000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000028/CAD.2_6854_10000_0.5395_0.6849_1.png
                gene_name: CAD
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.69 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000028
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 28 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4397845: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000029> was used as the working directory.
Started at Wed Oct 24 16:09:02 2012
Results reported at Wed Oct 24 16:11:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000029.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000029.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 29  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000029.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     69.90 sec.
    Max Memory :       985 MB
    Max Swap   :      3849 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
29
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 29
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 29: processing genes 2513 - 2602
Calculating significance of each gene.
Using projection method.
2513	CADM1	1
2514	CADM2	1
2515	CADM3	1
2516	CADM4	1
2517	CADPS	1
2518	CADPS2	1.001118e-01
2519	CAGE1	2.721262e-01
2520	CALB1	1
2521	CALB2	1
2522	CALCA	1
2523	CALCB	1
2524	CALCOCO1	2.436510e-01
2525	CALCOCO2	5.551573e-02
2526	CALCR	1
2527	CALCRL	1
2528	CALD1	1.473979e-01
2529	CALHM1	1
2530	CALHM2	1
2531	CALM1	5.404543e-02
2532	CALM2	1
2533	CALM3	9.962381e-02
2534	CALML3	1
2535	CALML4	1
2536	CALML5	1
2537	CALML6	1
2538	CALN1	1
2539	CALR	1
2540	CALR3	1
2541	CALU	1
2542	CALY	1
2543	CAMK1	1
2544	CAMK1D	1
2545	CAMK1G	1
2546	CAMK2A	1
2547	CAMK2B	1
2548	CAMK2D	1
2549	CAMK2G	1
2550	CAMK2N1	1
2551	CAMK2N2	8.086588e-03
2552	CAMK4	1
2553	CAMKK1	1
2554	CAMKK2	1
2555	CAMKV	1.682777e-01
2556	CAMLG	1
2557	CAMP	1
2558	CAMSAP1	1
2559	CAMSAP1L1	1
2560	CAMTA1	3.802045e-01
2561	CAMTA2	2.034256e-01
2562	CAND1	2.127085e-01
2563	CAND2	1
2564	CANT1	1
2565	CANX	1
2566	CAP1	1
2567	CAP2	1
2568	CAPG	1
2569	CAPN1	1
2570	CAPN10	1
2571	CAPN11	1
2572	CAPN12	1
2573	CAPN13	1
2574	CAPN2	1
2575	CAPN3	3.902275e-01
2576	CAPN5	1
2577	CAPN6	1
2578	CAPN7	1
2579	CAPN9	1
2580	CAPNS1	3.804051e-03
2581	CAPNS2	1
2582	CAPRIN1	1
2583	CAPRIN2	1
2584	CAPS	1.015182e-01
2585	CAPS2	1
2586	CAPSL	1
2587	CAPZA1	1
2588	CAPZA2	1
2589	CAPZA3	1
2590	CAPZB	1
2591	CARD10	1
2592	CARD11	1
2593	CARD14	1
2594	CARD16	1
2595	CARD17	1
2596	CARD18	1
2597	CARD6	1
2598	CARD8	1
2599	CARD9	1
2600	CARHSP1	1
2601	CARKD	1
2602	CARM1	1
Done

Running MutSig 2:
Scatter job 29: processing genes 2513 - 2602
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CAPNS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.641595e-02	ci left: 3.163183e-01	ci right 3.347835e-01	k: 3255	n:10000
Cons ci ratio: 6.958397e-02	ci left: 2.324462e-01	ci right 2.493050e-01	k: 2408	n:10000
KS ci ratio: 1.283710e-02	ci left: 8.972367e-01	ci right 9.089273e-01	k: 9032	n:10000
CAPNS1   10000 perm   2 sec   (5400 perm/sec)   p_kst 9.032000e-01   p_cons 2.408000e-01   p_joint 3.255000e-01

Outputting figure to mutsig2_images.part000000000029/CAPNS1.2_847_10000_0.9032_0.2408_0.3255.png
                gene_name: CAPNS1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.33 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000029
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 29 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4397848: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000030> was used as the working directory.
Started at Wed Oct 24 16:09:10 2012
Results reported at Wed Oct 24 16:11:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000030.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000030.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 30  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000030.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    157.51 sec.
    Max Memory :      1547 MB
    Max Swap   :      4051 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
30
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 30
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 30: processing genes 2603 - 2691
Calculating significance of each gene.
Using projection method.
2603	CARNS1	1
2604	CARS	1
2605	CARS2	1
2606	CARTPT	1
2607	CASC1	1
2608	CASC3	2.666842e-01
2609	CASC4	1
2610	CASC5	1
2611	CASD1	1.180966e-02
2612	CASK	1
2613	CASKIN1	3.253687e-01
2614	CASKIN2	1
2615	CASP1	1
2616	CASP10	1.670000e-01
2617	CASP14	1
2618	CASP2	1
2619	CASP3	1
2620	CASP4	1
2621	CASP5	1
2622	CASP6	1
2623	CASP7	1
In gene CASP8 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 1721    n = 1	mu =   4.43e-07
2624	CASP8	6.365668e-02
2625	CASP8AP2	4.460271e-01
2626	CASP9	1
2627	CASQ1	1
2628	CASQ2	1
2629	CASR	1.668501e-01
2630	CASS4	2.276518e-01
2631	CAST	1
2632	CASZ1	1
2633	CAT	1.298604e-01
2634	CATSPER1	1
2635	CATSPER2	1
2636	CATSPER3	3.223539e-02
2637	CATSPER4	1
2638	CATSPERB	1
2639	CATSPERG	1
2640	CAV1	1
2641	CAV2	1
2642	CAV3	1
2643	CBARA1	1
2644	CBFA2T2	1
2645	CBFA2T3	1
2646	CBFB	1
2647	CBL	1
2648	CBLB	1.282231e-01
2649	CBLC	1.591050e-01
2650	CBLL1	1.054939e-01
2651	CBLN1	1
2652	CBLN2	1
2653	CBLN3	1
2654	CBLN4	1
2655	CBR1	1
2656	CBR3	1
2657	CBR4	1
2658	CBS	1
2659	CBWD1	1
2660	CBWD2	1
2661	CBWD6	1
2662	CBX1	1.585883e-02
2663	CBX2	1
2664	CBX3	1
2665	CBX4	8.510929e-03
2666	CBX5	1
2667	CBX6	1
2668	CBX7	1
2669	CBX8	1
2670	CBY1	1
2671	CC2D1A	2.521895e-01
2672	CC2D1B	3.230220e-01
2673	CC2D2A	1
2674	CC2D2B	1
2675	CCAR1	1.056093e-01
2676	CCBE1	1
2677	CCBL1	1.075258e-01
2678	CCBL2	2.171569e-01
2679	CCBP2	1
2680	CCDC101	1
2681	CCDC102A	1
2682	CCDC102B	1
2683	CCDC103	1
2684	CCDC104	1
2685	CCDC105	9.674923e-02
2686	CCDC106	1
2687	CCDC107	1
2688	CCDC108	4.094477e-01
2689	CCDC109A	1
2690	CCDC109B	1
2691	CCDC11	1
Done

Running MutSig 2:
Scatter job 30: processing genes 2603 - 2691
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CASD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.024770e-02	ci left: 9.311281e-01	ci right 9.408160e-01	k: 9361	n:10000
Cons ci ratio: 2.060037e-02	ci left: 7.753971e-01	ci right 7.916375e-01	k: 7836	n:10000
KS ci ratio: 2.526458e-02	ci left: 6.974658e-01	ci right 7.154138e-01	k: 7065	n:10000
CASD1   10000 perm   2 sec   (5670 perm/sec)   p_kst 7.065000e-01   p_cons 7.836000e-01   p_joint 9.361000e-01

Outputting figure to mutsig2_images.part000000000030/CASD1.2_2466_10000_0.7065_0.7836_0.9361.png
                gene_name: CASD1
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 17 percent done.
CASP8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.974894e-02	ci left: 1.529626e-01	ci right 1.674359e-01	k: 1601	n:10000
Cons ci ratio: 1.099875e-01	ci left: 1.064680e-01	ci right 1.189587e-01	k: 1126	n:10000
KS ci ratio: 3.128802e-02	ci left: 6.011627e-01	ci right 6.203727e-01	k: 6108	n:10000
CASP8   10000 perm   2 sec   (6318 perm/sec)   p_kst 6.108000e-01   p_cons 1.126000e-01   p_joint 1.601000e-01

Joint ci ratio: 3.715554e-02	ci left: 3.508540e-01	ci right 3.641875e-01	k: 7150	n:20000
Cons ci ratio: 7.759983e-02	ci left: 1.087421e-01	ci right 1.175707e-01	k: 2262	n:20000
KS ci ratio: 2.179610e-02	ci left: 6.111241e-01	ci right 6.246416e-01	k: 12358	n:20000
CASP8   20000 perm   4 sec   (5582 perm/sec)   p_kst 6.179000e-01   p_cons 1.131000e-01   p_joint 3.575000e-01

Outputting figure to mutsig2_images.part000000000030/CASP8.2_1753_20000_0.6179_0.1131_0.3575.png
                gene_name: CASP8
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.36 

Current progress: 33 percent done.
CBX1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.171276e-02	ci left: 9.125529e-01	ci right 9.234021e-01	k: 9181	n:10000
Cons ci ratio: 2.065500e-02	ci left: 7.744852e-01	ci right 7.907498e-01	k: 7827	n:10000
KS ci ratio: 3.699097e-02	ci left: 5.190593e-01	ci right 5.387238e-01	k: 5289	n:10000
CBX1   10000 perm   1 sec   (6953 perm/sec)   p_kst 5.289000e-01   p_cons 7.827000e-01   p_joint 9.181000e-01

Outputting figure to mutsig2_images.part000000000030/CBX1.2_574_10000_0.5289_0.7827_0.9181.png
                gene_name: CBX1
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 50 percent done.
CBX4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.135169e-02	ci left: 7.628386e-01	ci right 7.794031e-01	k: 7712	n:10000
Cons ci ratio: 3.928043e-02	ci left: 4.890517e-01	ci right 5.087489e-01	k: 4989	n:10000
KS ci ratio: 4.169550e-02	ci left: 4.592791e-01	ci right 4.789389e-01	k: 4691	n:10000
CBX4   10000 perm   2 sec   (6503 perm/sec)   p_kst 4.691000e-01   p_cons 4.989000e-01   p_joint 7.712000e-01

Outputting figure to mutsig2_images.part000000000030/CBX4.2_1703_10000_0.4691_0.4989_0.7712.png
                gene_name: CBX4
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.78 

Current progress: 67 percent done.
CCAR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.992989e-02	ci left: 4.808558e-01	ci right 5.005496e-01	k: 4907	n:10000
Cons ci ratio: 2.993534e-02	ci left: 6.220585e-01	ci right 6.410648e-01	k: 6316	n:10000
KS ci ratio: 8.455437e-02	ci left: 1.693677e-01	ci right 1.844210e-01	k: 1768	n:10000
CCAR1   10000 perm   2 sec   (5653 perm/sec)   p_kst 1.768000e-01   p_cons 6.316000e-01   p_joint 4.907000e-01

Outputting figure to mutsig2_images.part000000000030/CCAR1.2_3549_10000_0.1768_0.6316_0.4907.png
                gene_name: CCAR1
               theta_stop: 0.085 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 83 percent done.
CCDC108
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.044305e-02	ci left: 9.287493e-01	ci right 9.385962e-01	k: 9338	n:10000
Cons ci ratio: 4.053366e-02	ci left: 4.733618e-01	ci right 4.930480e-01	k: 4832	n:10000
KS ci ratio: 1.604104e-02	ci left: 8.495769e-01	ci right 8.634147e-01	k: 8566	n:10000
CCDC108   10000 perm   2 sec   (4964 perm/sec)   p_kst 8.566000e-01   p_cons 4.832000e-01   p_joint 9.338000e-01

Outputting figure to mutsig2_images.part000000000030/CCDC108.2_6058_10000_0.8566_0.4832_0.9338.png
                gene_name: CCDC108
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000030
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 30 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4397851: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000031> was used as the working directory.
Started at Wed Oct 24 16:09:16 2012
Results reported at Wed Oct 24 16:11:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000031.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000031.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 31  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000031.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    151.18 sec.
    Max Memory :      1550 MB
    Max Swap   :      3974 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
31
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 31
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 31: processing genes 2692 - 2781
Calculating significance of each gene.
Using projection method.
2692	CCDC110	2.725546e-01
2693	CCDC111	1
2694	CCDC112	1
2695	CCDC113	1
2696	CCDC114	8.697949e-02
2697	CCDC115	1
2698	CCDC116	1
2699	CCDC117	1
2700	CCDC12	1
2701	CCDC120	1.161872e-01
2702	CCDC121	1
2703	CCDC122	1
2704	CCDC123	3.484674e-01
2705	CCDC124	1
2706	CCDC125	2.521289e-01
2707	CCDC126	1
2708	CCDC127	1
2709	CCDC129	1.350734e-01
2710	CCDC13	1
2711	CCDC130	1
2712	CCDC132	1
2713	CCDC134	1
2714	CCDC135	2.392501e-02
2715	CCDC136	1
2716	CCDC137	1
2717	CCDC138	1
2718	CCDC14	2.110577e-01
2719	CCDC140	1
2720	CCDC141	1
2721	CCDC142	1
2722	CCDC144A	1
2723	CCDC144B	5.390477e-02
2724	CCDC144NL	1
2725	CCDC146	1
2726	CCDC147	1
2727	CCDC148	9.685468e-03
2728	CCDC149	1
2729	CCDC15	2.996895e-01
2730	CCDC150	1
2731	CCDC151	1
2732	CCDC153	1
2733	CCDC155	1
2734	CCDC157	1
2735	CCDC158	6.539316e-02
2736	CCDC159	1
2737	CCDC160	1
2738	CCDC17	1
2739	CCDC18	1.002413e-01
2740	CCDC19	1
2741	CCDC21	3.572339e-01
2742	CCDC22	1
2743	CCDC23	1
2744	CCDC24	1
2745	CCDC25	1
2746	CCDC27	1
2747	CCDC28A	1
2748	CCDC28B	1
2749	CCDC3	1
2750	CCDC30	1
2751	CCDC33	1
2752	CCDC34	1.056231e-01
2753	CCDC36	1
2754	CCDC37	9.063661e-02
2755	CCDC38	1
2756	CCDC39	1
2757	CCDC40	1
2758	CCDC41	1
2759	CCDC42	1
2760	CCDC43	1
2761	CCDC45	1
2762	CCDC46	1
2763	CCDC47	1
2764	CCDC48	1
2765	CCDC50	1
2766	CCDC51	1
2767	CCDC52	1
2768	CCDC53	1
2769	CCDC54	1
2770	CCDC55	9.320723e-02
2771	CCDC56	1
2772	CCDC57	1
2773	CCDC58	1
2774	CCDC59	1
2775	CCDC6	1
2776	CCDC60	1
2777	CCDC61	1
2778	CCDC62	1
2779	CCDC63	1
2780	CCDC64	1
2781	CCDC64B	1
Done

Running MutSig 2:
Scatter job 31: processing genes 2692 - 2781
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CCDC18
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.355274e-02	ci left: 5.673461e-01	ci right 5.868090e-01	k: 5771	n:10000
Cons ci ratio: 5.369191e-02	ci left: 3.382620e-01	ci right 3.570268e-01	k: 3476	n:10000
KS ci ratio: 1.824276e-02	ci left: 8.143595e-01	ci right 8.294525e-01	k: 8220	n:10000
CCDC18   10000 perm   2 sec   (4806 perm/sec)   p_kst 8.220000e-01   p_cons 3.476000e-01   p_joint 5.771000e-01

Outputting figure to mutsig2_images.part000000000031/CCDC18.3_4366_10000_0.822_0.3476_0.5771.png
                gene_name: CCDC18
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 25 percent done.
CCDC135
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.851646e-02	ci left: 6.444822e-01	ci right 6.632281e-01	k: 6539	n:10000
Cons ci ratio: 2.211887e-02	ci left: 7.499869e-01	ci right 7.668623e-01	k: 7585	n:10000
KS ci ratio: 1.121871e-01	ci left: 1.026640e-01	ci right 1.149650e-01	k: 1087	n:10000
CCDC135   10000 perm   2 sec   (6119 perm/sec)   p_kst 1.087000e-01   p_cons 7.585000e-01   p_joint 6.539000e-01

Joint ci ratio: 2.586330e-02	ci left: 5.276074e-01	ci right 5.414825e-01	k: 10691	n:20000
Cons ci ratio: 1.567035e-02	ci left: 7.518004e-01	ci right 7.637246e-01	k: 15156	n:20000
KS ci ratio: 8.001216e-02	ci left: 1.028466e-01	ci right 1.114680e-01	k: 2142	n:20000
CCDC135   20000 perm   4 sec   (5427 perm/sec)   p_kst 1.071000e-01   p_cons 7.578000e-01   p_joint 5.345500e-01

Outputting figure to mutsig2_images.part000000000031/CCDC135.2_2693_20000_0.1071_0.7578_0.53455.png
                gene_name: CCDC135
               theta_stop: 0.080 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.54 

Current progress: 50 percent done.
CCDC148
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.275439e-03	ci left: 9.718541e-01	ci right 9.780650e-01	k: 9751	n:10000
Cons ci ratio: 1.651450e-02	ci left: 8.421365e-01	ci right 8.562594e-01	k: 8493	n:10000
KS ci ratio: 1.455778e-01	ci left: 6.265923e-02	ci right 7.259445e-02	k: 675	n:10000
CCDC148   10000 perm   2 sec   (6102 perm/sec)   p_kst 6.750000e-02   p_cons 8.493000e-01   p_joint 9.751000e-01

Joint ci ratio: 1.453862e-02	ci left: 7.784831e-01	ci right 7.899342e-01	k: 15685	n:20000
Cons ci ratio: 1.177014e-02	ci left: 8.421888e-01	ci right 8.522100e-01	k: 16945	n:20000
KS ci ratio: 1.063118e-01	ci left: 6.025648e-02	ci right 6.707105e-02	k: 1272	n:20000
CCDC148   20000 perm   4 sec   (5445 perm/sec)   p_kst 6.360000e-02   p_cons 8.472500e-01   p_joint 7.842500e-01

Joint ci ratio: 1.416710e-02	ci left: 7.133397e-01	ci right 7.235513e-01	k: 21554	n:30000
Cons ci ratio: 1.014476e-02	ci left: 8.284276e-01	ci right 8.369079e-01	k: 24981	n:30000
KS ci ratio: 8.664648e-02	ci left: 6.109278e-02	ci right 6.665872e-02	k: 1915	n:30000
CCDC148   30000 perm   6 sec   (5192 perm/sec)   p_kst 6.383333e-02   p_cons 8.327000e-01   p_joint 7.184667e-01

Outputting figure to mutsig2_images.part000000000031/CCDC148.2_1884_30000_0.063833_0.8327_0.71847.png
                gene_name: CCDC148
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.064 
        ci_ks_bounds_left: 0.061 
       ci_ks_bounds_right: 0.067 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.71 
    ci_joint_bounds_right: 0.72 

Current progress: 75 percent done.
CCDC158
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.317679e-01	ci left: 7.591905e-02	ci right 8.672633e-02	k: 812	n:10000
Cons ci ratio: 3.402247e-01	ci left: 1.087258e-02	ci right 1.541759e-02	k: 130	n:10000
KS ci ratio: 4.533675e-02	ci left: 4.179754e-01	ci right 4.374667e-01	k: 4277	n:10000
CCDC158   10000 perm   2 sec   (5495 perm/sec)   p_kst 4.277000e-01   p_cons 1.300000e-02   p_joint 8.120000e-02

Joint ci ratio: 1.425113e-01	ci left: 3.384702e-02	ci right 3.908886e-02	k: 728	n:20000
Cons ci ratio: 2.369421e-01	ci left: 1.189959e-02	ci right 1.514412e-02	k: 269	n:20000
KS ci ratio: 3.200193e-02	ci left: 4.217273e-01	ci right 4.354935e-01	k: 8572	n:20000
CCDC158   20000 perm   4 sec   (4937 perm/sec)   p_kst 4.286000e-01   p_cons 1.345000e-02   p_joint 3.640000e-02

Joint ci ratio: 1.657610e-01	ci left: 1.678143e-02	ci right 1.984620e-02	k: 548	n:30000
Cons ci ratio: 1.917907e-01	ci left: 1.241520e-02	ci right 1.508019e-02	k: 411	n:30000
KS ci ratio: 2.625689e-02	ci left: 4.206280e-01	ci right 4.318529e-01	k: 12787	n:30000
CCDC158   30000 perm   6 sec   (4713 perm/sec)   p_kst 4.262333e-01   p_cons 1.370000e-02   p_joint 1.826667e-02

Joint ci ratio: 1.044323e-01	ci left: 3.224538e-02	ci right 3.582268e-02	k: 1360	n:40000
Cons ci ratio: 1.659942e-01	ci left: 1.260773e-02	ci right 1.491366e-02	k: 549	n:40000
KS ci ratio: 2.263557e-02	ci left: 4.236183e-01	ci right 4.333421e-01	k: 17139	n:40000
CCDC158   40000 perm   9 sec   (4573 perm/sec)   p_kst 4.284750e-01   p_cons 1.372500e-02   p_joint 3.400000e-02

Joint ci ratio: 8.154030e-02	ci left: 4.237569e-02	ci right 4.599747e-02	k: 2208	n:50000
Cons ci ratio: 1.099304e-01	ci left: 2.343505e-02	ci right 2.618050e-02	k: 1239	n:50000
KS ci ratio: 2.016997e-02	ci left: 4.259743e-01	ci right 4.346738e-01	k: 21516	n:50000
CCDC158   50000 perm   11 sec   (4466 perm/sec)   p_kst 4.303200e-01   p_cons 2.478000e-02   p_joint 4.416000e-02

Joint ci ratio: 4.806311e-02	ci left: 9.739625e-02	ci right 1.022092e-01	k: 5987	n:60000
Cons ci ratio: 9.973560e-02	ci left: 2.384675e-02	ci right 2.636614e-02	k: 1505	n:60000
KS ci ratio: 1.833292e-02	ci left: 4.284809e-01	ci right 4.364256e-01	k: 25947	n:60000
CCDC158   60000 perm   14 sec   (4361 perm/sec)   p_kst 4.324500e-01   p_cons 2.508333e-02   p_joint 9.978333e-02

Outputting figure to mutsig2_images.part000000000031/CCDC158.2_3434_60000_0.43245_0.025083_0.099783.png
                gene_name: CCDC158
               theta_stop: 0.100 
                    nperm: 60000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.025 
      ci_cons_bounds_left: 0.024 
     ci_cons_bounds_right: 0.026 
                  p_joint: 0.100 
     ci_joint_bounds_left: 0.097 
    ci_joint_bounds_right: 0.10 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000031
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 31 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4397859: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000032> was used as the working directory.
Started at Wed Oct 24 16:09:23 2012
Results reported at Wed Oct 24 16:12:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000032.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000032.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 32  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000032.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    185.83 sec.
    Max Memory :       689 MB
    Max Swap   :      3464 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
32
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 32
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 32: processing genes 2782 - 2871
Calculating significance of each gene.
Using projection method.
2782	CCDC65	1
2783	CCDC66	1
2784	CCDC67	1
2785	CCDC68	1
2786	CCDC69	1
2787	CCDC7	1
2788	CCDC70	1
2789	CCDC71	1
2790	CCDC72	1
2791	CCDC73	2.248789e-01
2792	CCDC74A	1
2793	CCDC74B	1
2794	CCDC75	1
2795	CCDC76	1.111896e-01
2796	CCDC77	2.565660e-01
2797	CCDC78	2.573374e-02
2798	CCDC8	8.785303e-02
2799	CCDC80	3.059070e-02
2800	CCDC81	1
2801	CCDC82	1
2802	CCDC83	1
2803	CCDC84	1
2804	CCDC85A	6.084258e-02
2805	CCDC86	1
2806	CCDC87	1
2807	CCDC88A	1.622233e-01
2808	CCDC88B	1
2809	CCDC88C	1
2810	CCDC89	1
2811	CCDC9	1
2812	CCDC90A	1.170578e-01
2813	CCDC90B	1
2814	CCDC91	4.255356e-02
2815	CCDC92	1
2816	CCDC93	1.672679e-01
2817	CCDC94	1
2818	CCDC96	1
2819	CCDC97	1
2820	CCDC99	1
2821	CCHCR1	1
2822	CCIN	1
2823	CCK	1
2824	CCKAR	1
2825	CCKBR	1
2826	CCL1	1
2827	CCL11	1
2828	CCL13	1
2829	CCL14	1
2830	CCL15	1
2831	CCL16	1
2832	CCL17	1
2833	CCL18	1
2834	CCL19	1
2835	CCL2	1
2836	CCL20	2.142515e-02
2837	CCL21	1
2838	CCL22	1
2839	CCL23	1.128377e-02
2840	CCL24	1
2841	CCL25	1
2842	CCL26	1
2843	CCL27	1
2844	CCL28	1
2845	CCL3	1
2846	CCL4	1
2847	CCL5	1
2848	CCL7	1
2849	CCL8	1
2850	CCM2	1
2851	CCNA1	1
2852	CCNA2	1
2853	CCNB1	1
2854	CCNB1IP1	1
2855	CCNB2	1
2856	CCNB3	5.463731e-01
2857	CCNC	1
2858	CCND1	1
2859	CCND2	1
2860	CCND3	1
2861	CCNDBP1	1
2862	CCNE1	1
2863	CCNE2	1
2864	CCNF	2.533793e-01
2865	CCNG1	1
2866	CCNG2	1
2867	CCNH	1
2868	CCNI	1
2869	CCNI2	1
2870	CCNJ	1
2871	CCNJL	1
Done

Running MutSig 2:
Scatter job 32: processing genes 2782 - 2871
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CCDC88A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.047174e-01	ci left: 1.164278e-01	ci right 1.293928e-01	k: 1228	n:10000
Cons ci ratio: 5.822401e-02	ci left: 3.027268e-01	ci right 3.209830e-01	k: 3118	n:10000
KS ci ratio: 1.397872e-01	ci left: 6.778282e-02	ci right 7.806763e-02	k: 728	n:10000
CCDC88A   10000 perm   3 sec   (3862 perm/sec)   p_kst 7.280000e-02   p_cons 3.118000e-01   p_joint 1.228000e-01

Joint ci ratio: 7.777433e-02	ci left: 1.082998e-01	ci right 1.171132e-01	k: 2253	n:20000
Cons ci ratio: 4.184691e-02	ci left: 2.985235e-01	ci right 3.113332e-01	k: 6098	n:20000
KS ci ratio: 1.018547e-01	ci left: 6.542758e-02	ci right 7.249836e-02	k: 1378	n:20000
CCDC88A   20000 perm   8 sec   (2531 perm/sec)   p_kst 6.890000e-02   p_cons 3.049000e-01   p_joint 1.126500e-01

Joint ci ratio: 5.811154e-02	ci left: 1.278596e-01	ci right 1.355452e-01	k: 3950	n:30000
Cons ci ratio: 3.419882e-02	ci left: 2.993281e-01	ci right 3.097764e-01	k: 9136	n:30000
KS ci ratio: 8.317542e-02	ci left: 6.605905e-02	ci right 7.182476e-02	k: 2067	n:30000
CCDC88A   30000 perm   11 sec   (2804 perm/sec)   p_kst 6.890000e-02   p_cons 3.045333e-01   p_joint 1.316667e-01

Outputting figure to mutsig2_images.part000000000032/CCDC88A.3_5744_30000_0.0689_0.30453_0.13167.png
                gene_name: CCDC88A
               theta_stop: 0.083 
                    nperm: 30000 
                     p_ks: 0.069 
        ci_ks_bounds_left: 0.066 
       ci_ks_bounds_right: 0.072 
                   p_cons: 0.30 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 33 percent done.
CCDC80
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.187825e-03	ci left: 9.434661e-01	ci right 9.522706e-01	k: 9480	n:10000
Cons ci ratio: 4.867731e-02	ci left: 3.837082e-01	ci right 4.029540e-01	k: 3933	n:10000
KS ci ratio: 2.356124e-02	ci left: 7.258284e-01	ci right 7.432348e-01	k: 7346	n:10000
CCDC80   10000 perm   2 sec   (5782 perm/sec)   p_kst 7.346000e-01   p_cons 3.933000e-01   p_joint 9.480000e-01

Outputting figure to mutsig2_images.part000000000032/CCDC80.2_2881_10000_0.7346_0.3933_0.948.png
                gene_name: CCDC80
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 67 percent done.
CCL23
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.628204e-02	ci left: 2.008694e-01	ci right 2.169006e-01	k: 2088	n:10000
Cons ci ratio: 8.808495e-02	ci left: 1.579697e-01	ci right 1.726258e-01	k: 1652	n:10000
KS ci ratio: 8.101469e-02	ci left: 1.819585e-01	ci right 1.974227e-01	k: 1896	n:10000
CCL23   10000 perm   1 sec   (7127 perm/sec)   p_kst 1.896000e-01   p_cons 1.652000e-01   p_joint 2.088000e-01

Outputting figure to mutsig2_images.part000000000032/CCL23.2_430_10000_0.1896_0.1652_0.2088.png
                gene_name: CCL23
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000032
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 32 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4397864: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000033> was used as the working directory.
Started at Wed Oct 24 16:09:23 2012
Results reported at Wed Oct 24 16:10:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000033.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000033.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 33  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000033.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     65.74 sec.
    Max Memory :      1211 MB
    Max Swap   :      3964 MB

    Max Processes  :         7
    Max Threads    :        71

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
33
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 33
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 33: processing genes 2872 - 2960
Calculating significance of each gene.
Using projection method.
2872	CCNK	1
2873	CCNL1	1
2874	CCNL2	1
2875	CCNO	1
2876	CCNT1	2.765607e-01
2877	CCNT2	1
2878	CCNY	8.453838e-02
2879	CCNYL1	1
2880	CCPG1	4.578334e-02
2881	CCR1	1
2882	CCR10	1
2883	CCR2	1
2884	CCR3	1
2885	CCR4	1
2886	CCR5	1
2887	CCR6	1
2888	CCR7	1.621194e-01
2889	CCR8	1
2890	CCR9	8.241737e-02
2891	CCRL1	1
2892	CCRL2	1
2893	CCRN4L	1
2894	CCS	1
2895	CCT2	2.420224e-01
2896	CCT3	1
2897	CCT4	1
2898	CCT5	1
2899	CCT6A	7.401401e-02
2900	CCT6B	2.462175e-01
2901	CCT7	1
2902	CCT8	4.957339e-02
2903	CCT8L2	1
2904	CD101	1
2905	CD109	1
2906	CD14	1
2907	CD151	1
2908	CD160	1
2909	CD163	4.863115e-01
2910	CD163L1	1
2911	CD164	1
2912	CD164L2	1
2913	CD177	1
2914	CD180	1.586792e-01
2915	CD19	1
2916	CD1A	1
2917	CD1B	1
2918	CD1C	1
2919	CD1D	1
2920	CD1E	1
2921	CD2	1
2922	CD200	1
2923	CD200R1	1.614239e-01
2924	CD200R1L	1
2925	CD207	1
2926	CD209	1
2927	CD22	2.681082e-01
2928	CD226	1.762267e-01
2929	CD244	2.402005e-02
2930	CD247	1
2931	CD248	1
2932	CD27	1
2933	CD274	1
2934	CD276	1
2935	CD28	1
2936	CD2AP	1
2937	CD2BP2	1
2938	CD300A	1
2939	CD300C	1
2940	CD300E	1
2941	CD300LB	1
2942	CD300LD	1
2943	CD300LF	1
2944	CD300LG	1
2945	CD302	1
2946	CD320	9.589132e-02
2947	CD33	1
2948	CD34	1
2949	CD36	1
2950	CD37	1
2951	CD38	1
2952	CD3D	1
2953	CD3E	1
2954	CD3EAP	7.182332e-02
2955	CD3G	1
2956	CD4	1
2957	CD40	1
2958	CD40LG	1
2959	CD44	1.842529e-01
2960	CD46	1
Done

Running MutSig 2:
Scatter job 33: processing genes 2872 - 2960
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CCPG1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.920630e-02	ci left: 6.335189e-01	ci right 6.523977e-01	k: 6430	n:10000
KS ci ratio: 4.151183e-02	ci left: 4.614759e-01	ci right 4.811408e-01	k: 4713	n:10000
CCPG1   10000 perm   2 sec   (6611 perm/sec)   p_kst 4.713000e-01   p_cons 6.430000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000033/CCPG1.2_2302_10000_0.4713_0.643_1.png
                gene_name: CCPG1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000033
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 33 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1547>
Subject: Job 4397871: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000034> was used as the working directory.
Started at Wed Oct 24 16:09:31 2012
Results reported at Wed Oct 24 16:11:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000034.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000034.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 34  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000034.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    210.62 sec.
    Max Memory :      1289 MB
    Max Swap   :      4015 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
34
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 34
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 34: processing genes 2961 - 3050
Calculating significance of each gene.
Using projection method.
2961	CD47	1.026712e-01
2962	CD48	1
2963	CD5	1
2964	CD52	1
2965	CD53	1
2966	CD55	1
2967	CD58	1
2968	CD59	1
2969	CD5L	1
2970	CD6	1
2971	CD63	1
2972	CD68	1
2973	CD69	1
2974	CD7	1
2975	CD70	1
2976	CD72	1
2977	CD74	1
2978	CD79A	1
2979	CD79B	1
2980	CD80	1
2981	CD81	1
2982	CD82	1
2983	CD83	1
2984	CD84	2.739650e-02
2985	CD86	1.389280e-01
2986	CD8A	1
2987	CD8B	1
2988	CD9	1
2989	CD93	1
2990	CD96	1
2991	CD97	2.603936e-01
2992	CD99	1
2993	CD99L2	1
2994	CDA	1
2995	CDADC1	1
2996	CDAN1	1
2997	CDC123	1
2998	CDC14A	1
2999	CDC14B	1.811676e-01
3000/17942 3000	CDC16	1
3001	CDC20	1.006674e-01
3002	CDC20B	1
3003	CDC23	1
3004	CDC25A	1
3005	CDC25B	1.471768e-01
3006	CDC25C	1
3007	CDC26	1
3008	CDC27	9.487288e-02
3009	CDC34	1
3010	CDC37	1
3011	CDC37L1	1
3012	CDC40	1
3013	CDC42	1
3014	CDC42BPA	3.521201e-01
3015	CDC42BPB	1
3016	CDC42BPG	1
3017	CDC42EP1	1
3018	CDC42EP2	1
3019	CDC42EP3	4.935544e-02
3020	CDC42EP4	8.256662e-02
3021	CDC42SE1	1
3022	CDC42SE2	1
3023	CDC45	1
3024	CDC5L	1
3025	CDC6	1
3026	CDC7	1
3027	CDC73	2.559719e-01
3028	CDCA2	6.894422e-02
3029	CDCA3	1
3030	CDCA4	1
3031	CDCA5	1
3032	CDCA7	1
3033	CDCA7L	1
3034	CDCA8	1
3035	CDCP1	3.738036e-01
3036	CDCP2	1
3037	CDH1	1
3038	CDH10	2.641685e-01
3039	CDH11	1.443683e-01
3040	CDH12	1.825303e-01
3041	CDH13	2.053390e-01
3042	CDH15	1
3043	CDH16	1
3044	CDH17	1
3045	CDH18	1
3046	CDH19	1
3047	CDH2	1.323422e-01
3048	CDH20	8.625838e-02
3049	CDH22	2.181123e-01
3050	CDH23	6.829673e-01
Done

Running MutSig 2:
Scatter job 34: processing genes 2961 - 3050
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CDC42BPA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.460821e-02	ci left: 7.083616e-01	ci right 7.261116e-01	k: 7173	n:10000
Cons ci ratio: 1.231453e-01	ci left: 8.630741e-02	ci right 9.773155e-02	k: 919	n:10000
KS ci ratio: 4.325118e-02	ci left: 4.411130e-01	ci right 4.607156e-01	k: 4509	n:10000
CDC42BPA   10000 perm   2 sec   (4399 perm/sec)   p_kst 4.509000e-01   p_cons 9.190000e-02   p_joint 7.173000e-01

Joint ci ratio: 1.748898e-02	ci left: 7.089395e-01	ci right 7.214979e-01	k: 14305	n:20000
Cons ci ratio: 8.803028e-02	ci left: 8.621560e-02	ci right 9.420400e-02	k: 1803	n:20000
KS ci ratio: 3.060742e-02	ci left: 4.436371e-01	ci right 4.574773e-01	k: 9011	n:20000
CDC42BPA   20000 perm   8 sec   (2460 perm/sec)   p_kst 4.505500e-01   p_cons 9.015000e-02   p_joint 7.152500e-01

Outputting figure to mutsig2_images.part000000000034/CDC42BPA.2_5304_20000_0.45055_0.09015_0.71525.png
                gene_name: CDC42BPA
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.090 
      ci_cons_bounds_left: 0.086 
     ci_cons_bounds_right: 0.094 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.71 
    ci_joint_bounds_right: 0.72 

Current progress: 50 percent done.
CDCA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.679164e-02	ci left: 1.340383e-01	ci right 1.477716e-01	k: 1408	n:10000
Cons ci ratio: 7.752686e-02	ci left: 1.956464e-01	ci right 2.115267e-01	k: 2035	n:10000
KS ci ratio: 6.555229e-02	ci left: 2.546878e-01	ci right 2.720503e-01	k: 2633	n:10000
CDCA2   10000 perm   2 sec   (5663 perm/sec)   p_kst 2.633000e-01   p_cons 2.035000e-01   p_joint 1.408000e-01

Outputting figure to mutsig2_images.part000000000034/CDCA2.2_3128_10000_0.2633_0.2035_0.1408.png
                gene_name: CDCA2
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.15 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000034
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 34 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4397878: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000035> was used as the working directory.
Started at Wed Oct 24 16:09:49 2012
Results reported at Wed Oct 24 16:11:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000035.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000035.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 35  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000035.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     96.38 sec.
    Max Memory :      1653 MB
    Max Swap   :      4090 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
35
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 35
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 35: processing genes 3051 - 3140
Calculating significance of each gene.
Using projection method.
3051	CDH24	1
3052	CDH26	1
3053	CDH3	1
3054	CDH4	1
3055	CDH5	1
3056	CDH6	1
3057	CDH7	2.083548e-02
3058	CDH8	1.240127e-01
3059	CDH9	1
3060	CDHR1	1
3061	CDHR2	1
3062	CDHR3	3.839528e-01
3063	CDHR5	1
3064	CDIPT	1
3065	CDK1	1
3066	CDK10	1
3067	CDK11A	1
3068	CDK11B	8.848010e-04
3069	CDK12	1.233724e-01
3070	CDK13	1.960655e-02
3071	CDK14	1
3072	CDK15	1
3073	CDK16	1
3074	CDK17	1
3075	CDK18	1
3076	CDK19	1
3077	CDK2	1
3078	CDK20	1
3079	CDK2AP1	1
3080	CDK2AP2	1
3081	CDK3	1.657419e-01
3082	CDK4	1
3083	CDK5	1
3084	CDK5R1	1
3085	CDK5R2	1
3086	CDK5RAP1	1
3087	CDK5RAP2	5.015399e-01
3088	CDK5RAP3	7.435674e-03
3089	CDK6	1
3090	CDK7	1
3091	CDK8	1
3092	CDK9	1.152756e-01
3093	CDKAL1	1
3094	CDKL1	1
3095	CDKL2	1
3096	CDKL3	1
3097	CDKL4	3.539545e-02
3098	CDKL5	1
3099	CDKN1A	1
3100	CDKN1B	1
3101	CDKN2A	1
3102	CDKN2AIP	1.471222e-01
3103	CDKN2AIPNL	1
3104	CDKN2B	1
3105	CDKN2C	1
3106	CDKN2D	1
3107	CDKN3	1
3108	CDNF	1
3109	CDO1	1
3110	CDON	1
3111	CDR1	2.859195e-02
3112	CDR2	1.454602e-01
3113	CDRT1	1
3114	CDRT15	1
3115	CDRT4	1
3116	CDS1	1
3117	CDS2	2.217031e-01
3118	CDSN	1
3119	CDT1	2.264334e-02
3120	CDV3	1
3121	CDX1	1
3122	CDX2	1
3123	CDX4	1
3124	CDYL	1
3125	CDYL2	1
3126	CEACAM1	1
3127	CEACAM16	2.826016e-02
3128	CEACAM18	1
3129	CEACAM19	1
3130	CEACAM20	1
3131	CEACAM21	1
3132	CEACAM3	1
3133	CEACAM4	1
3134	CEACAM5	1
3135	CEACAM6	1
3136	CEACAM7	1
3137	CEACAM8	1
3138	CEBPD	1
3139	CEBPE	1
3140	CEBPG	1
Done

Running MutSig 2:
Scatter job 35: processing genes 3051 - 3140
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CDHR3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.737222e-02	ci left: 6.629006e-01	ci right 6.813991e-01	k: 6722	n:10000
Cons ci ratio: 5.710380e-02	ci left: 3.110592e-01	ci right 3.294457e-01	k: 3202	n:10000
KS ci ratio: 2.383317e-02	ci left: 7.212834e-01	ci right 7.387824e-01	k: 7301	n:10000
CDHR3   10000 perm   2 sec   (5970 perm/sec)   p_kst 7.301000e-01   p_cons 3.202000e-01   p_joint 6.722000e-01

Outputting figure to mutsig2_images.part000000000035/CDHR3.3_2734_10000_0.7301_0.3202_0.6722.png
                gene_name: CDHR3
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    ci_joint_bounds_right: 0.68 

Current progress: 17 percent done.
CDK11B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.067200e-02	ci left: 2.854779e-01	ci right 3.034419e-01	k: 2944	n:10000
KS ci ratio: 2.014424e-02	ci left: 7.829981e-01	ci right 7.990320e-01	k: 7911	n:10000
CDK11B   10000 perm   2 sec   (5782 perm/sec)   p_kst 7.911000e-01   p_cons 2.944000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000035/CDK11B.3_2459_10000_0.7911_0.2944_1.png
                gene_name: CDK11B
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.29 
     ci_cons_bounds_right: 0.30 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
CDK13
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.466723e-02	ci left: 4.252535e-01	ci right 4.447844e-01	k: 4350	n:10000
Cons ci ratio: 8.369350e-02	ci left: 1.723174e-01	ci right 1.874696e-01	k: 1798	n:10000
KS ci ratio: 6.920559e-02	ci left: 2.344220e-01	ci right 2.513280e-01	k: 2428	n:10000
CDK13   10000 perm   2 sec   (5272 perm/sec)   p_kst 2.428000e-01   p_cons 1.798000e-01   p_joint 4.350000e-01

Outputting figure to mutsig2_images.part000000000035/CDK13.3_4595_10000_0.2428_0.1798_0.435.png
                gene_name: CDK13
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.44 

Current progress: 50 percent done.
CDH7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.017051e-02	ci left: 9.320594e-01	ci right 9.416842e-01	k: 9370	n:10000
Cons ci ratio: 5.542886e-02	ci left: 3.240605e-01	ci right 3.426367e-01	k: 3333	n:10000
KS ci ratio: 2.989034e-02	ci left: 6.227620e-01	ci right 6.417609e-01	k: 6323	n:10000
CDH7   10000 perm   2 sec   (6087 perm/sec)   p_kst 6.323000e-01   p_cons 3.333000e-01   p_joint 9.370000e-01

Outputting figure to mutsig2_images.part000000000035/CDH7.2_2402_10000_0.6323_0.3333_0.937.png
                gene_name: CDH7
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 67 percent done.
CDK12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.462512e-03	ci left: 9.849077e-01	ci right 9.894019e-01	k: 9873	n:10000
KS ci ratio: 4.005790e-02	ci left: 4.792569e-01	ci right 4.989495e-01	k: 4891	n:10000
CDK12   10000 perm   2 sec   (5124 perm/sec)   p_kst 4.891000e-01   p_cons 9.873000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000035/CDK12.2_4529_10000_0.4891_0.9873_1.png
                gene_name: CDK12
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
CDK5RAP3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.863244e-03	ci left: 9.574375e-01	ci right 9.650907e-01	k: 9614	n:10000
Cons ci ratio: 5.877849e-03	ci left: 9.750383e-01	ci right 9.808786e-01	k: 9781	n:10000
KS ci ratio: 4.323372e-02	ci left: 4.413126e-01	ci right 4.609159e-01	k: 4511	n:10000
CDK5RAP3   10000 perm   2 sec   (6460 perm/sec)   p_kst 4.511000e-01   p_cons 9.781000e-01   p_joint 9.614000e-01

Outputting figure to mutsig2_images.part000000000035/CDK5RAP3.2_1577_10000_0.4511_0.9781_0.9614.png
                gene_name: CDK5RAP3
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000035
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 35 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4397902: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000036> was used as the working directory.
Started at Wed Oct 24 16:09:49 2012
Results reported at Wed Oct 24 16:12:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000036.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000036.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 36  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000036.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    179.50 sec.
    Max Memory :      1511 MB
    Max Swap   :      3998 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
36
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 36
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 36: processing genes 3141 - 3230
Calculating significance of each gene.
Using projection method.
3141	CEBPZ	2.688009e-01
3142	CECR1	1
3143	CECR2	7.182904e-02
3144	CECR5	1
3145	CEL	1
3146	CELA1	1
3147	CELA2A	1
3148	CELA2B	1
3149	CELA3A	1
3150	CELA3B	1
3151	CELF1	1
3152	CELF2	1
3153	CELF3	1
3154	CELF4	1
3155	CELF5	1
3156	CELF6	1
3157	CELSR1	1
3158	CELSR2	1.656487e-02
3159	CELSR3	1
3160	CEMP1	1
3161	CEND1	2.454003e-02
3162	CENPA	1
3163	CENPB	1.686738e-01
3164	CENPBD1	1
3165	CENPC1	1
3166	CENPE	5.658558e-01
3167	CENPF	4.734049e-01
3168	CENPH	1
3169	CENPI	1
3170	CENPJ	1
3171	CENPK	1
3172	CENPL	1
3173	CENPM	1
3174	CENPN	1
3175	CENPO	1
3176	CENPP	1
3177	CENPQ	1
3178	CENPT	1
3179	CENPV	1
3180	CENPW	1
3181	CEP110	1.397380e-02
3182	CEP120	4.070255e-01
3183	CEP135	2.539807e-01
3184	CEP152	4.525262e-01
3185	CEP164	1
3186	CEP170	2.700596e-01
3187	CEP192	8.022912e-02
3188	CEP250	1.480201e-01
3189	CEP290	1
3190	CEP350	3.705015e-01
3191	CEP55	1
3192	CEP57	1
3193	CEP63	1
3194	CEP68	1
3195	CEP70	1
3196	CEP72	1.643178e-01
3197	CEP76	1
3198	CEP78	1
3199	CEP97	1
3200	CEPT1	1
3201	CER1	1
3202	CERCAM	1
3203	CERK	1.663571e-02
3204	CERKL	1
3205	CES1	1
3206	CES2	1
3207	CES3	1.599179e-01
3208	CES7	3.628736e-03
3209	CES8	1
3210	CETN1	1
3211	CETN2	1
3212	CETN3	1
3213	CETP	1
3214	CFB	1
3215	CFDP1	1
3216	CFH	1
3217	CFHR1	1
3218	CFHR2	1
3219	CFHR3	1
3220	CFHR4	1
3221	CFHR5	1
3222	CFI	1
3223	CFL1	1
3224	CFL2	1
3225	CFLAR	1
3226	CFP	7.395981e-02
3227	CFTR	4.112244e-01
3228	CGA	2.345148e-02
3229	CGB	1
3230	CGB1	1
Done

Running MutSig 2:
Scatter job 36: processing genes 3141 - 3230
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CELSR2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.164184e-02	ci left: 7.579801e-01	ci right 7.746645e-01	k: 7664	n:10000
Cons ci ratio: 2.234215e-02	ci left: 7.462447e-01	ci right 7.632067e-01	k: 7548	n:10000
KS ci ratio: 4.552242e-02	ci left: 4.159818e-01	ci right 4.354615e-01	k: 4257	n:10000
CELSR2   10000 perm   3 sec   (3828 perm/sec)   p_kst 4.257000e-01   p_cons 7.548000e-01   p_joint 7.664000e-01

Outputting figure to mutsig2_images.part000000000036/CELSR2.6_8908_10000_0.4257_0.7548_0.7664.png
                gene_name: CELSR2
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.77 

Current progress: 12 percent done.
CEP110
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.102425e-02	ci left: 2.831000e-01	ci right 3.010213e-01	k: 2920	n:10000
Cons ci ratio: 8.978231e-02	ci left: 1.528644e-01	ci right 1.673342e-01	k: 1600	n:10000
KS ci ratio: 3.942995e-02	ci left: 4.871524e-01	ci right 5.068493e-01	k: 4970	n:10000
CEP110   10000 perm   2 sec   (4523 perm/sec)   p_kst 4.970000e-01   p_cons 1.600000e-01   p_joint 2.920000e-01

Outputting figure to mutsig2_images.part000000000036/CEP110.4_7146_10000_0.497_0.16_0.292.png
                gene_name: CEP110
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.30 

Current progress: 25 percent done.
CEP192
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.886187e-01	ci left: 3.748413e-02	ci right 4.538584e-02	k: 413	n:10000
Cons ci ratio: 1.393752e-01	ci left: 6.816984e-02	ci right 7.848038e-02	k: 732	n:10000
KS ci ratio: 1.591398e-01	ci left: 5.263174e-02	ci right 6.182831e-02	k: 571	n:10000
CEP192   10000 perm   2 sec   (4340 perm/sec)   p_kst 5.710000e-02   p_cons 7.320000e-02   p_joint 4.130000e-02

Joint ci ratio: 1.750839e-01	ci left: 2.230608e-02	ci right 2.663369e-02	k: 488	n:20000
Cons ci ratio: 1.023338e-01	ci left: 6.484186e-02	ci right 7.188426e-02	k: 1366	n:20000
KS ci ratio: 1.140188e-01	ci left: 5.260997e-02	ci right 5.901994e-02	k: 1115	n:20000
CEP192   20000 perm   5 sec   (3972 perm/sec)   p_kst 5.575000e-02   p_cons 6.830000e-02   p_joint 2.440000e-02

Joint ci ratio: 1.236128e-01	ci left: 3.042513e-02	ci right 3.446608e-02	k: 972	n:30000
Cons ci ratio: 8.306762e-02	ci left: 6.622250e-02	ci right 7.199462e-02	k: 2072	n:30000
KS ci ratio: 9.384106e-02	ci left: 5.238154e-02	ci right 5.757173e-02	k: 1648	n:30000
CEP192   30000 perm   8 sec   (3826 perm/sec)   p_kst 5.493333e-02   p_cons 6.906667e-02   p_joint 3.240000e-02

Joint ci ratio: 9.919391e-02	ci left: 3.570814e-02	ci right 3.945938e-02	k: 1502	n:40000
Cons ci ratio: 7.144041e-02	ci left: 6.749380e-02	ci right 7.251884e-02	k: 2799	n:40000
KS ci ratio: 8.108708e-02	ci left: 5.295734e-02	ci right 5.745750e-02	k: 2207	n:40000
CEP192   40000 perm   11 sec   (3729 perm/sec)   p_kst 5.517500e-02   p_cons 6.997500e-02   p_joint 3.755000e-02

Outputting figure to mutsig2_images.part000000000036/CEP192.3_7790_40000_0.055175_0.069975_0.03755.png
                gene_name: CEP192
               theta_stop: 0.099 
                    nperm: 40000 
                     p_ks: 0.055 
        ci_ks_bounds_left: 0.053 
       ci_ks_bounds_right: 0.057 
                   p_cons: 0.070 
      ci_cons_bounds_left: 0.067 
     ci_cons_bounds_right: 0.073 
                  p_joint: 0.038 
     ci_joint_bounds_left: 0.036 
    ci_joint_bounds_right: 0.039 

Current progress: 38 percent done.
CECR2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.252495e-02	ci left: 4.494958e-01	ci right 4.691280e-01	k: 4593	n:10000
Cons ci ratio: 1.968030e-02	ci left: 7.907046e-01	ci right 8.065211e-01	k: 7987	n:10000
KS ci ratio: 2.595468e-01	ci left: 1.940213e-02	ci right 2.528070e-02	k: 222	n:10000
CECR2   10000 perm   2 sec   (5448 perm/sec)   p_kst 2.220000e-02   p_cons 7.987000e-01   p_joint 4.593000e-01

Joint ci ratio: 4.369440e-02	ci left: 2.806377e-01	ci right 2.932243e-01	k: 5738	n:20000
Cons ci ratio: 1.402823e-02	ci left: 7.904484e-01	ci right 8.016654e-01	k: 15922	n:20000
KS ci ratio: 1.824882e-01	ci left: 2.048931e-02	ci right 2.465110e-02	k: 450	n:20000
CECR2   20000 perm   4 sec   (4869 perm/sec)   p_kst 2.250000e-02   p_cons 7.961000e-01   p_joint 2.869000e-01

Joint ci ratio: 4.175976e-02	ci left: 2.222698e-01	ci right 2.317831e-01	k: 6810	n:30000
Cons ci ratio: 1.136098e-02	ci left: 7.941508e-01	ci right 8.032580e-01	k: 23962	n:30000
KS ci ratio: 1.482750e-01	ci left: 2.107635e-02	ci right 2.448360e-02	k: 682	n:30000
CECR2   30000 perm   6 sec   (4660 perm/sec)   p_kst 2.273333e-02   p_cons 7.987333e-01   p_joint 2.270000e-01

Joint ci ratio: 3.338055e-02	ci left: 2.520765e-01	ci right 2.606589e-01	k: 10254	n:40000
Cons ci ratio: 9.827644e-03	ci left: 7.951393e-01	ci right 8.030172e-01	k: 31964	n:40000
KS ci ratio: 1.291134e-01	ci left: 2.106890e-02	ci right 2.400098e-02	k: 900	n:40000
CECR2   40000 perm   9 sec   (4519 perm/sec)   p_kst 2.250000e-02   p_cons 7.991000e-01   p_joint 2.563500e-01

Joint ci ratio: 2.783130e-02	ci left: 2.800899e-01	ci right 2.880152e-01	k: 14202	n:50000
Cons ci ratio: 8.812538e-03	ci left: 7.947354e-01	ci right 8.017900e-01	k: 39914	n:50000
KS ci ratio: 1.167213e-01	ci left: 2.077095e-02	ci right 2.336495e-02	k: 1102	n:50000
CECR2   50000 perm   11 sec   (4410 perm/sec)   p_kst 2.204000e-02   p_cons 7.982800e-01   p_joint 2.840400e-01

Joint ci ratio: 2.479427e-02	ci left: 2.904227e-01	ci right 2.977306e-01	k: 17644	n:60000
Cons ci ratio: 8.058768e-03	ci left: 7.944797e-01	ci right 8.009248e-01	k: 47863	n:60000
KS ci ratio: 1.066176e-01	ci left: 2.085737e-02	ci right 2.322251e-02	k: 1321	n:60000
CECR2   60000 perm   14 sec   (4302 perm/sec)   p_kst 2.201667e-02   p_cons 7.977167e-01   p_joint 2.940667e-01

Joint ci ratio: 1.542968e-02	ci left: 4.760071e-01	ci right 4.834231e-01	k: 33580	n:70000
Cons ci ratio: 7.471915e-03	ci left: 7.942450e-01	ci right 8.002160e-01	k: 55807	n:70000
KS ci ratio: 9.836160e-02	ci left: 2.109337e-02	ci right 2.328934e-02	k: 1552	n:70000
CECR2   70000 perm   17 sec   (4187 perm/sec)   p_kst 2.217143e-02   p_cons 7.972429e-01   p_joint 4.797143e-01

Outputting figure to mutsig2_images.part000000000036/CECR2.2_4403_70000_0.022171_0.79724_0.47971.png
                gene_name: CECR2
               theta_stop: 0.098 
                    nperm: 70000 
                     p_ks: 0.022 
        ci_ks_bounds_left: 0.021 
       ci_ks_bounds_right: 0.023 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.48 

Current progress: 50 percent done.
CEP152
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.519761e-02	ci left: 6.985753e-01	ci right 7.165037e-01	k: 7076	n:10000
Cons ci ratio: 5.648024e-02	ci left: 3.158221e-01	ci right 3.342799e-01	k: 3250	n:10000
KS ci ratio: 6.762478e-02	ci left: 2.429207e-01	ci right 2.600243e-01	k: 2514	n:10000
CEP152   10000 perm   2 sec   (5094 perm/sec)   p_kst 2.514000e-01   p_cons 3.250000e-01   p_joint 7.076000e-01

Outputting figure to mutsig2_images.part000000000036/CEP152.2_5065_10000_0.2514_0.325_0.7076.png
                gene_name: CEP152
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 62 percent done.
CEP250
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.422738e-02	ci left: 2.626030e-01	ci right 2.801304e-01	k: 2713	n:10000
Cons ci ratio: 6.911164e-02	ci left: 2.349160e-01	ci right 2.518337e-01	k: 2433	n:10000
KS ci ratio: 1.001686e-01	ci left: 1.261085e-01	ci right 1.395062e-01	k: 1327	n:10000
CEP250   10000 perm   2 sec   (4434 perm/sec)   p_kst 1.327000e-01   p_cons 2.433000e-01   p_joint 2.713000e-01

Joint ci ratio: 4.269618e-02	ci left: 2.901256e-01	ci right 3.028336e-01	k: 5929	n:20000
Cons ci ratio: 4.866496e-02	ci left: 2.389526e-01	ci right 2.509216e-01	k: 4898	n:20000
KS ci ratio: 7.124930e-02	ci left: 1.267467e-01	ci right 1.361607e-01	k: 2628	n:20000
CEP250   20000 perm   5 sec   (4025 perm/sec)   p_kst 1.314000e-01   p_cons 2.449000e-01   p_joint 2.964500e-01

Outputting figure to mutsig2_images.part000000000036/CEP250.2_7457_20000_0.1314_0.2449_0.29645.png
                gene_name: CEP250
               theta_stop: 0.071 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.30 

Current progress: 75 percent done.
CERK
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.307477e-02	ci left: 1.744810e-01	ci right 1.897046e-01	k: 1820	n:10000
Cons ci ratio: 9.990851e-02	ci left: 1.266956e-01	ci right 1.401187e-01	k: 1333	n:10000
KS ci ratio: 5.082408e-02	ci left: 3.634102e-01	ci right 3.824638e-01	k: 3729	n:10000
CERK   10000 perm   2 sec   (6651 perm/sec)   p_kst 3.729000e-01   p_cons 1.333000e-01   p_joint 1.820000e-01

Outputting figure to mutsig2_images.part000000000036/CERK.2_1666_10000_0.3729_0.1333_0.182.png
                gene_name: CERK
               theta_stop: 0.100 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.19 

Current progress: 88 percent done.
CES7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.503941e-02	ci left: 7.011979e-01	ci right 7.190795e-01	k: 7102	n:10000
Cons ci ratio: 4.768235e-02	ci left: 3.935649e-01	ci right 4.128915e-01	k: 4032	n:10000
KS ci ratio: 6.051180e-02	ci left: 2.865679e-01	ci right 3.045513e-01	k: 2955	n:10000
CES7   10000 perm   2 sec   (6520 perm/sec)   p_kst 2.955000e-01   p_cons 4.032000e-01   p_joint 7.102000e-01

Outputting figure to mutsig2_images.part000000000036/CES7.2_1948_10000_0.2955_0.4032_0.7102.png
                gene_name: CES7
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000036
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 36 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4397906: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000037> was used as the working directory.
Started at Wed Oct 24 16:09:49 2012
Results reported at Wed Oct 24 16:27:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000037.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000037.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 37  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000037.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :   1060.72 sec.
    Max Memory :      1371 MB
    Max Swap   :      3988 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
37
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 37
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 37: processing genes 3231 - 3319
Calculating significance of each gene.
Using projection method.
3231	CGB2	1
3232	CGB5	1
3233	CGB7	1
3234	CGB8	1
3235	CGGBP1	1
3236	CGN	5.936696e-02
3237	CGNL1	3.272613e-01
3238	CGREF1	1
3239	CGRRF1	1
3240	CH25H	2.761768e-02
3241	CHAC1	1
3242	CHAC2	7.469839e-02
3243	CHAD	1
3244	CHAF1A	2.940851e-01
3245	CHAF1B	1
3246	CHAT	1
3247	CHCHD1	1
3248	CHCHD10	1
3249	CHCHD2	1
3250	CHCHD3	1
3251	CHCHD4	1
3252	CHCHD5	1
3253	CHCHD6	1
3254	CHCHD7	1
3255	CHCHD8	1
3256	CHD1	2.329740e-01
3257	CHD1L	1
3258	CHD2	1
3259	CHD3	1.114839e-01
3260	CHD4	2.782585e-01
3261	CHD5	1
3262	CHD6	1
3263	CHD7	1.836683e-01
3264	CHD8	4.250486e-02
3265	CHD9	1
3266	CHDH	7.857796e-02
3267	CHEK1	1
3268	CHEK2	4.873672e-02
3269	CHERP	1.107397e-01
3270	CHFR	1
3271	CHGA	9.780176e-02
3272	CHGB	1
3273	CHI3L1	1
3274	CHI3L2	1
3275	CHIA	1
3276	CHIC2	1
3277	CHID1	1
3278	CHIT1	1
3279	CHKA	1
3280	CHKB	1.669704e-01
3281	CHL1	1.659142e-01
3282	CHM	1
3283	CHML	1
3284	CHMP1A	1
3285	CHMP1B	1
3286	CHMP2A	1
3287	CHMP2B	8.231185e-02
3288	CHMP4A	1
3289	CHMP4B	1
3290	CHMP4C	1
3291	CHMP5	1
3292	CHMP6	1
3293	CHMP7	1
3294	CHN1	1
3295	CHN2	1
3296	CHODL	1
3297	CHORDC1	1
3298	CHP	1
3299	CHP2	1
3300	CHPF	1
3301	CHPF2	1
3302	CHPT1	1
3303	CHRAC1	1
3304	CHRD	1
3305	CHRDL1	1.617133e-01
3306	CHRDL2	1
3307	CHRFAM7A	1
3308	CHRM1	1
3309	CHRM2	1
3310	CHRM3	1
3311	CHRM4	1
3312	CHRM5	1
3313	CHRNA1	1
3314	CHRNA10	1
3315	CHRNA2	1
3316	CHRNA3	7.197334e-02
3317	CHRNA4	1
3318	CHRNA5	8.910589e-02
3319	CHRNA6	1
Done

Running MutSig 2:
Scatter job 37: processing genes 3231 - 3319
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CHD8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.650251e-01	ci left: 9.321618e-03	ci right 1.357016e-02	k: 113	n:10000
Cons ci ratio: 1.011330e+00	ci left: 7.655977e-04	ci right 2.347848e-03	k: 14	n:10000
KS ci ratio: 1.445485e-01	ci left: 6.352868e-02	ci right 7.352445e-02	k: 684	n:10000
CHD8   10000 perm   3 sec   (3898 perm/sec)   p_kst 6.840000e-02   p_cons 1.400000e-03   p_joint 1.130000e-02

Joint ci ratio: 4.033559e-01	ci left: 3.754742e-03	ci right 5.693581e-03	k: 93	n:20000
Cons ci ratio: 8.168860e-01	ci left: 6.894885e-04	ci right 1.664942e-03	k: 22	n:20000
KS ci ratio: 1.024545e-01	ci left: 6.469544e-02	ci right 7.173072e-02	k: 1363	n:20000
CHD8   20000 perm   8 sec   (2615 perm/sec)   p_kst 6.815000e-02   p_cons 1.100000e-03   p_joint 4.650000e-03

Joint ci ratio: 2.366011e-01	ci left: 7.993789e-03	ci right 1.016955e-02	k: 271	n:30000
Cons ci ratio: 6.718822e-01	ci left: 7.573066e-04	ci right 1.544465e-03	k: 33	n:30000
KS ci ratio: 8.569486e-02	ci left: 6.239923e-02	ci right 6.801866e-02	k: 1955	n:30000
CHD8   30000 perm   11 sec   (2810 perm/sec)   p_kst 6.516667e-02   p_cons 1.100000e-03   p_joint 9.033333e-03

Joint ci ratio: 2.582951e-01	ci left: 4.985810e-03	ci right 6.487312e-03	k: 228	n:40000
Cons ci ratio: 7.037711e-01	ci left: 5.060773e-04	ci right 1.070500e-03	k: 30	n:40000
KS ci ratio: 7.397175e-02	ci left: 6.316828e-02	ci right 6.804502e-02	k: 2623	n:40000
CHD8   40000 perm   14 sec   (2909 perm/sec)   p_kst 6.557500e-02   p_cons 7.500000e-04   p_joint 5.700000e-03

Joint ci ratio: 2.327711e-01	ci left: 4.983585e-03	ci right 6.314797e-03	k: 281	n:50000
Cons ci ratio: 6.046090e-01	ci left: 5.885084e-04	ci right 1.112260e-03	k: 41	n:50000
KS ci ratio: 6.636844e-02	ci left: 6.305134e-02	ci right 6.739930e-02	k: 3260	n:50000
CHD8   50000 perm   17 sec   (2961 perm/sec)   p_kst 6.520000e-02   p_cons 8.200000e-04   p_joint 5.620000e-03

Joint ci ratio: 2.188918e-01	ci left: 4.734727e-03	ci right 5.913900e-03	k: 318	n:60000
Cons ci ratio: 5.597666e-01	ci left: 5.899139e-04	ci right 1.060546e-03	k: 48	n:60000
KS ci ratio: 6.067886e-02	ci left: 6.305659e-02	ci right 6.701894e-02	k: 3901	n:60000
CHD8   60000 perm   20 sec   (2984 perm/sec)   p_kst 6.501667e-02   p_cons 8.000000e-04   p_joint 5.300000e-03

Joint ci ratio: 2.317259e-01	ci left: 3.599760e-03	ci right 4.556355e-03	k: 284	n:70000
Cons ci ratio: 5.101218e-01	ci left: 6.292273e-04	ci right 1.070991e-03	k: 58	n:70000
KS ci ratio: 5.407535e-02	ci left: 6.793720e-02	ci right 7.172712e-02	k: 4887	n:70000
CHD8   70000 perm   23 sec   (2990 perm/sec)   p_kst 6.981429e-02   p_cons 8.285714e-04   p_joint 4.057143e-03

Joint ci ratio: 2.180116e-01	ci left: 3.586255e-03	ci right 4.475307e-03	k: 321	n:80000
Cons ci ratio: 4.787007e-01	ci left: 6.381106e-04	ci right 1.049484e-03	k: 66	n:80000
KS ci ratio: 5.052597e-02	ci left: 6.820426e-02	ci right 7.175200e-02	k: 5597	n:80000
CHD8   80000 perm   27 sec   (2987 perm/sec)   p_kst 6.996250e-02   p_cons 8.250000e-04   p_joint 4.012500e-03

Joint ci ratio: 1.545205e-01	ci left: 6.551153e-03	ci right 7.658751e-03	k: 638	n:90000
Cons ci ratio: 3.769737e-01	ci left: 9.744223e-04	ci right 1.436473e-03	k: 107	n:90000
KS ci ratio: 4.777415e-02	ci left: 6.793483e-02	ci right 7.127075e-02	k: 6263	n:90000
CHD8   90000 perm   30 sec   (2976 perm/sec)   p_kst 6.958889e-02   p_cons 1.188889e-03   p_joint 7.088889e-03

Joint ci ratio: 1.571967e-01	ci left: 5.694027e-03	ci right 6.674947e-03	k: 617	n:100000
Cons ci ratio: 3.621903e-01	ci left: 9.586222e-04	ci right 1.391149e-03	k: 116	n:100000
KS ci ratio: 4.533306e-02	ci left: 6.799072e-02	ci right 7.115430e-02	k: 6956	n:100000
CHD8   100000 perm   34 sec   (2961 perm/sec)   p_kst 6.956000e-02   p_cons 1.160000e-03   p_joint 6.170000e-03

Joint ci ratio: 1.665781e-01	ci left: 4.591730e-03	ci right 5.434693e-03	k: 550	n:110000
Cons ci ratio: 3.422864e-01	ci left: 9.874975e-04	ci right 1.403158e-03	k: 130	n:110000
KS ci ratio: 4.320429e-02	ci left: 6.812101e-02	ci right 7.113809e-02	k: 7658	n:110000
CHD8   110000 perm   37 sec   (2942 perm/sec)   p_kst 6.961818e-02   p_cons 1.181818e-03   p_joint 5.000000e-03

Joint ci ratio: 1.603048e-01	ci left: 4.560752e-03	ci right 5.363459e-03	k: 594	n:120000
Cons ci ratio: 3.299282e-01	ci left: 9.815083e-04	ci right 1.376568e-03	k: 140	n:120000
KS ci ratio: 4.138966e-02	ci left: 6.810869e-02	ci right 7.099549e-02	k: 8345	n:120000
CHD8   120000 perm   41 sec   (2919 perm/sec)   p_kst 6.954167e-02   p_cons 1.166667e-03   p_joint 4.950000e-03

Joint ci ratio: 1.540860e-01	ci left: 4.572026e-03	ci right 5.342618e-03	k: 643	n:130000
Cons ci ratio: 3.198807e-01	ci left: 9.695923e-04	ci right 1.345537e-03	k: 149	n:130000
KS ci ratio: 3.965408e-02	ci left: 6.852733e-02	ci right 7.130728e-02	k: 9088	n:130000
CHD8   130000 perm   45 sec   (2896 perm/sec)   p_kst 6.990769e-02   p_cons 1.146154e-03   p_joint 4.946154e-03

Joint ci ratio: 1.609060e-01	ci left: 3.881682e-03	ci right 4.567673e-03	k: 590	n:140000
Cons ci ratio: 3.087605e-01	ci left: 9.727115e-04	ci right 1.334175e-03	k: 160	n:140000
KS ci ratio: 3.813660e-02	ci left: 6.883166e-02	ci right 7.151475e-02	k: 9823	n:140000
CHD8   140000 perm   49 sec   (2876 perm/sec)   p_kst 7.016429e-02   p_cons 1.142857e-03   p_joint 4.214286e-03

Joint ci ratio: 1.200323e-01	ci left: 6.636041e-03	ci right 7.489846e-03	k: 1058	n:150000
Cons ci ratio: 2.978592e-01	ci left: 9.817788e-04	ci right 1.331297e-03	k: 172	n:150000
KS ci ratio: 3.813077e-02	ci left: 6.456360e-02	ci right 6.707989e-02	k: 9872	n:150000
CHD8   150000 perm   53 sec   (2833 perm/sec)   p_kst 6.581333e-02   p_cons 1.146667e-03   p_joint 7.053333e-03

Joint ci ratio: 1.362072e-01	ci left: 4.799100e-03	ci right 5.506514e-03	k: 823	n:160000
Cons ci ratio: 2.904035e-01	ci left: 9.725175e-04	ci right 1.308480e-03	k: 181	n:160000
KS ci ratio: 3.685295e-02	ci left: 6.482536e-02	ci right 6.726539e-02	k: 10566	n:160000
CHD8   160000 perm   57 sec   (2810 perm/sec)   p_kst 6.603750e-02   p_cons 1.131250e-03   p_joint 5.143750e-03

Joint ci ratio: 1.338019e-01	ci left: 4.687292e-03	ci right 5.365051e-03	k: 853	n:170000
Cons ci ratio: 2.820067e-01	ci left: 9.753731e-04	ci right 1.300848e-03	k: 192	n:170000
KS ci ratio: 3.576872e-02	ci left: 6.480673e-02	ci right 6.717280e-02	k: 11217	n:170000
CHD8   170000 perm   61 sec   (2775 perm/sec)   p_kst 6.598235e-02   p_cons 1.129412e-03   p_joint 5.017647e-03

Joint ci ratio: 1.319702e-01	ci left: 4.555767e-03	ci right 5.204782e-03	k: 877	n:180000
Cons ci ratio: 2.777270e-01	ci left: 9.521782e-04	ci right 1.264248e-03	k: 198	n:180000
KS ci ratio: 3.480471e-02	ci left: 6.468641e-02	ci right 6.698316e-02	k: 11849	n:180000
CHD8   180000 perm   66 sec   (2718 perm/sec)   p_kst 6.582778e-02   p_cons 1.100000e-03   p_joint 4.872222e-03

Joint ci ratio: 1.116840e-01	ci left: 6.082169e-03	ci right 6.806698e-03	k: 1223	n:190000
Cons ci ratio: 2.647357e-01	ci left: 1.000176e-03	ci right 1.310104e-03	k: 218	n:190000
KS ci ratio: 3.384216e-02	ci left: 6.484061e-02	ci right 6.707792e-02	k: 12531	n:190000
CHD8   190000 perm   70 sec   (2696 perm/sec)   p_kst 6.595263e-02   p_cons 1.147368e-03   p_joint 6.436842e-03

Joint ci ratio: 1.093880e-01	ci left: 6.030863e-03	ci right 6.733559e-03	k: 1275	n:200000
Cons ci ratio: 2.606065e-01	ci left: 9.828617e-04	ci right 1.281900e-03	k: 225	n:200000
KS ci ratio: 3.293795e-02	ci left: 6.504467e-02	ci right 6.722792e-02	k: 13226	n:200000
CHD8   200000 perm   75 sec   (2674 perm/sec)   p_kst 6.613000e-02   p_cons 1.125000e-03   p_joint 6.375000e-03

Joint ci ratio: 1.110362e-01	ci left: 5.572272e-03	ci right 6.231955e-03	k: 1238	n:210000
Cons ci ratio: 2.550262e-01	ci left: 9.806008e-04	ci right 1.271547e-03	k: 235	n:210000
KS ci ratio: 3.213467e-02	ci left: 6.510713e-02	ci right 6.723819e-02	k: 13895	n:210000
CHD8   210000 perm   80 sec   (2637 perm/sec)   p_kst 6.616667e-02   p_cons 1.119048e-03   p_joint 5.895238e-03

Joint ci ratio: 1.091621e-01	ci left: 5.509049e-03	ci right 6.149531e-03	k: 1281	n:220000
Cons ci ratio: 2.534254e-01	ci left: 9.487935e-04	ci right 1.228256e-03	k: 238	n:220000
KS ci ratio: 3.142095e-02	ci left: 6.503365e-02	ci right 6.711417e-02	k: 14535	n:220000
CHD8   220000 perm   85 sec   (2603 perm/sec)   p_kst 6.606818e-02   p_cons 1.081818e-03   p_joint 5.822727e-03

Joint ci ratio: 1.069745e-01	ci left: 5.493729e-03	ci right 6.118824e-03	k: 1334	n:230000
Cons ci ratio: 2.513347e-01	ci left: 9.238314e-04	ci right 1.193345e-03	k: 242	n:230000
KS ci ratio: 3.072351e-02	ci left: 6.508359e-02	ci right 6.711867e-02	k: 15202	n:230000
CHD8   230000 perm   89 sec   (2582 perm/sec)   p_kst 6.609565e-02   p_cons 1.052174e-03   p_joint 5.800000e-03

Joint ci ratio: 1.145686e-01	ci left: 4.575966e-03	ci right 5.136095e-03	k: 1164	n:240000
Cons ci ratio: 2.448688e-01	ci left: 9.361386e-04	ci right 1.201148e-03	k: 255	n:240000
KS ci ratio: 3.008678e-02	ci left: 6.506363e-02	ci right 6.705520e-02	k: 15853	n:240000
CHD8   240000 perm   94 sec   (2561 perm/sec)   p_kst 6.605417e-02   p_cons 1.062500e-03   p_joint 4.850000e-03

Joint ci ratio: 1.121861e-01	ci left: 4.587257e-03	ci right 5.136319e-03	k: 1214	n:250000
Cons ci ratio: 2.406755e-01	ci left: 9.325031e-04	ci right 1.191288e-03	k: 264	n:250000
KS ci ratio: 2.949955e-02	ci left: 6.499801e-02	ci right 6.694807e-02	k: 16492	n:250000
CHD8   250000 perm   99 sec   (2538 perm/sec)   p_kst 6.596800e-02   p_cons 1.056000e-03   p_joint 4.856000e-03

Joint ci ratio: 9.745297e-02	ci left: 5.883105e-03	ci right 6.489521e-03	k: 1607	n:260000
Cons ci ratio: 2.337207e-01	ci left: 9.545209e-04	ci right 1.210656e-03	k: 280	n:260000
KS ci ratio: 2.892373e-02	ci left: 6.502947e-02	ci right 6.694176e-02	k: 17155	n:260000
CHD8   260000 perm   103 sec   (2515 perm/sec)   p_kst 6.598077e-02   p_cons 1.076923e-03   p_joint 6.180769e-03

Joint ci ratio: 9.656216e-02	ci left: 5.773612e-03	ci right 6.362993e-03	k: 1637	n:270000
Cons ci ratio: 2.304644e-01	ci left: 9.470747e-04	ci right 1.197167e-03	k: 288	n:270000
KS ci ratio: 2.836844e-02	ci left: 6.511045e-02	ci right 6.698776e-02	k: 17832	n:270000
CHD8   270000 perm   108 sec   (2495 perm/sec)   p_kst 6.604444e-02   p_cons 1.066667e-03   p_joint 6.062963e-03

Joint ci ratio: 9.428384e-02	ci left: 5.846317e-03	ci right 6.428262e-03	k: 1717	n:280000
Cons ci ratio: 2.265780e-01	ci left: 9.469205e-04	ci right 1.192166e-03	k: 298	n:280000
KS ci ratio: 2.786087e-02	ci left: 6.511146e-02	ci right 6.695467e-02	k: 18488	n:280000
CHD8   280000 perm   113 sec   (2475 perm/sec)   p_kst 6.602857e-02   p_cons 1.064286e-03   p_joint 6.132143e-03

Joint ci ratio: 9.267957e-02	ci left: 5.846780e-03	ci right 6.418330e-03	k: 1777	n:290000
Cons ci ratio: 2.243401e-01	ci left: 9.337886e-04	ci right 1.172914e-03	k: 304	n:290000
KS ci ratio: 2.739723e-02	ci left: 6.503388e-02	ci right 6.684377e-02	k: 19121	n:290000
CHD8   290000 perm   118 sec   (2455 perm/sec)   p_kst 6.593448e-02   p_cons 1.048276e-03   p_joint 6.127586e-03

Joint ci ratio: 9.383744e-02	ci left: 5.511852e-03	ci right 6.057762e-03	k: 1734	n:300000
Cons ci ratio: 2.193608e-01	ci left: 9.467368e-04	ci right 1.183072e-03	k: 318	n:300000
KS ci ratio: 2.693775e-02	ci left: 6.504452e-02	ci right 6.682388e-02	k: 19779	n:300000
CHD8   300000 perm   123 sec   (2434 perm/sec)   p_kst 6.593000e-02   p_cons 1.060000e-03   p_joint 5.780000e-03

Joint ci ratio: 9.338726e-02	ci left: 5.387589e-03	ci right 5.918491e-03	k: 1751	n:310000
Cons ci ratio: 2.153473e-01	ci left: 9.527998e-04	ci right 1.185721e-03	k: 330	n:310000
KS ci ratio: 2.651730e-02	ci left: 6.497777e-02	ci right 6.672713e-02	k: 20413	n:310000
CHD8   310000 perm   128 sec   (2414 perm/sec)   p_kst 6.584839e-02   p_cons 1.064516e-03   p_joint 5.648387e-03

Joint ci ratio: 9.994392e-02	ci left: 4.545178e-03	ci right 5.026357e-03	k: 1530	n:320000
Cons ci ratio: 2.115463e-01	ci left: 9.585206e-04	ci right 1.188169e-03	k: 342	n:320000
KS ci ratio: 2.608016e-02	ci left: 6.508312e-02	ci right 6.680600e-02	k: 21101	n:320000
CHD8   320000 perm   134 sec   (2393 perm/sec)   p_kst 6.594063e-02   p_cons 1.068750e-03   p_joint 4.781250e-03

Joint ci ratio: 9.959240e-02	ci left: 4.439935e-03	ci right 4.908222e-03	k: 1541	n:330000
Cons ci ratio: 2.082336e-01	ci left: 9.610560e-04	ci right 1.187246e-03	k: 353	n:330000
KS ci ratio: 2.567466e-02	ci left: 6.513110e-02	ci right 6.682805e-02	k: 21772	n:330000
CHD8   330000 perm   139 sec   (2371 perm/sec)   p_kst 6.597576e-02   p_cons 1.069697e-03   p_joint 4.669697e-03

Joint ci ratio: 8.281262e-02	ci left: 6.275835e-03	ci right 6.820862e-03	k: 2225	n:340000
Cons ci ratio: 2.064924e-01	ci left: 9.495198e-04	ci right 1.170890e-03	k: 359	n:340000
KS ci ratio: 2.528992e-02	ci left: 6.516475e-02	ci right 6.683677e-02	k: 22439	n:340000
CHD8   340000 perm   145 sec   (2352 perm/sec)   p_kst 6.599706e-02   p_cons 1.055882e-03   p_joint 6.544118e-03

Joint ci ratio: 9.934724e-02	ci left: 4.208488e-03	ci right 4.651207e-03	k: 1549	n:350000
Cons ci ratio: 2.039592e-01	ci left: 9.467834e-04	ci right 1.164470e-03	k: 368	n:350000
KS ci ratio: 2.422013e-02	ci left: 6.878750e-02	ci right 7.047678e-02	k: 24370	n:350000
CHD8   350000 perm   150 sec   (2331 perm/sec)   p_kst 6.962857e-02   p_cons 1.051429e-03   p_joint 4.425714e-03

Joint ci ratio: 9.092825e-02	ci left: 4.902493e-03	ci right 5.372194e-03	k: 1848	n:360000
Cons ci ratio: 1.999347e-01	ci left: 9.600444e-04	ci right 1.175894e-03	k: 383	n:360000
KS ci ratio: 2.384117e-02	ci left: 6.901667e-02	ci right 7.068470e-02	k: 25145	n:360000
CHD8   360000 perm   156 sec   (2302 perm/sec)   p_kst 6.984722e-02   p_cons 1.063889e-03   p_joint 5.133333e-03

Joint ci ratio: 9.063947e-02	ci left: 4.801678e-03	ci right 5.260181e-03	k: 1860	n:370000
Cons ci ratio: 1.983920e-01	ci left: 9.495043e-04	ci right 1.161137e-03	k: 389	n:370000
KS ci ratio: 2.351116e-02	ci left: 6.905893e-02	ci right 7.070457e-02	k: 25855	n:370000
CHD8   370000 perm   162 sec   (2279 perm/sec)   p_kst 6.987838e-02   p_cons 1.051351e-03   p_joint 5.027027e-03

Joint ci ratio: 9.136363e-02	ci left: 4.600717e-03	ci right 5.043728e-03	k: 1831	n:380000
Cons ci ratio: 1.966361e-01	ci left: 9.420271e-04	ci right 1.149913e-03	k: 396	n:380000
KS ci ratio: 2.319966e-02	ci left: 6.907033e-02	ci right 7.069413e-02	k: 26554	n:380000
CHD8   380000 perm   168 sec   (2261 perm/sec)   p_kst 6.987895e-02   p_cons 1.042105e-03   p_joint 4.818421e-03

Joint ci ratio: 7.985372e-02	ci left: 5.895718e-03	ci right 6.388586e-03	k: 2394	n:390000
Cons ci ratio: 1.932572e-01	ci left: 9.520184e-04	ci right 1.158074e-03	k: 410	n:390000
KS ci ratio: 2.291332e-02	ci left: 6.900731e-02	ci right 7.060935e-02	k: 27224	n:390000
CHD8   390000 perm   174 sec   (2243 perm/sec)   p_kst 6.980513e-02   p_cons 1.051282e-03   p_joint 6.138462e-03

Joint ci ratio: 7.883971e-02	ci left: 5.900250e-03	ci right 6.386946e-03	k: 2456	n:400000
Cons ci ratio: 1.909483e-01	ci left: 9.520157e-04	ci right 1.155323e-03	k: 420	n:400000
KS ci ratio: 2.263079e-02	ci left: 6.898486e-02	ci right 7.056638e-02	k: 27909	n:400000
CHD8   400000 perm   180 sec   (2225 perm/sec)   p_kst 6.977250e-02   p_cons 1.050000e-03   p_joint 6.140000e-03

Joint ci ratio: 7.915413e-02	ci left: 5.710893e-03	ci right 6.183935e-03	k: 2437	n:410000
Cons ci ratio: 1.885015e-01	ci left: 9.543509e-04	ci right 1.155247e-03	k: 431	n:410000
KS ci ratio: 2.235552e-02	ci left: 6.898061e-02	ci right 7.054255e-02	k: 28601	n:410000
CHD8   410000 perm   186 sec   (2209 perm/sec)   p_kst 6.975854e-02   p_cons 1.051220e-03   p_joint 5.943902e-03

Joint ci ratio: 7.822921e-02	ci left: 5.710297e-03	ci right 6.177511e-03	k: 2495	n:420000
Cons ci ratio: 1.865684e-01	ci left: 9.520507e-04	ci right 1.150174e-03	k: 440	n:420000
KS ci ratio: 2.209613e-02	ci left: 6.894115e-02	ci right 7.048384e-02	k: 29278	n:420000
CHD8   420000 perm   193 sec   (2181 perm/sec)   p_kst 6.970952e-02   p_cons 1.047619e-03   p_joint 5.940476e-03

Joint ci ratio: 7.581303e-02	ci left: 5.944735e-03	ci right 6.415445e-03	k: 2656	n:430000
Cons ci ratio: 1.844886e-01	ci left: 9.520857e-04	ci right 1.147761e-03	k: 450	n:430000
KS ci ratio: 2.183499e-02	ci left: 6.896609e-02	ci right 7.049088e-02	k: 29982	n:430000
CHD8   430000 perm   199 sec   (2159 perm/sec)   p_kst 6.972558e-02   p_cons 1.046512e-03   p_joint 6.176744e-03

Joint ci ratio: 7.547620e-02	ci left: 5.863131e-03	ci right 6.325227e-03	k: 2680	n:440000
Cons ci ratio: 1.832744e-01	ci left: 9.434557e-04	ci right 1.135939e-03	k: 456	n:440000
KS ci ratio: 2.158744e-02	ci left: 6.896287e-02	ci right 7.047008e-02	k: 30674	n:440000
CHD8   440000 perm   205 sec   (2142 perm/sec)   p_kst 6.971364e-02   p_cons 1.036364e-03   p_joint 6.090909e-03

Joint ci ratio: 9.531714e-02	ci left: 3.565914e-03	ci right 3.924967e-03	k: 1684	n:450000
Cons ci ratio: 1.568166e-01	ci left: 1.277918e-03	ci right 1.497471e-03	k: 623	n:450000
KS ci ratio: 2.135068e-02	ci left: 6.894440e-02	ci right 7.043448e-02	k: 31359	n:450000
CHD8   450000 perm   212 sec   (2125 perm/sec)   p_kst 6.968667e-02   p_cons 1.384444e-03   p_joint 3.742222e-03

Joint ci ratio: 7.874271e-02	ci left: 5.147622e-03	ci right 5.571688e-03	k: 2464	n:460000
Cons ci ratio: 1.548436e-01	ci left: 1.283564e-03	ci right 1.501055e-03	k: 639	n:460000
KS ci ratio: 2.112332e-02	ci left: 6.891601e-02	ci right 7.038942e-02	k: 32039	n:460000
CHD8   460000 perm   218 sec   (2110 perm/sec)   p_kst 6.965000e-02   p_cons 1.389130e-03   p_joint 5.356522e-03

Joint ci ratio: 7.951287e-02	ci left: 4.940056e-03	ci right 5.351187e-03	k: 2417	n:470000
Cons ci ratio: 1.531773e-01	ci left: 1.284894e-03	ci right 1.500052e-03	k: 653	n:470000
KS ci ratio: 2.090066e-02	ci left: 6.890372e-02	ci right 7.036116e-02	k: 32726	n:470000
CHD8   470000 perm   225 sec   (2093 perm/sec)   p_kst 6.962979e-02   p_cons 1.389362e-03   p_joint 5.142553e-03

Joint ci ratio: 7.353509e-02	ci left: 5.668928e-03	ci right 6.103736e-03	k: 2824	n:480000
Cons ci ratio: 1.516774e-01	ci left: 1.284175e-03	ci right 1.496916e-03	k: 666	n:480000
KS ci ratio: 2.068091e-02	ci left: 6.891691e-02	ci right 7.035912e-02	k: 33425	n:480000
CHD8   480000 perm   231 sec   (2079 perm/sec)   p_kst 6.963542e-02   p_cons 1.387500e-03   p_joint 5.883333e-03

Joint ci ratio: 7.517625e-02	ci left: 5.310851e-03	ci right 5.727682e-03	k: 2703	n:490000
Cons ci ratio: 1.505536e-01	ci left: 1.277604e-03	ci right 1.487547e-03	k: 676	n:490000
KS ci ratio: 2.046472e-02	ci left: 6.894995e-02	ci right 7.037759e-02	k: 34134	n:490000
CHD8   490000 perm   238 sec   (2063 perm/sec)   p_kst 6.966122e-02   p_cons 1.379592e-03   p_joint 5.516327e-03

Joint ci ratio: 7.488860e-02	ci left: 5.245839e-03	ci right 5.655923e-03	k: 2724	n:500000
Cons ci ratio: 1.488051e-01	ci left: 1.282854e-03	ci right 1.490993e-03	k: 692	n:500000
KS ci ratio: 2.025174e-02	ci left: 6.900364e-02	ci right 7.041735e-02	k: 34854	n:500000
CHD8   500000 perm   244 sec   (2048 perm/sec)   p_kst 6.970800e-02   p_cons 1.384000e-03   p_joint 5.448000e-03

Joint ci ratio: 7.431898e-02	ci left: 5.223794e-03	ci right 5.628914e-03	k: 2766	n:510000
Cons ci ratio: 1.467024e-01	ci left: 1.295466e-03	ci right 1.502421e-03	k: 712	n:510000
KS ci ratio: 2.005194e-02	ci left: 6.901236e-02	ci right 7.041214e-02	k: 35552	n:510000
CHD8   510000 perm   251 sec   (2030 perm/sec)   p_kst 6.970980e-02   p_cons 1.396078e-03   p_joint 5.423529e-03

Joint ci ratio: 7.436342e-02	ci left: 5.117664e-03	ci right 5.514801e-03	k: 2763	n:520000
Cons ci ratio: 1.452829e-01	ci left: 1.296493e-03	ci right 1.501434e-03	k: 726	n:520000
KS ci ratio: 1.985205e-02	ci left: 6.905910e-02	ci right 7.044570e-02	k: 36270	n:520000
CHD8   520000 perm   258 sec   (2015 perm/sec)   p_kst 6.975000e-02   p_cons 1.396154e-03   p_joint 5.313462e-03

Joint ci ratio: 7.399136e-02	ci left: 5.072950e-03	ci right 5.464563e-03	k: 2791	n:530000
Cons ci ratio: 1.438068e-01	ci left: 1.299309e-03	ci right 1.502430e-03	k: 741	n:530000
KS ci ratio: 1.967318e-02	ci left: 6.900459e-02	ci right 7.037747e-02	k: 36935	n:530000
CHD8   530000 perm   265 sec   (2001 perm/sec)   p_kst 6.968868e-02   p_cons 1.398113e-03   p_joint 5.266038e-03

Joint ci ratio: 7.362480e-02	ci left: 5.029898e-03	ci right 5.416181e-03	k: 2819	n:540000
Cons ci ratio: 1.419063e-01	ci left: 1.310962e-03	ci right 1.512967e-03	k: 761	n:540000
KS ci ratio: 1.949153e-02	ci left: 6.900193e-02	ci right 7.036195e-02	k: 37627	n:540000
CHD8   540000 perm   272 sec   (1986 perm/sec)   p_kst 6.967963e-02   p_cons 1.409259e-03   p_joint 5.220370e-03

Joint ci ratio: 7.284061e-02	ci left: 5.047325e-03	ci right 5.430643e-03	k: 2880	n:550000
Cons ci ratio: 1.407112e-01	ci left: 1.309927e-03	ci right 1.509930e-03	k: 774	n:550000
KS ci ratio: 1.931375e-02	ci left: 6.900667e-02	ci right 7.035423e-02	k: 38323	n:550000
CHD8   550000 perm   279 sec   (1972 perm/sec)   p_kst 6.967818e-02   p_cons 1.407273e-03   p_joint 5.236364e-03

Joint ci ratio: 6.752434e-02	ci left: 5.780087e-03	ci right 6.185764e-03	k: 3349	n:560000
Cons ci ratio: 1.398126e-01	ci left: 1.303766e-03	ci right 1.501450e-03	k: 784	n:560000
KS ci ratio: 1.914258e-02	ci left: 6.899885e-02	ci right 7.033418e-02	k: 39012	n:560000
CHD8   560000 perm   286 sec   (1958 perm/sec)   p_kst 6.966429e-02   p_cons 1.400000e-03   p_joint 5.980357e-03

Joint ci ratio: 6.740657e-02	ci left: 5.699371e-03	ci right 6.098658e-03	k: 3361	n:570000
Cons ci ratio: 1.382362e-01	ci left: 1.311373e-03	ci right 1.507785e-03	k: 802	n:570000
KS ci ratio: 1.897949e-02	ci left: 6.896689e-02	ci right 7.029012e-02	k: 39687	n:570000
CHD8   570000 perm   293 sec   (1944 perm/sec)   p_kst 6.962632e-02   p_cons 1.407018e-03   p_joint 5.896491e-03

Joint ci ratio: 6.685228e-02	ci left: 5.696037e-03	ci right 6.091682e-03	k: 3417	n:580000
Cons ci ratio: 1.371308e-01	ci left: 1.310405e-03	ci right 1.504975e-03	k: 815	n:580000
KS ci ratio: 1.881398e-02	ci left: 6.898072e-02	ci right 7.029254e-02	k: 40388	n:580000
CHD8   580000 perm   300 sec   (1931 perm/sec)   p_kst 6.963448e-02   p_cons 1.405172e-03   p_joint 5.891379e-03

Joint ci ratio: 6.715270e-02	ci left: 5.549484e-03	ci right 5.936749e-03	k: 3387	n:590000
Cons ci ratio: 1.362161e-01	ci left: 1.306201e-03	ci right 1.498748e-03	k: 826	n:590000
KS ci ratio: 1.865907e-02	ci left: 6.895026e-02	ci right 7.025059e-02	k: 41063	n:590000
CHD8   590000 perm   308 sec   (1917 perm/sec)   p_kst 6.959831e-02   p_cons 1.400000e-03   p_joint 5.740678e-03

Joint ci ratio: 6.656572e-02	ci left: 5.555322e-03	ci right 5.939474e-03	k: 3447	n:600000
Cons ci ratio: 1.357255e-01	ci left: 1.294091e-03	ci right 1.484109e-03	k: 832	n:600000
KS ci ratio: 1.850721e-02	ci left: 6.892582e-02	ci right 7.021500e-02	k: 41741	n:600000
CHD8   600000 perm   315 sec   (1902 perm/sec)   p_kst 6.956833e-02   p_cons 1.386667e-03   p_joint 5.745000e-03

Joint ci ratio: 6.661746e-02	ci left: 5.456181e-03	ci right 5.833783e-03	k: 3442	n:610000
Cons ci ratio: 1.345991e-01	ci left: 1.295051e-03	ci right 1.483506e-03	k: 846	n:610000
KS ci ratio: 1.834762e-02	ci left: 6.898222e-02	ci right 7.026121e-02	k: 42468	n:610000
CHD8   610000 perm   326 sec   (1873 perm/sec)   p_kst 6.961967e-02   p_cons 1.386885e-03   p_joint 5.642623e-03

Joint ci ratio: 6.951147e-02	ci left: 4.925787e-03	ci right 5.282088e-03	k: 3163	n:620000
Cons ci ratio: 1.333453e-01	ci left: 1.299105e-03	ci right 1.486249e-03	k: 862	n:620000
KS ci ratio: 1.820590e-02	ci left: 6.893888e-02	ci right 7.020709e-02	k: 43134	n:620000
CHD8   620000 perm   333 sec   (1861 perm/sec)   p_kst 6.957097e-02   p_cons 1.390323e-03   p_joint 5.101613e-03

Joint ci ratio: 6.964717e-02	ci left: 4.828875e-03	ci right 5.178875e-03	k: 3151	n:630000
Cons ci ratio: 1.320507e-01	ci left: 1.304572e-03	ci right 1.490537e-03	k: 879	n:630000
KS ci ratio: 1.807118e-02	ci left: 6.887007e-02	ci right 7.012754e-02	k: 43783	n:630000
CHD8   630000 perm   341 sec   (1848 perm/sec)   p_kst 6.949683e-02   p_cons 1.395238e-03   p_joint 5.001587e-03

Joint ci ratio: 7.050930e-02	ci left: 4.636739e-03	ci right 4.977143e-03	k: 3075	n:640000
Cons ci ratio: 1.316037e-01	ci left: 1.293254e-03	ci right 1.476932e-03	k: 885	n:640000
KS ci ratio: 1.792685e-02	ci left: 6.889370e-02	ci right 7.014145e-02	k: 44490	n:640000
CHD8   640000 perm   349 sec   (1836 perm/sec)   p_kst 6.951562e-02   p_cons 1.382812e-03   p_joint 4.804687e-03

Joint ci ratio: 6.995427e-02	ci left: 4.639465e-03	ci right 4.977279e-03	k: 3124	n:650000
Cons ci ratio: 1.303587e-01	ci left: 1.298655e-03	ci right 1.481220e-03	k: 902	n:650000
KS ci ratio: 1.778760e-02	ci left: 6.890438e-02	ci right 7.014254e-02	k: 45189	n:650000
CHD8   650000 perm   357 sec   (1822 perm/sec)   p_kst 6.952154e-02   p_cons 1.387692e-03   p_joint 4.806154e-03

Joint ci ratio: 6.951124e-02	ci left: 4.628719e-03	ci right 4.963530e-03	k: 3164	n:660000
Cons ci ratio: 1.292187e-01	ci left: 1.302434e-03	ci right 1.483806e-03	k: 918	n:660000
KS ci ratio: 1.765031e-02	ci left: 6.892383e-02	ci right 7.015268e-02	k: 45894	n:660000
CHD8   660000 perm   365 sec   (1809 perm/sec)   p_kst 6.953636e-02   p_cons 1.390909e-03   p_joint 4.793939e-03

Joint ci ratio: 6.893619e-02	ci left: 4.637369e-03	ci right 4.969920e-03	k: 3217	n:670000
Cons ci ratio: 1.283144e-01	ci left: 1.301772e-03	ci right 1.481688e-03	k: 931	n:670000
KS ci ratio: 1.751171e-02	ci left: 6.897544e-02	ci right 7.019545e-02	k: 46621	n:670000
CHD8   670000 perm   373 sec   (1796 perm/sec)   p_kst 6.958358e-02   p_cons 1.389552e-03   p_joint 4.801493e-03

Joint ci ratio: 5.990636e-02	ci left: 6.069850e-03	ci right 6.446139e-03	k: 4254	n:680000
Cons ci ratio: 1.271597e-01	ci left: 1.306830e-03	ci right 1.485696e-03	k: 948	n:680000
KS ci ratio: 1.738185e-02	ci left: 6.898455e-02	ci right 7.019559e-02	k: 47320	n:680000
CHD8   680000 perm   381 sec   (1784 perm/sec)   p_kst 6.958824e-02   p_cons 1.394118e-03   p_joint 6.255882e-03

Joint ci ratio: 6.286056e-02	ci left: 5.428132e-03	ci right 5.781836e-03	k: 3866	n:690000
Cons ci ratio: 1.259051e-01	ci left: 1.314555e-03	ci right 1.492572e-03	k: 967	n:690000
KS ci ratio: 1.725079e-02	ci left: 6.902375e-02	ci right 7.022625e-02	k: 48040	n:690000
CHD8   690000 perm   389 sec   (1774 perm/sec)   p_kst 6.962319e-02   p_cons 1.401449e-03   p_joint 5.602899e-03

Joint ci ratio: 6.473270e-02	ci left: 5.042687e-03	ci right 5.381428e-03	k: 3647	n:700000
Cons ci ratio: 1.250044e-01	ci left: 1.315148e-03	ci right 1.491876e-03	k: 981	n:700000
KS ci ratio: 1.712623e-02	ci left: 6.903482e-02	ci right 7.022874e-02	k: 48741	n:700000
CHD8   700000 perm   398 sec   (1758 perm/sec)   p_kst 6.963000e-02   p_cons 1.401429e-03   p_joint 5.210000e-03

Joint ci ratio: 6.417170e-02	ci left: 5.060353e-03	ci right 5.397225e-03	k: 3711	n:710000
Cons ci ratio: 1.238739e-01	ci left: 1.321188e-03	ci right 1.497005e-03	k: 999	n:710000
KS ci ratio: 1.699675e-02	ci left: 6.910313e-02	ci right 7.028911e-02	k: 49483	n:710000
CHD8   710000 perm   407 sec   (1746 perm/sec)   p_kst 6.969437e-02   p_cons 1.407042e-03   p_joint 5.226761e-03

Joint ci ratio: 6.405274e-02	ci left: 5.009199e-03	ci right 5.342024e-03	k: 3725	n:720000
Cons ci ratio: 1.228339e-01	ci left: 1.325721e-03	ci right 1.500552e-03	k: 1016	n:720000
KS ci ratio: 1.687866e-02	ci left: 6.910456e-02	ci right 7.028224e-02	k: 50178	n:720000
CHD8   720000 perm   415 sec   (1734 perm/sec)   p_kst 6.969167e-02   p_cons 1.411111e-03   p_joint 5.173611e-03

Joint ci ratio: 6.514472e-02	ci left: 4.774789e-03	ci right 5.097652e-03	k: 3602	n:730000
Cons ci ratio: 1.221752e-01	ci left: 1.322167e-03	ci right 1.495527e-03	k: 1027	n:730000
KS ci ratio: 1.676282e-02	ci left: 6.910733e-02	ci right 7.027690e-02	k: 50874	n:730000
CHD8   730000 perm   424 sec   (1723 perm/sec)   p_kst 6.969041e-02   p_cons 1.406849e-03   p_joint 4.934247e-03

Joint ci ratio: 6.478650e-02	ci left: 4.763440e-03	ci right 5.083698e-03	k: 3642	n:740000
Cons ci ratio: 1.216443e-01	ci left: 1.316091e-03	ci right 1.487850e-03	k: 1036	n:740000
KS ci ratio: 1.665107e-02	ci left: 6.909660e-02	ci right 7.025812e-02	k: 51560	n:740000
CHD8   740000 perm   432 sec   (1712 perm/sec)   p_kst 6.967568e-02   p_cons 1.400000e-03   p_joint 4.921622e-03

Joint ci ratio: 6.547854e-02	ci left: 4.600232e-03	ci right 4.912946e-03	k: 3566	n:750000
Cons ci ratio: 1.211203e-01	ci left: 1.310179e-03	ci right 1.480377e-03	k: 1045	n:750000
KS ci ratio: 1.654050e-02	ci left: 6.909415e-02	ci right 7.024784e-02	k: 52252	n:750000
CHD8   750000 perm   441 sec   (1700 perm/sec)   p_kst 6.966933e-02   p_cons 1.393333e-03   p_joint 4.754667e-03

Joint ci ratio: 5.929193e-02	ci left: 5.548828e-03	ci right 5.889167e-03	k: 4345	n:760000
Cons ci ratio: 1.202043e-01	ci left: 1.313357e-03	ci right 1.482586e-03	k: 1061	n:760000
KS ci ratio: 1.643978e-02	ci left: 6.903149e-02	ci right 7.017705e-02	k: 52898	n:760000
CHD8   760000 perm   453 sec   (1678 perm/sec)   p_kst 6.960263e-02   p_cons 1.396053e-03   p_joint 5.717105e-03

Joint ci ratio: 5.732420e-02	ci left: 5.863283e-03	ci right 6.210579e-03	k: 4647	n:770000
Cons ci ratio: 1.193642e-01	ci left: 1.315197e-03	ci right 1.483395e-03	k: 1076	n:770000
KS ci ratio: 1.632352e-02	ci left: 6.910763e-02	ci right 7.024626e-02	k: 53650	n:770000
CHD8   770000 perm   462 sec   (1667 perm/sec)   p_kst 6.967532e-02   p_cons 1.397403e-03   p_joint 6.035065e-03

Joint ci ratio: 5.717196e-02	ci left: 5.819701e-03	ci right 6.163470e-03	k: 4672	n:780000
Cons ci ratio: 1.187049e-01	ci left: 1.313262e-03	ci right 1.480220e-03	k: 1088	n:780000
KS ci ratio: 1.621739e-02	ci left: 6.912053e-02	ci right 7.025190e-02	k: 54354	n:780000
CHD8   780000 perm   471 sec   (1655 perm/sec)   p_kst 6.968462e-02   p_cons 1.394872e-03   p_joint 5.989744e-03

Joint ci ratio: 5.834096e-02	ci left: 5.516461e-03	ci right 5.849205e-03	k: 4488	n:790000
Cons ci ratio: 1.182177e-01	ci left: 1.307693e-03	ci right 1.473213e-03	k: 1097	n:790000
KS ci ratio: 1.611141e-02	ci left: 6.914826e-02	ci right 7.027262e-02	k: 55070	n:790000
CHD8   790000 perm   481 sec   (1644 perm/sec)   p_kst 6.970886e-02   p_cons 1.388608e-03   p_joint 5.681013e-03

Joint ci ratio: 5.824526e-02	ci left: 5.465978e-03	ci right 5.795118e-03	k: 4503	n:800000
Cons ci ratio: 1.174712e-01	ci left: 1.308331e-03	ci right 1.472813e-03	k: 1111	n:800000
KS ci ratio: 1.601720e-02	ci left: 6.909686e-02	ci right 7.021376e-02	k: 55723	n:800000
CHD8   800000 perm   490 sec   (1633 perm/sec)   p_kst 6.965375e-02   p_cons 1.388750e-03   p_joint 5.628750e-03

Joint ci ratio: 5.795046e-02	ci left: 5.454461e-03	ci right 5.781189e-03	k: 4549	n:810000
Cons ci ratio: 1.168426e-01	ci left: 1.306559e-03	ci right 1.469879e-03	k: 1123	n:810000
KS ci ratio: 1.592448e-02	ci left: 6.904798e-02	ci right 7.015757e-02	k: 56377	n:810000
CHD8   810000 perm   499 sec   (1623 perm/sec)   p_kst 6.960123e-02   p_cons 1.386420e-03   p_joint 5.616049e-03

Joint ci ratio: 5.759082e-02	ci left: 5.456451e-03	ci right 5.781203e-03	k: 4606	n:820000
Cons ci ratio: 1.159178e-01	ci left: 1.311938e-03	ci right 1.474544e-03	k: 1141	n:820000
KS ci ratio: 1.582887e-02	ci left: 6.903676e-02	ci right 7.013945e-02	k: 57061	n:820000
CHD8   820000 perm   509 sec   (1612 perm/sec)   p_kst 6.958659e-02   p_cons 1.391463e-03   p_joint 5.617073e-03

Joint ci ratio: 5.805070e-02	ci left: 5.305206e-03	ci right 5.623562e-03	k: 4534	n:830000
Cons ci ratio: 1.152637e-01	ci left: 1.311341e-03	ci right 1.472893e-03	k: 1154	n:830000
KS ci ratio: 1.573790e-02	ci left: 6.900183e-02	ci right 7.009757e-02	k: 57725	n:830000
CHD8   830000 perm   518 sec   (1601 perm/sec)   p_kst 6.954819e-02   p_cons 1.390361e-03   p_joint 5.462651e-03

Joint ci ratio: 5.777783e-02	ci left: 5.292497e-03	ci right 5.608547e-03	k: 4577	n:840000
Cons ci ratio: 1.148670e-01	ci left: 1.304980e-03	ci right 1.465157e-03	k: 1162	n:840000
KS ci ratio: 1.564488e-02	ci left: 6.899739e-02	ci right 7.008653e-02	k: 58414	n:840000
CHD8   840000 perm   528 sec   (1590 perm/sec)   p_kst 6.954048e-02   p_cons 1.383333e-03   p_joint 5.448810e-03

Joint ci ratio: 5.765952e-02	ci left: 5.252259e-03	ci right 5.565243e-03	k: 4596	n:850000
Cons ci ratio: 1.144254e-01	ci left: 1.299911e-03	ci right 1.458812e-03	k: 1171	n:850000
KS ci ratio: 1.555080e-02	ci left: 6.901536e-02	ci right 7.009817e-02	k: 59122	n:850000
CHD8   850000 perm   538 sec   (1580 perm/sec)   p_kst 6.955529e-02   p_cons 1.377647e-03   p_joint 5.407059e-03

Joint ci ratio: 5.744814e-02	ci left: 5.230151e-03	ci right 5.540637e-03	k: 4630	n:860000
Cons ci ratio: 1.137000e-01	ci left: 1.301741e-03	ci right 1.459788e-03	k: 1186	n:860000
KS ci ratio: 1.545603e-02	ci left: 6.905262e-02	ci right 7.012935e-02	k: 59847	n:860000
CHD8   860000 perm   548 sec   (1568 perm/sec)   p_kst 6.958953e-02   p_cons 1.379070e-03   p_joint 5.383721e-03

Joint ci ratio: 5.710384e-02	ci left: 5.233480e-03	ci right 5.542241e-03	k: 4686	n:870000
Cons ci ratio: 1.131770e-01	ci left: 1.299063e-03	ci right 1.456011e-03	k: 1197	n:870000
KS ci ratio: 1.536735e-02	ci left: 6.905239e-02	ci right 7.012289e-02	k: 60540	n:870000
CHD8   870000 perm   558 sec   (1558 perm/sec)   p_kst 6.958621e-02   p_cons 1.375862e-03   p_joint 5.386207e-03

Joint ci ratio: 5.684404e-02	ci left: 5.222176e-03	ci right 5.528821e-03	k: 4729	n:880000
Cons ci ratio: 1.124750e-01	ci left: 1.300865e-03	ci right 1.456992e-03	k: 1212	n:880000
KS ci ratio: 1.527856e-02	ci left: 6.906578e-02	ci right 7.013024e-02	k: 61245	n:880000
CHD8   880000 perm   568 sec   (1549 perm/sec)   p_kst 6.959659e-02   p_cons 1.377273e-03   p_joint 5.373864e-03

Joint ci ratio: 5.658179e-02	ci left: 5.212236e-03	ci right 5.516840e-03	k: 4773	n:890000
Cons ci ratio: 1.120144e-01	ci left: 1.297169e-03	ci right 1.452173e-03	k: 1222	n:890000
KS ci ratio: 1.519340e-02	ci left: 6.906096e-02	ci right 7.011937e-02	k: 61934	n:890000
CHD8   890000 perm   580 sec   (1535 perm/sec)   p_kst 6.958876e-02   p_cons 1.373034e-03   p_joint 5.362921e-03

Joint ci ratio: 5.738658e-02	ci left: 5.009730e-03	ci right 5.306802e-03	k: 4641	n:900000
Cons ci ratio: 1.113337e-01	ci left: 1.298957e-03	ci right 1.453169e-03	k: 1237	n:900000
KS ci ratio: 1.510939e-02	ci left: 6.905849e-02	ci right 7.011095e-02	k: 62625	n:900000
CHD8   900000 perm   590 sec   (1526 perm/sec)   p_kst 6.958333e-02   p_cons 1.374444e-03   p_joint 5.156667e-03

Joint ci ratio: 5.818087e-02	ci left: 4.819287e-03	ci right 5.109153e-03	k: 4516	n:910000
Cons ci ratio: 1.108425e-01	ci left: 1.296435e-03	ci right 1.449624e-03	k: 1248	n:910000
KS ci ratio: 1.502766e-02	ci left: 6.904842e-02	ci right 7.009498e-02	k: 63309	n:910000
CHD8   910000 perm   600 sec   (1516 perm/sec)   p_kst 6.957033e-02   p_cons 1.371429e-03   p_joint 4.962637e-03

Joint ci ratio: 5.789336e-02	ci left: 4.815106e-03	ci right 5.103242e-03	k: 4561	n:920000
Cons ci ratio: 1.104456e-01	ci left: 1.291855e-03	ci right 1.443921e-03	k: 1257	n:920000
KS ci ratio: 1.494673e-02	ci left: 6.904291e-02	ci right 7.008371e-02	k: 63997	n:920000
CHD8   920000 perm   610 sec   (1507 perm/sec)   p_kst 6.956196e-02   p_cons 1.366304e-03   p_joint 4.957609e-03

Joint ci ratio: 5.768561e-02	ci left: 4.798301e-03	ci right 5.084366e-03	k: 4594	n:930000
Cons ci ratio: 1.098361e-01	ci left: 1.292603e-03	ci right 1.443863e-03	k: 1271	n:930000
KS ci ratio: 1.486611e-02	ci left: 6.904611e-02	ci right 7.008130e-02	k: 64693	n:930000
CHD8   930000 perm   625 sec   (1487 perm/sec)   p_kst 6.956237e-02   p_cons 1.366667e-03   p_joint 4.939785e-03

Joint ci ratio: 5.736808e-02	ci left: 4.800730e-03	ci right 5.085313e-03	k: 4645	n:940000
Cons ci ratio: 1.092366e-01	ci left: 1.293338e-03	ci right 1.443804e-03	k: 1285	n:940000
KS ci ratio: 1.478957e-02	ci left: 6.902488e-02	ci right 7.005437e-02	k: 65366	n:940000
CHD8   940000 perm   645 sec   (1458 perm/sec)   p_kst 6.953830e-02   p_cons 1.367021e-03   p_joint 4.941489e-03

Joint ci ratio: 5.712299e-02	ci left: 4.791698e-03	ci right 5.074492e-03	k: 4685	n:950000
Cons ci ratio: 1.088566e-01	ci left: 1.288939e-03	ci right 1.438339e-03	k: 1294	n:950000
KS ci ratio: 1.471385e-02	ci left: 6.900725e-02	ci right 7.003117e-02	k: 66042	n:950000
CHD8   950000 perm   655 sec   (1451 perm/sec)   p_kst 6.951789e-02   p_cons 1.362105e-03   p_joint 4.931579e-03

Joint ci ratio: 5.679052e-02	ci left: 4.798261e-03	ci right 5.079739e-03	k: 4740	n:960000
Cons ci ratio: 1.083973e-01	ci left: 1.286659e-03	ci right 1.435126e-03	k: 1305	n:960000
KS ci ratio: 1.463326e-02	ci left: 6.904295e-02	ci right 7.006174e-02	k: 66769	n:960000
CHD8   960000 perm   665 sec   (1444 perm/sec)   p_kst 6.955104e-02   p_cons 1.359375e-03   p_joint 4.937500e-03

Joint ci ratio: 5.699163e-02	ci left: 4.715252e-03	ci right 4.992872e-03	k: 4707	n:970000
Cons ci ratio: 1.079439e-01	ci left: 1.284428e-03	ci right 1.431977e-03	k: 1316	n:970000
KS ci ratio: 1.455770e-02	ci left: 6.904504e-02	ci right 7.005856e-02	k: 67464	n:970000
CHD8   970000 perm   675 sec   (1437 perm/sec)   p_kst 6.955052e-02   p_cons 1.356701e-03   p_joint 4.852577e-03

Joint ci ratio: 5.713345e-02	ci left: 4.643997e-03	ci right 4.918126e-03	k: 4684	n:980000
Cons ci ratio: 1.076178e-01	ci left: 1.279265e-03	ci right 1.425749e-03	k: 1324	n:980000
KS ci ratio: 1.448044e-02	ci left: 6.907254e-02	ci right 7.008103e-02	k: 68184	n:980000
CHD8   980000 perm   686 sec   (1429 perm/sec)   p_kst 6.957551e-02   p_cons 1.351020e-03   p_joint 4.779592e-03

Joint ci ratio: 5.592433e-02	ci left: 4.800247e-03	ci right 5.077409e-03	k: 4888	n:990000
Cons ci ratio: 1.069338e-01	ci left: 1.283054e-03	ci right 1.428979e-03	k: 1341	n:990000
KS ci ratio: 1.440507e-02	ci left: 6.909345e-02	ci right 7.009695e-02	k: 68898	n:990000
CHD8   990000 perm   697 sec   (1420 perm/sec)   p_kst 6.959394e-02   p_cons 1.354545e-03   p_joint 4.937374e-03

Joint ci ratio: 5.566885e-02	ci left: 4.796617e-03	ci right 5.072263e-03	k: 4933	n:1000000
Cons ci ratio: 1.066168e-01	ci left: 1.278010e-03	ci right 1.422903e-03	k: 1349	n:1000000
KS ci ratio: 1.433109e-02	ci left: 6.911196e-02	ci right 7.011054e-02	k: 69610	n:1000000
CHD8   1000000 perm   709 sec   (1411 perm/sec)   p_kst 6.961000e-02   p_cons 1.349000e-03   p_joint 4.933000e-03

Joint ci ratio: 5.325122e-02	ci left: 5.194493e-03	ci right 5.479642e-03	k: 5389	n:1010000
Cons ci ratio: 1.060682e-01	ci left: 1.278849e-03	ci right 1.423045e-03	k: 1363	n:1010000
KS ci ratio: 1.425660e-02	ci left: 6.914492e-02	ci right 7.013874e-02	k: 70337	n:1010000
CHD8   1010000 perm   721 sec   (1401 perm/sec)   p_kst 6.964059e-02   p_cons 1.349505e-03   p_joint 5.335644e-03

Joint ci ratio: 5.299623e-02	ci left: 5.193870e-03	ci right 5.477578e-03	k: 5441	n:1020000
Cons ci ratio: 1.053750e-01	ci left: 1.283492e-03	ci right 1.427207e-03	k: 1381	n:1020000
KS ci ratio: 1.418015e-02	ci left: 6.920559e-02	ci right 7.019490e-02	k: 71093	n:1020000
CHD8   1020000 perm   732 sec   (1393 perm/sec)   p_kst 6.969902e-02   p_cons 1.353922e-03   p_joint 5.334314e-03

Joint ci ratio: 5.278835e-02	ci left: 5.184639e-03	ci right 5.466698e-03	k: 5484	n:1030000
Cons ci ratio: 1.048076e-01	ci left: 1.285211e-03	ci right 1.428296e-03	k: 1396	n:1030000
KS ci ratio: 1.410756e-02	ci left: 6.924089e-02	ci right 7.022560e-02	k: 71824	n:1030000
CHD8   1030000 perm   743 sec   (1387 perm/sec)   p_kst 6.973204e-02   p_cons 1.355340e-03   p_joint 5.324272e-03

Joint ci ratio: 5.238321e-02	ci left: 5.215445e-03	ci right 5.496936e-03	k: 5569	n:1040000
Cons ci ratio: 1.042494e-01	ci left: 1.286899e-03	ci right 1.429363e-03	k: 1411	n:1040000
KS ci ratio: 1.403898e-02	ci left: 6.924870e-02	ci right 7.022870e-02	k: 72527	n:1040000
CHD8   1040000 perm   754 sec   (1380 perm/sec)   p_kst 6.973750e-02   p_cons 1.356731e-03   p_joint 5.354808e-03

Joint ci ratio: 5.224799e-02	ci left: 5.193030e-03	ci right 5.472567e-03	k: 5598	n:1050000
Cons ci ratio: 1.038458e-01	ci left: 1.284846e-03	ci right 1.426499e-03	k: 1422	n:1050000
KS ci ratio: 1.396996e-02	ci left: 6.926966e-02	ci right 7.024509e-02	k: 73244	n:1050000
CHD8   1050000 perm   765 sec   (1373 perm/sec)   p_kst 6.975619e-02   p_cons 1.354286e-03   p_joint 5.331429e-03

Joint ci ratio: 5.198859e-02	ci left: 5.196181e-03	ci right 5.474457e-03	k: 5654	n:1060000
Cons ci ratio: 1.033747e-01	ci left: 1.284672e-03	ci right 1.425623e-03	k: 1435	n:1060000
KS ci ratio: 1.390103e-02	ci left: 6.929870e-02	ci right 7.026969e-02	k: 73970	n:1060000
CHD8   1060000 perm   776 sec   (1366 perm/sec)   p_kst 6.978302e-02   p_cons 1.353774e-03   p_joint 5.333962e-03

Joint ci ratio: 5.193913e-02	ci left: 5.157763e-03	ci right 5.433711e-03	k: 5665	n:1070000
Cons ci ratio: 1.027680e-01	ci left: 1.288144e-03	ci right 1.428596e-03	k: 1452	n:1070000
KS ci ratio: 1.383989e-02	ci left: 6.926386e-02	ci right 7.023006e-02	k: 74628	n:1070000
CHD8   1070000 perm   787 sec   (1360 perm/sec)   p_kst 6.974579e-02   p_cons 1.357009e-03   p_joint 5.294393e-03

Joint ci ratio: 5.175707e-02	ci left: 5.146562e-03	ci right 5.420916e-03	k: 5705	n:1080000
Cons ci ratio: 1.023114e-01	ci left: 1.287945e-03	ci right 1.427714e-03	k: 1465	n:1080000
KS ci ratio: 1.377778e-02	ci left: 6.924629e-02	ci right 7.020787e-02	k: 75304	n:1080000
CHD8   1080000 perm   798 sec   (1354 perm/sec)   p_kst 6.972593e-02   p_cons 1.356481e-03   p_joint 5.282407e-03

Joint ci ratio: 5.149140e-02	ci left: 5.152776e-03	ci right 5.426010e-03	k: 5764	n:1090000
Cons ci ratio: 1.017919e-01	ci left: 1.289539e-03	ci right 1.428729e-03	k: 1480	n:1090000
KS ci ratio: 1.371165e-02	ci left: 6.927477e-02	ci right 7.023210e-02	k: 76030	n:1090000
CHD8   1090000 perm   809 sec   (1348 perm/sec)   p_kst 6.975229e-02   p_cons 1.357798e-03   p_joint 5.288073e-03

Joint ci ratio: 5.208632e-02	ci left: 4.989270e-03	ci right 5.256982e-03	k: 5634	n:1100000
Cons ci ratio: 1.014842e-01	ci left: 1.285790e-03	ci right 1.424130e-03	k: 1489	n:1100000
KS ci ratio: 1.364713e-02	ci left: 6.929641e-02	ci right 7.024949e-02	k: 76749	n:1100000
CHD8   1100000 perm   820 sec   (1341 perm/sec)   p_kst 6.977182e-02   p_cons 1.353636e-03   p_joint 5.121818e-03

Joint ci ratio: 5.287124e-02	ci left: 4.797611e-03	ci right 5.059037e-03	k: 5469	n:1110000
Cons ci ratio: 1.010781e-01	ci left: 1.284743e-03	ci right 1.422385e-03	k: 1501	n:1110000
KS ci ratio: 1.358888e-02	ci left: 6.926648e-02	ci right 7.021505e-02	k: 77411	n:1110000
CHD8   1110000 perm   831 sec   (1335 perm/sec)   p_kst 6.973964e-02   p_cons 1.352252e-03   p_joint 4.927027e-03

Joint ci ratio: 5.306283e-02	ci left: 4.720410e-03	ci right 4.978589e-03	k: 5430	n:1120000
Cons ci ratio: 1.007434e-01	ci left: 1.281975e-03	ci right 1.418839e-03	k: 1511	n:1120000
KS ci ratio: 1.352887e-02	ci left: 6.926112e-02	ci right 7.020540e-02	k: 78100	n:1120000
CHD8   1120000 perm   843 sec   (1329 perm/sec)   p_kst 6.973214e-02   p_cons 1.349107e-03   p_joint 4.848214e-03

Joint ci ratio: 5.379543e-02	ci left: 4.551148e-03	ci right 4.803613e-03	k: 5284	n:1130000
Cons ci ratio: 1.004121e-01	ci left: 1.279257e-03	ci right 1.415355e-03	k: 1521	n:1130000
KS ci ratio: 1.347120e-02	ci left: 6.924086e-02	ci right 7.018081e-02	k: 78772	n:1130000
CHD8   1130000 perm   854 sec   (1323 perm/sec)   p_kst 6.970973e-02   p_cons 1.346018e-03   p_joint 4.676106e-03

Joint ci ratio: 4.954012e-02	ci left: 5.326935e-03	ci right 5.598394e-03	k: 6226	n:1140000
Cons ci ratio: 1.000840e-01	ci left: 1.276588e-03	ci right 1.411931e-03	k: 1531	n:1140000
KS ci ratio: 1.341199e-02	ci left: 6.924284e-02	ci right 7.017865e-02	k: 79469	n:1140000
CHD8   1140000 perm   866 sec   (1316 perm/sec)   p_kst 6.970965e-02   p_cons 1.342982e-03   p_joint 5.461404e-03

Joint ci ratio: 4.928335e-02	ci left: 5.336438e-03	ci right 5.606932e-03	k: 6291	n:1150000
Cons ci ratio: 9.962974e-02	ci left: 1.277357e-03	ci right 1.412131e-03	k: 1545	n:1150000
KS ci ratio: 1.334980e-02	ci left: 6.928119e-02	ci right 7.021315e-02	k: 80208	n:1150000
CHD8   1150000 perm   878 sec   (1310 perm/sec)   p_kst 6.974609e-02   p_cons 1.343478e-03   p_joint 5.470435e-03

Outputting figure to mutsig2_images.part000000000037/CHD8.5_7904_1150000_0.069746_0.0013435_0.0054704.png
                gene_name: CHD8
               theta_stop: 0.100 
                    nperm: 1150000 
                     p_ks: 0.070 
        ci_ks_bounds_left: 0.069 
       ci_ks_bounds_right: 0.070 
                   p_cons: 0.0013 
      ci_cons_bounds_left: 0.0013 
     ci_cons_bounds_right: 0.0014 
                  p_joint: 0.0055 
     ci_joint_bounds_left: 0.0053 
    ci_joint_bounds_right: 0.0056 

Current progress: 20 percent done.
CHD7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.870972e-01	ci left: 1.567108e-02	ci right 2.101476e-02	k: 182	n:10000
Cons ci ratio: 4.496832e-02	ci left: 4.219631e-01	ci right 4.414767e-01	k: 4317	n:10000
KS ci ratio: 3.541838e-01	ci left: 9.958933e-03	ci right 1.433217e-02	k: 120	n:10000
CHD7   10000 perm   3 sec   (3977 perm/sec)   p_kst 1.200000e-02   p_cons 4.317000e-01   p_joint 1.820000e-02

Joint ci ratio: 1.730984e-01	ci left: 2.283264e-02	ci right 2.720694e-02	k: 499	n:20000
Cons ci ratio: 3.211980e-02	ci left: 4.199312e-01	ci right 4.336901e-01	k: 8536	n:20000
KS ci ratio: 2.410476e-01	ci left: 1.147624e-02	ci right 1.466766e-02	k: 260	n:20000
CHD7   20000 perm   6 sec   (3633 perm/sec)   p_kst 1.300000e-02   p_cons 4.268000e-01   p_joint 2.495000e-02

Joint ci ratio: 1.743706e-01	ci left: 1.512069e-02	ci right 1.804068e-02	k: 496	n:30000
Cons ci ratio: 2.614092e-02	ci left: 4.227909e-01	ci right 4.340230e-01	k: 12852	n:30000
KS ci ratio: 1.990167e-01	ci left: 1.149527e-02	ci right 1.406704e-02	k: 382	n:30000
CHD7   30000 perm   9 sec   (3509 perm/sec)   p_kst 1.273333e-02   p_cons 4.284000e-01   p_joint 1.653333e-02

Joint ci ratio: 1.517883e-01	ci left: 1.515398e-02	ci right 1.766693e-02	k: 655	n:40000
Cons ci ratio: 2.254798e-02	ci left: 4.255155e-01	ci right 4.352446e-01	k: 17215	n:40000
KS ci ratio: 1.742065e-01	ci left: 1.141029e-02	ci right 1.361132e-02	k: 499	n:40000
CHD7   40000 perm   12 sec   (3429 perm/sec)   p_kst 1.247500e-02   p_cons 4.303750e-01   p_joint 1.637500e-02

Joint ci ratio: 1.243743e-01	ci left: 1.826717e-02	ci right 2.070906e-02	k: 973	n:50000
Cons ci ratio: 2.017491e-02	ci left: 4.258545e-01	ci right 4.345536e-01	k: 21510	n:50000
KS ci ratio: 1.511105e-01	ci left: 1.227572e-02	ci right 1.430138e-02	k: 663	n:50000
CHD7   50000 perm   15 sec   (3364 perm/sec)   p_kst 1.326000e-02   p_cons 4.302000e-01   p_joint 1.946000e-02

Joint ci ratio: 1.134785e-01	ci left: 1.839235e-02	ci right 2.062114e-02	k: 1169	n:60000
Cons ci ratio: 1.839030e-02	ci left: 4.269494e-01	ci right 4.348907e-01	k: 25855	n:60000
KS ci ratio: 1.382792e-01	ci left: 1.230205e-02	ci right 1.414548e-02	k: 792	n:60000
CHD7   60000 perm   18 sec   (3304 perm/sec)   p_kst 1.320000e-02   p_cons 4.309167e-01   p_joint 1.948333e-02

Joint ci ratio: 1.046316e-01	ci left: 1.862766e-02	ci right 2.069814e-02	k: 1375	n:70000
Cons ci ratio: 1.705108e-02	ci left: 4.265281e-01	ci right 4.338777e-01	k: 30114	n:70000
KS ci ratio: 1.281740e-01	ci left: 1.233994e-02	ci right 1.404362e-02	k: 922	n:70000
CHD7   70000 perm   22 sec   (3253 perm/sec)   p_kst 1.317143e-02   p_cons 4.302000e-01   p_joint 1.964286e-02

Joint ci ratio: 9.808323e-02	ci left: 1.861402e-02	ci right 2.054604e-02	k: 1565	n:80000
Cons ci ratio: 1.593037e-02	ci left: 4.273649e-01	ci right 4.342401e-01	k: 34464	n:80000
KS ci ratio: 1.205845e-01	ci left: 1.225077e-02	ci right 1.383484e-02	k: 1042	n:80000
CHD7   80000 perm   25 sec   (3206 perm/sec)   p_kst 1.302500e-02   p_cons 4.308000e-01   p_joint 1.956250e-02

Joint ci ratio: 9.196268e-02	ci left: 1.887807e-02	ci right 2.070862e-02	k: 1780	n:90000
Cons ci ratio: 1.502887e-02	ci left: 4.272507e-01	ci right 4.337315e-01	k: 38744	n:90000
KS ci ratio: 1.124506e-01	ci left: 1.257255e-02	ci right 1.408129e-02	k: 1198	n:90000
CHD7   90000 perm   28 sec   (3162 perm/sec)   p_kst 1.331111e-02   p_cons 4.304889e-01   p_joint 1.977778e-02

Joint ci ratio: 8.724100e-02	ci left: 1.892593e-02	ci right 2.066209e-02	k: 1978	n:100000
Cons ci ratio: 1.427509e-02	ci left: 4.268187e-01	ci right 4.329654e-01	k: 42989	n:100000
KS ci ratio: 1.069743e-01	ci left: 1.254071e-02	ci right 1.396773e-02	k: 1324	n:100000
CHD7   100000 perm   32 sec   (3120 perm/sec)   p_kst 1.324000e-02   p_cons 4.298900e-01   p_joint 1.978000e-02

Joint ci ratio: 8.277275e-02	ci left: 1.915408e-02	ci right 2.081682e-02	k: 2197	n:110000
Cons ci ratio: 1.363123e-02	ci left: 4.262270e-01	ci right 4.320859e-01	k: 47207	n:110000
KS ci ratio: 1.016257e-01	ci left: 1.266679e-02	ci right 1.403178e-02	k: 1467	n:110000
CHD7   110000 perm   36 sec   (3081 perm/sec)   p_kst 1.333636e-02   p_cons 4.291545e-01   p_joint 1.997273e-02

Joint ci ratio: 7.939801e-02	ci left: 1.911728e-02	ci right 2.070604e-02	k: 2388	n:120000
Cons ci ratio: 1.305282e-02	ci left: 4.262805e-01	ci right 4.318896e-01	k: 51490	n:120000
KS ci ratio: 9.740580e-02	ci left: 1.266760e-02	ci right 1.397275e-02	k: 1597	n:120000
CHD7   120000 perm   41 sec   (2902 perm/sec)   p_kst 1.330833e-02   p_cons 4.290833e-01   p_joint 1.990000e-02

Outputting figure to mutsig2_images.part000000000037/CHD7.3_9142_120000_0.013308_0.42908_0.0199.png
                gene_name: CHD7
               theta_stop: 0.097 
                    nperm: 120000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.013 
       ci_ks_bounds_right: 0.014 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.020 
     ci_joint_bounds_left: 0.019 
    ci_joint_bounds_right: 0.021 

Current progress: 40 percent done.
CGN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.534259e-02	ci left: 8.603917e-01	ci right 8.737937e-01	k: 8672	n:10000
Cons ci ratio: 2.499077e-02	ci left: 7.020050e-01	ci right 7.198720e-01	k: 7110	n:10000
KS ci ratio: 5.372743e-02	ci left: 3.379640e-01	ci right 3.567250e-01	k: 3473	n:10000
CGN   10000 perm   2 sec   (5402 perm/sec)   p_kst 3.473000e-01   p_cons 7.110000e-01   p_joint 8.672000e-01

Outputting figure to mutsig2_images.part000000000037/CGN.2_3692_10000_0.3473_0.711_0.8672.png
                gene_name: CGN
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 60 percent done.
CHD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.073802e-02	ci left: 6.095991e-01	ci right 6.287314e-01	k: 6192	n:10000
Cons ci ratio: 1.037238e-03	ci left: 9.986945e-01	ci right 9.997798e-01	k: 9994	n:10000
KS ci ratio: 3.329228e-02	ci left: 5.711569e-01	ci right 5.905960e-01	k: 5809	n:10000
CHD3   10000 perm   3 sec   (3985 perm/sec)   p_kst 5.809000e-01   p_cons 9.994000e-01   p_joint 6.192000e-01

Outputting figure to mutsig2_images.part000000000037/CHD3.2_6444_10000_0.5809_0.9994_0.6192.png
                gene_name: CHD3
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   p_cons: 1.00 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.63 

Current progress: 80 percent done.
CHD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.216715e-02	ci left: 7.491777e-01	ci right 7.660720e-01	k: 7577	n:10000
Cons ci ratio: 2.143635e-02	ci left: 7.614214e-01	ci right 7.780212e-01	k: 7698	n:10000
KS ci ratio: 3.576934e-02	ci left: 5.357789e-01	ci right 5.553945e-01	k: 5456	n:10000
CHD4   10000 perm   3 sec   (3520 perm/sec)   p_kst 5.456000e-01   p_cons 7.698000e-01   p_joint 7.577000e-01

Outputting figure to mutsig2_images.part000000000037/CHD4.2_5895_10000_0.5456_0.7698_0.7577.png
                gene_name: CHD4
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.76 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.77 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000037
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 37 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4397909: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000038> was used as the working directory.
Started at Wed Oct 24 16:10:07 2012
Results reported at Wed Oct 24 16:12:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000038.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000038.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 38  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000038.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    143.70 sec.
    Max Memory :      1199 MB
    Max Swap   :      3933 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
38
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 38
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 38: processing genes 3320 - 3409
Calculating significance of each gene.
Using projection method.
3320	CHRNA7	1
3321	CHRNA9	1
3322	CHRNB1	1
3323	CHRNB2	1
3324	CHRNB3	1
3325	CHRNB4	1
3326	CHRND	1
3327	CHRNE	1.930349e-01
3328	CHRNG	1.050812e-01
3329	CHST1	1
3330	CHST10	6.204904e-02
3331	CHST11	1
3332	CHST12	1
3333	CHST13	1
3334	CHST14	1
3335	CHST15	1
3336	CHST2	1
3337	CHST3	8.450073e-02
3338	CHST4	1.914843e-01
3339	CHST5	1.814249e-01
3340	CHST6	1.678627e-01
3341	CHST7	1
3342	CHST8	1
3343	CHST9	1
3344	CHSY1	1.818560e-01
3345	CHSY3	1
3346	CHTF18	1
3347	CHTF8	1
3348	CHUK	1
3349	CHURC1	1
3350	CIAO1	1
3351	CIAPIN1	1.634168e-01
3352	CIB1	1
3353	CIB2	1
3354	CIB3	1.030733e-01
3355	CIB4	7.858793e-02
3356	CIC	3.322255e-02
3357	CIDEA	1
3358	CIDEB	1
3359	CIDEC	1
3360	CIITA	1
3361	CILP	1
3362	CILP2	1
3363	CINP	1
3364	CIR1	1
3365	CIRBP	1
3366	CIRH1A	1
3367	CISD1	1
3368	CISD2	1
3369	CISH	1
3370	CIT	1
3371	CITED1	1
3372	CITED2	1
3373	CIZ1	3.213866e-01
3374	CKAP2	2.474411e-01
3375	CKAP2L	1.802468e-01
3376	CKAP4	1
3377	CKAP5	5.573383e-01
3378	CKB	1
3379	CKLF	1
3380	CKM	1.905433e-01
3381	CKMT1A	1
3382	CKMT1B	1
3383	CKMT2	3.801965e-02
3384	CKS1B	1
3385	CKS2	1
3386	CLASP1	2.231958e-01
3387	CLASP2	1
3388	CLC	1
3389	CLCA1	1
3390	CLCA2	1
3391	CLCA4	4.796949e-02
3392	CLCC1	1
3393	CLCF1	1
3394	CLCN1	1
3395	CLCN2	1.383499e-01
3396	CLCN3	1
3397	CLCN4	1
3398	CLCN5	8.313290e-03
3399	CLCN6	1
3400	CLCN7	1
3401	CLCNKA	2.616119e-01
3402	CLCNKB	1
3403	CLDN1	1
3404	CLDN10	1
3405	CLDN11	1
3406	CLDN12	1
3407	CLDN14	1
3408	CLDN15	1
3409	CLDN16	1
Done

Running MutSig 2:
Scatter job 38: processing genes 3320 - 3409
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CKAP5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.829303e-01	ci left: 3.987233e-02	ci right 4.799604e-02	k: 438	n:10000
Cons ci ratio: 3.187005e-02	ci left: 5.923277e-01	ci right 6.116129e-01	k: 6020	n:10000
KS ci ratio: 2.148972e-01	ci left: 2.873209e-02	ci right 3.574387e-02	k: 321	n:10000
CKAP5   10000 perm   2 sec   (4641 perm/sec)   p_kst 3.210000e-02   p_cons 6.020000e-01   p_joint 4.380000e-02

Joint ci ratio: 1.386114e-01	ci left: 3.577914e-02	ci right 4.115611e-02	k: 768	n:20000
Cons ci ratio: 2.233272e-02	ci left: 5.995390e-01	ci right 6.131301e-01	k: 12127	n:20000
KS ci ratio: 1.538196e-01	ci left: 2.902635e-02	ci right 3.391111e-02	k: 628	n:20000
CKAP5   20000 perm   7 sec   (2933 perm/sec)   p_kst 3.140000e-02   p_cons 6.063500e-01   p_joint 3.840000e-02

Joint ci ratio: 1.035781e-01	ci left: 4.320175e-02	ci right 4.795342e-02	k: 1366	n:30000
Cons ci ratio: 1.805020e-02	ci left: 6.056566e-01	ci right 6.167219e-01	k: 18336	n:30000
KS ci ratio: 1.256285e-01	ci left: 2.945537e-02	ci right 3.343605e-02	k: 942	n:30000
CKAP5   30000 perm   9 sec   (3176 perm/sec)   p_kst 3.140000e-02   p_cons 6.112000e-01   p_joint 4.553333e-02

Joint ci ratio: 8.941077e-02	ci left: 4.379634e-02	ci right 4.791992e-02	k: 1833	n:40000
Cons ci ratio: 1.557785e-02	ci left: 6.080560e-01	ci right 6.176276e-01	k: 24514	n:40000
KS ci ratio: 1.087235e-01	ci left: 2.976121e-02	ci right 3.320724e-02	k: 1258	n:40000
CKAP5   40000 perm   12 sec   (3303 perm/sec)   p_kst 3.145000e-02   p_cons 6.128500e-01   p_joint 4.582500e-02

Joint ci ratio: 8.075930e-02	ci left: 4.317978e-02	ci right 4.683328e-02	k: 2249	n:50000
Cons ci ratio: 1.392892e-02	ci left: 6.087143e-01	ci right 6.172726e-01	k: 30650	n:50000
KS ci ratio: 9.827376e-02	ci left: 2.932240e-02	ci right 3.237239e-02	k: 1541	n:50000
CKAP5   50000 perm   15 sec   (3364 perm/sec)   p_kst 3.082000e-02   p_cons 6.130000e-01   p_joint 4.498000e-02

Outputting figure to mutsig2_images.part000000000038/CKAP5.3_6271_50000_0.03082_0.613_0.04498.png
                gene_name: CKAP5
               theta_stop: 0.098 
                    nperm: 50000 
                     p_ks: 0.031 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.62 
                  p_joint: 0.045 
     ci_joint_bounds_left: 0.043 
    ci_joint_bounds_right: 0.047 

Current progress: 20 percent done.
CIC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.237972e-02	ci left: 4.511926e-01	ci right 4.708301e-01	k: 4610	n:10000
Cons ci ratio: 7.822696e-02	ci left: 1.927894e-01	ci right 2.085854e-01	k: 2006	n:10000
KS ci ratio: 2.987106e-02	ci left: 6.230635e-01	ci right 6.420592e-01	k: 6326	n:10000
CIC   10000 perm   2 sec   (5087 perm/sec)   p_kst 6.326000e-01   p_cons 2.006000e-01   p_joint 4.610000e-01

Outputting figure to mutsig2_images.part000000000038/CIC.2_4907_10000_0.6326_0.2006_0.461.png
                gene_name: CIC
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 40 percent done.
CLASP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.192571e-02	ci left: 7.532242e-01	ci right 7.700231e-01	k: 7617	n:10000
KS ci ratio: 7.308596e-02	ci left: 2.151691e-01	ci right 2.315924e-01	k: 2233	n:10000
CLASP1   10000 perm   2 sec   (5315 perm/sec)   p_kst 2.233000e-01   p_cons 7.617000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000038/CLASP1.2_4825_10000_0.2233_0.7617_1.png
                gene_name: CLASP1
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
CLCA4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.774183e-02	ci left: 3.929674e-01	ci right 4.122893e-01	k: 4026	n:10000
KS ci ratio: 4.993416e-02	ci left: 3.716666e-01	ci right 3.908027e-01	k: 3812	n:10000
CLCA4   10000 perm   2 sec   (5793 perm/sec)   p_kst 3.812000e-01   p_cons 4.026000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000038/CLCA4.2_2816_10000_0.3812_0.4026_1.png
                gene_name: CLCA4
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
CLCN5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 7.879218e-02	ci left: 1.905240e-01	ci right 2.062521e-01	k: 1983	n:10000
KS ci ratio: 1.028188e-02	ci left: 9.307143e-01	ci right 9.404301e-01	k: 9357	n:10000
CLCN5   10000 perm   2 sec   (5997 perm/sec)   p_kst 9.357000e-01   p_cons 1.983000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000038/CLCN5.2_2503_10000_0.9357_0.1983_1.png
                gene_name: CLCN5
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.21 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000038
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 38 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 4397912: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000039> was used as the working directory.
Started at Wed Oct 24 16:10:28 2012
Results reported at Wed Oct 24 16:12:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000039.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000039.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 39  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000039.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    143.85 sec.
    Max Memory :      1403 MB
    Max Swap   :      3950 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
39
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 39
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 39: processing genes 3410 - 3499
Calculating significance of each gene.
Using projection method.
3410	CLDN17	1
3411	CLDN18	1.146667e-01
3412	CLDN19	1
3413	CLDN2	1
3414	CLDN20	1
3415	CLDN22	1
3416	CLDN23	1
3417	CLDN25	1
3418	CLDN3	1
3419	CLDN4	1
3420	CLDN5	1
3421	CLDN6	1
3422	CLDN7	1
3423	CLDN8	1
3424	CLDN9	1
3425	CLDND1	1
3426	CLDND2	1
3427	CLEC10A	1
3428	CLEC11A	2.945622e-03
3429	CLEC12A	1
3430	CLEC12B	1
3431	CLEC14A	9.685987e-02
3432	CLEC16A	1
3433	CLEC17A	1
3434	CLEC18A	1
3435	CLEC18B	1
3436	CLEC18C	1
3437	CLEC1A	1
3438	CLEC1B	1
3439	CLEC2B	1
3440	CLEC2D	1
3441	CLEC2L	1
3442	CLEC3A	1
3443	CLEC3B	1
3444	CLEC4A	1
3445	CLEC4C	1
3446	CLEC4D	8.774428e-02
3447	CLEC4E	1
3448	CLEC4F	1
3449	CLEC4G	1
3450	CLEC4M	1
3451	CLEC5A	1
3452	CLEC6A	1
3453	CLEC7A	1
3454	CLEC9A	1
3455	CLECL1	1
3456	CLGN	2.433892e-01
3457	CLIC1	1
3458	CLIC2	1
3459	CLIC3	1
3460	CLIC4	1
3461	CLIC5	2.153369e-02
3462	CLIC6	1
3463	CLINT1	1
3464	CLIP1	1
3465	CLIP2	1.864413e-01
3466	CLIP3	8.221309e-02
3467	CLIP4	1
3468	CLK1	1
3469	CLK2	1
3470	CLK3	2.432987e-01
3471	CLK4	1
3472	CLLU1	1
3473	CLLU1OS	1
3474	CLMN	6.129151e-02
3475	CLN3	1
3476	CLN5	1
3477	CLN6	1
3478	CLN8	1
3479	CLNK	1
3480	CLNS1A	1
3481	CLOCK	1
3482	CLP1	1
3483	CLPB	5.320239e-02
3484	CLPP	1
3485	CLPS	1
3486	CLPTM1	1
3487	CLPTM1L	1
3488	CLPX	1
3489	CLRN1	1
3490	CLRN2	4.521618e-02
3491	CLRN3	1
3492	CLSPN	1
3493	CLSTN1	1
3494	CLSTN2	1
3495	CLSTN3	2.584401e-02
3496	CLTA	1
3497	CLTB	1
3498	CLTC	1
3499	CLTCL1	1.611341e-02
Done

Running MutSig 2:
Scatter job 39: processing genes 3410 - 3499
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CLEC11A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.115553e-01	ci left: 1.037366e-01	ci right 1.160916e-01	k: 1098	n:10000
Cons ci ratio: 1.323893e-01	ci left: 7.524035e-02	ci right 8.600545e-02	k: 805	n:10000
KS ci ratio: 1.067067e-01	ci left: 1.125202e-01	ci right 1.253028e-01	k: 1188	n:10000
CLEC11A   10000 perm   2 sec   (6493 perm/sec)   p_kst 1.188000e-01   p_cons 8.050000e-02   p_joint 1.098000e-01

Joint ci ratio: 6.946510e-02	ci left: 1.325582e-01	ci right 1.421475e-01	k: 2746	n:20000
Cons ci ratio: 9.189018e-02	ci left: 7.955498e-02	ci right 8.726664e-02	k: 1667	n:20000
KS ci ratio: 7.523915e-02	ci left: 1.149858e-01	ci right 1.240251e-01	k: 2389	n:20000
CLEC11A   20000 perm   5 sec   (3644 perm/sec)   p_kst 1.194500e-01   p_cons 8.335000e-02   p_joint 1.373000e-01

Outputting figure to mutsig2_images.part000000000039/CLEC11A.2_988_20000_0.11945_0.08335_0.1373.png
                gene_name: CLEC11A
               theta_stop: 0.092 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.083 
      ci_cons_bounds_left: 0.080 
     ci_cons_bounds_right: 0.087 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 25 percent done.
CLMN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.222604e-02	ci left: 2.751757e-01	ci right 2.929502e-01	k: 2840	n:10000
Cons ci ratio: 9.776290e-02	ci left: 1.316879e-01	ci right 1.453234e-01	k: 1384	n:10000
KS ci ratio: 3.541019e-02	ci left: 5.407869e-01	ci right 5.603836e-01	k: 5506	n:10000
CLMN   10000 perm   2 sec   (5937 perm/sec)   p_kst 5.506000e-01   p_cons 1.384000e-01   p_joint 2.840000e-01

Outputting figure to mutsig2_images.part000000000039/CLMN.2_3061_10000_0.5506_0.1384_0.284.png
                gene_name: CLMN
               theta_stop: 0.098 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 50 percent done.
CLSTN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.405044e-02	ci left: 1.409954e-01	ci right 1.550103e-01	k: 1479	n:10000
Cons ci ratio: 7.686376e-02	ci left: 1.984054e-01	ci right 2.143660e-01	k: 2063	n:10000
KS ci ratio: 9.922299e-02	ci left: 1.282615e-01	ci right 1.417519e-01	k: 1349	n:10000
CLSTN3   10000 perm   2 sec   (5714 perm/sec)   p_kst 1.349000e-01   p_cons 2.063000e-01   p_joint 1.479000e-01

Outputting figure to mutsig2_images.part000000000039/CLSTN3.2_2943_10000_0.1349_0.2063_0.1479.png
                gene_name: CLSTN3
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.16 

Current progress: 75 percent done.
CLTCL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.780176e-02	ci left: 6.559541e-01	ci right 6.745495e-01	k: 6653	n:10000
KS ci ratio: 1.691880e-02	ci left: 8.357199e-01	ci right 8.500797e-01	k: 8430	n:10000
CLTCL1   10000 perm   2 sec   (5167 perm/sec)   p_kst 8.430000e-01   p_cons 6.653000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000039/CLTCL1.2_5051_10000_0.843_0.6653_1.png
                gene_name: CLTCL1
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.67 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000039
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 39 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4397915: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000040> was used as the working directory.
Started at Wed Oct 24 16:10:28 2012
Results reported at Wed Oct 24 16:12:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000040.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000040.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 40  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000040.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     93.97 sec.
    Max Memory :      1178 MB
    Max Swap   :      3958 MB

    Max Processes  :         7
    Max Threads    :        72

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
40
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 40
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 40: processing genes 3500 - 3588
Calculating significance of each gene.
Using projection method.
3500	CLU	1
3501	CLUAP1	1.870636e-01
3502	CLUL1	1.795558e-01
3503	CLVS1	1
3504	CLVS2	1.549979e-03
3505	CLYBL	1
3506	CMA1	1
3507	CMAS	1
3508	CMBL	1
3509	CMC1	1
3510	CMIP	1
3511	CMKLR1	7.364618e-02
3512	CMPK1	1
3513	CMPK2	1
3514	CMTM1	1
3515	CMTM2	1
3516	CMTM3	1
3517	CMTM4	1
3518	CMTM5	1
3519	CMTM6	1
3520	CMTM7	1
3521	CMTM8	1
3522	CMYA5	1
3523	CNBD1	1
3524	CNBP	1
3525	CNDP1	1
3526	CNDP2	1.804233e-01
3527	CNFN	1
3528	CNGA1	1
3529	CNGA2	1
3530	CNGA3	1
3531	CNGA4	1
3532	CNGB1	1.085561e-01
3533	CNGB3	1
3534	CNIH	4.289620e-02
3535	CNIH2	1
3536	CNIH3	1
3537	CNIH4	1
3538	CNKSR1	5.454154e-02
3539	CNKSR2	1
3540	CNKSR3	1
3541	CNN1	1
3542	CNN2	1
3543	CNN3	1
3544	CNNM1	1
3545	CNNM2	1.440944e-01
3546	CNNM3	1
3547	CNNM4	1
3548	CNO	1
3549	CNOT1	1
3550	CNOT10	3.223572e-01
3551	CNOT2	1
3552	CNOT3	1
3553	CNOT4	1
3554	CNOT6	1
3555	CNOT6L	1
3556	CNOT7	1
3557	CNOT8	1
3558	CNP	1
3559	CNPY1	1
3560	CNPY2	1
3561	CNPY3	1
3562	CNPY4	1
3563	CNR1	1.423145e-01
3564	CNR2	1
3565	CNRIP1	1
3566	CNST	1
3567	CNTD1	1
3568	CNTD2	1
3569	CNTF	1
3570	CNTFR	1
3571	CNTLN	1
3572	CNTN1	1
3573	CNTN2	1
3574	CNTN3	2.527060e-01
3575	CNTN4	1
3576	CNTN5	1
3577	CNTN6	1
3578	CNTNAP1	3.187300e-01
3579	CNTNAP2	3.330131e-01
3580	CNTNAP3	2.464117e-01
3581	CNTNAP4	3.535897e-02
3582	CNTNAP5	3.209086e-01
3583	CNTROB	1
3584	COASY	3.130885e-02
3585	COBL	1
3586	COBLL1	3.354978e-01
3587	COBRA1	1
3588	COCH	2.474331e-01
Done

Running MutSig 2:
Scatter job 40: processing genes 3500 - 3588
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CNTNAP4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.028651e-01	ci left: 1.202398e-01	ci right 1.333784e-01	k: 1267	n:10000
Cons ci ratio: 5.356197e-02	ci left: 3.393548e-01	ci right 3.581334e-01	k: 3487	n:10000
KS ci ratio: 2.408683e-01	ci left: 2.268733e-02	ci right 2.899301e-02	k: 257	n:10000
CNTNAP4   10000 perm   2 sec   (5732 perm/sec)   p_kst 2.570000e-02   p_cons 3.487000e-01   p_joint 1.267000e-01

Joint ci ratio: 8.053930e-02	ci left: 1.016188e-01	ci right 1.101961e-01	k: 2117	n:20000
Cons ci ratio: 3.646613e-02	ci left: 3.594682e-01	ci right 3.728707e-01	k: 7323	n:20000
KS ci ratio: 1.667107e-01	ci left: 2.465375e-02	ci right 2.918520e-02	k: 537	n:20000
CNTNAP4   20000 perm   6 sec   (3518 perm/sec)   p_kst 2.685000e-02   p_cons 3.661500e-01   p_joint 1.058500e-01

Joint ci ratio: 6.438617e-02	ci left: 1.064149e-01	ci right 1.135275e-01	k: 3298	n:30000
Cons ci ratio: 2.982796e-02	ci left: 3.598811e-01	ci right 3.708117e-01	k: 10960	n:30000
KS ci ratio: 1.360332e-01	ci left: 2.509845e-02	ci right 2.879393e-02	k: 807	n:30000
CNTNAP4   30000 perm   8 sec   (3836 perm/sec)   p_kst 2.690000e-02   p_cons 3.653333e-01   p_joint 1.099333e-01

Joint ci ratio: 7.224828e-02	ci left: 6.606801e-02	ci right 7.104484e-02	k: 2741	n:40000
Cons ci ratio: 2.584383e-02	ci left: 3.604042e-01	ci right 3.698654e-01	k: 14605	n:40000
KS ci ratio: 1.171031e-01	ci left: 2.565209e-02	ci right 2.886704e-02	k: 1089	n:40000
CNTNAP4   40000 perm   10 sec   (4003 perm/sec)   p_kst 2.722500e-02   p_cons 3.651250e-01   p_joint 6.852500e-02

Joint ci ratio: 7.634991e-02	ci left: 4.816474e-02	ci right 5.200771e-02	k: 2503	n:50000
Cons ci ratio: 2.313686e-02	ci left: 3.604788e-01	ci right 3.689369e-01	k: 18235	n:50000
KS ci ratio: 1.051178e-01	ci left: 2.563579e-02	ci right 2.849947e-02	k: 1352	n:50000
CNTNAP4   50000 perm   12 sec   (4080 perm/sec)   p_kst 2.704000e-02   p_cons 3.647000e-01   p_joint 5.006000e-02

Joint ci ratio: 6.489074e-02	ci left: 5.546985e-02	ci right 5.920644e-02	k: 3439	n:60000
Cons ci ratio: 2.114925e-02	ci left: 3.602315e-01	ci right 3.679483e-01	k: 21845	n:60000
KS ci ratio: 9.634402e-02	ci left: 2.555491e-02	ci right 2.815779e-02	k: 1610	n:60000
CNTNAP4   60000 perm   15 sec   (4116 perm/sec)   p_kst 2.683333e-02   p_cons 3.640833e-01   p_joint 5.731667e-02

Outputting figure to mutsig2_images.part000000000040/CNTNAP4.3_4036_60000_0.026833_0.36408_0.057317.png
                gene_name: CNTNAP4
               theta_stop: 0.096 
                    nperm: 60000 
                     p_ks: 0.027 
        ci_ks_bounds_left: 0.026 
       ci_ks_bounds_right: 0.028 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.057 
     ci_joint_bounds_left: 0.055 
    ci_joint_bounds_right: 0.059 

Current progress: 25 percent done.
CLVS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.500759e-02	ci left: 3.274362e-01	ci right 3.460590e-01	k: 3367	n:10000
KS ci ratio: 2.254729e-02	ci left: 7.428065e-01	ci right 7.598468e-01	k: 7514	n:10000
CLVS2   10000 perm   1 sec   (7896 perm/sec)   p_kst 7.514000e-01   p_cons 3.367000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000040/CLVS2.2_1004_10000_0.7514_0.3367_1.png
                gene_name: CLVS2
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
CNGB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.648931e-02	ci left: 5.258660e-01	ci right 5.455132e-01	k: 5357	n:10000
Cons ci ratio: 4.222657e-02	ci left: 4.529894e-01	ci right 4.726323e-01	k: 4628	n:10000
KS ci ratio: 3.047793e-02	ci left: 6.136175e-01	ci right 6.327106e-01	k: 6232	n:10000
CNGB1   10000 perm   2 sec   (6242 perm/sec)   p_kst 6.232000e-01   p_cons 4.628000e-01   p_joint 5.357000e-01

Outputting figure to mutsig2_images.part000000000040/CNGB1.2_3914_10000_0.6232_0.4628_0.5357.png
                gene_name: CNGB1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 75 percent done.
COASY
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.022198e-01	ci left: 1.216088e-01	ci right 1.348087e-01	k: 1281	n:10000
Cons ci ratio: 3.381460e-02	ci left: 5.635359e-01	ci right 5.830214e-01	k: 5733	n:10000
KS ci ratio: 1.816359e-01	ci left: 4.044604e-02	ci right 4.862195e-02	k: 444	n:10000
COASY   10000 perm   1 sec   (7196 perm/sec)   p_kst 4.440000e-02   p_cons 5.733000e-01   p_joint 1.281000e-01

Joint ci ratio: 7.063193e-02	ci left: 1.287164e-01	ci right 1.381905e-01	k: 2668	n:20000
Cons ci ratio: 2.343878e-02	ci left: 5.761801e-01	ci right 5.898958e-01	k: 11661	n:20000
KS ci ratio: 1.285145e-01	ci left: 4.158670e-02	ci right 4.734668e-02	k: 888	n:20000
COASY   20000 perm   3 sec   (6457 perm/sec)   p_kst 4.440000e-02   p_cons 5.830500e-01   p_joint 1.334000e-01

Joint ci ratio: 7.996158e-02	ci left: 7.119339e-02	ci right 7.715605e-02	k: 2224	n:30000
Cons ci ratio: 1.898039e-02	ci left: 5.814703e-01	ci right 5.926462e-01	k: 17612	n:30000
KS ci ratio: 1.055343e-01	ci left: 4.164178e-02	ci right 4.631372e-02	k: 1318	n:30000
COASY   30000 perm   5 sec   (6146 perm/sec)   p_kst 4.393333e-02   p_cons 5.870667e-01   p_joint 7.413333e-02

Joint ci ratio: 3.167720e-02	ci left: 2.724441e-01	ci right 2.812383e-01	k: 11073	n:40000
Cons ci ratio: 1.645857e-02	ci left: 5.816053e-01	ci right 5.912822e-01	k: 23458	n:40000
KS ci ratio: 9.179683e-02	ci left: 4.159509e-02	ci right 4.562151e-02	k: 1743	n:40000
COASY   40000 perm   7 sec   (5952 perm/sec)   p_kst 4.357500e-02   p_cons 5.864500e-01   p_joint 2.768250e-01

Outputting figure to mutsig2_images.part000000000040/COASY.2_1822_40000_0.043575_0.58645_0.27682.png
                gene_name: COASY
               theta_stop: 0.092 
                    nperm: 40000 
                     p_ks: 0.044 
        ci_ks_bounds_left: 0.042 
       ci_ks_bounds_right: 0.046 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.28 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000040
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 40 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4397917: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000041> was used as the working directory.
Started at Wed Oct 24 16:10:36 2012
Results reported at Wed Oct 24 16:12:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000041.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000041.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 41  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000041.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    159.82 sec.
    Max Memory :      1632 MB
    Max Swap   :      3975 MB

    Max Processes  :         7
    Max Threads    :        60

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
41
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 41
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 41: processing genes 3589 - 3678
Calculating significance of each gene.
Using projection method.
3589	COG1	1
3590	COG2	7.802808e-02
3591	COG3	1.506136e-01
3592	COG4	1
3593	COG5	1
3594	COG6	1
3595	COG7	1
3596	COG8	1
3597	COIL	1
3598	COL10A1	1
3599	COL11A1	1
3600	COL11A2	8.409353e-03
3601	COL12A1	5.237140e-01
3602	COL13A1	1
3603	COL14A1	1
3604	COL15A1	2.374208e-01
3605	COL16A1	4.349301e-02
3606	COL17A1	4.431521e-01
3607	COL18A1	1.418203e-01
3608	COL19A1	1.785296e-01
3609	COL1A1	1
3610	COL1A2	2.031066e-02
3611	COL20A1	1
3612	COL21A1	1.726533e-01
3613	COL22A1	1.233643e-02
3614	COL23A1	1
3615	COL24A1	4.322764e-01
3616	COL25A1	3.350406e-01
3617	COL27A1	1
3618	COL28A1	1
3619	COL2A1	1
3620	COL3A1	4.204015e-01
3621	COL4A1	3.990705e-01
3622	COL4A2	1
3623	COL4A3	1
3624	COL4A3BP	7.437002e-02
3625	COL4A4	1
3626	COL4A5	8.030102e-02
3627	COL4A6	1
3628	COL5A1	5.077718e-01
3629	COL5A2	1
3630	COL5A3	1.067549e-01
3631	COL6A1	1
3632	COL6A2	3.804202e-01
3633	COL6A3	2.219914e-01
3634	COL6A6	4.722507e-01
3635	COL7A1	1
3636	COL8A1	1
3637	COL8A2	1
3638	COL9A1	1
3639	COL9A2	1
3640	COL9A3	1
3641	COLEC10	1
3642	COLEC11	1
3643	COLEC12	8.540201e-02
3644	COLQ	1
3645	COMMD1	1
3646	COMMD10	1
3647	COMMD2	1
3648	COMMD3	1
3649	COMMD4	1
3650	COMMD5	1
3651	COMMD6	1
3652	COMMD7	1
3653	COMMD8	1
3654	COMMD9	1
3655	COMP	1.911246e-01
3656	COMT	1
3657	COPA	1
3658	COPB1	1.001346e-01
3659	COPB2	1
3660	COPE	1
3661	COPG	2.729778e-01
3662	COPG2	1
3663	COPS2	5.710546e-02
3664	COPS3	1
3665	COPS4	1
3666	COPS5	1
3667	COPS6	1
3668	COPS7A	1
3669	COPS7B	1
3670	COPS8	1
3671	COPZ1	1
3672	COPZ2	1
3673	COQ10A	1
3674	COQ10B	1
3675	COQ2	1
3676	COQ3	8.022966e-02
3677	COQ4	1
3678	COQ5	5.563379e-02
Done

Running MutSig 2:
Scatter job 41: processing genes 3589 - 3678
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
COL11A2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.617279e-02	ci left: 3.182039e-01	ci right 3.366967e-01	k: 3274	n:10000
Cons ci ratio: 1.075182e-02	ci left: 9.249261e-01	ci right 9.350217e-01	k: 9301	n:10000
KS ci ratio: 7.817824e-02	ci left: 1.929864e-01	ci right 2.087882e-01	k: 2008	n:10000
COL11A2   10000 perm   2 sec   (4403 perm/sec)   p_kst 2.008000e-01   p_cons 9.301000e-01   p_joint 3.274000e-01

Outputting figure to mutsig2_images.part000000000041/COL11A2.4_5550_10000_0.2008_0.9301_0.3274.png
                gene_name: COL11A2
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 12 percent done.
COL6A3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.542946e-02	ci left: 4.169786e-01	ci right 4.364641e-01	k: 4267	n:10000
Cons ci ratio: 5.345604e-02	ci left: 3.402490e-01	ci right 3.590387e-01	k: 3496	n:10000
KS ci ratio: 7.396041e-02	ci left: 2.111242e-01	ci right 2.274396e-01	k: 2192	n:10000
COL6A3   10000 perm   3 sec   (3931 perm/sec)   p_kst 2.192000e-01   p_cons 3.496000e-01   p_joint 4.267000e-01

Outputting figure to mutsig2_images.part000000000041/COL6A3.4_9753_10000_0.2192_0.3496_0.4267.png
                gene_name: COL6A3
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 25 percent done.
COL22A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.982620e-02	ci left: 4.821550e-01	ci right 5.018497e-01	k: 4920	n:10000
Cons ci ratio: 4.140372e-02	ci left: 4.627741e-01	ci right 4.824419e-01	k: 4726	n:10000
KS ci ratio: 4.311172e-02	ci left: 4.427095e-01	ci right 4.623181e-01	k: 4525	n:10000
COL22A1   10000 perm   2 sec   (5162 perm/sec)   p_kst 4.525000e-01   p_cons 4.726000e-01   p_joint 4.920000e-01

Outputting figure to mutsig2_images.part000000000041/COL22A1.3_5137_10000_0.4525_0.4726_0.492.png
                gene_name: COL22A1
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 38 percent done.
COL16A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.096203e-02	ci left: 1.821553e-01	ci right 1.976258e-01	k: 1898	n:10000
Cons ci ratio: 5.877102e-02	ci left: 2.987602e-01	ci right 3.169519e-01	k: 3078	n:10000
KS ci ratio: 1.541967e-01	ci left: 5.600212e-02	ci right 6.545578e-02	k: 606	n:10000
COL16A1   10000 perm   2 sec   (4964 perm/sec)   p_kst 6.060000e-02   p_cons 3.078000e-01   p_joint 1.898000e-01

Joint ci ratio: 7.752260e-02	ci left: 1.089387e-01	ci right 1.177741e-01	k: 2266	n:20000
Cons ci ratio: 4.165521e-02	ci left: 3.004618e-01	ci right 3.132943e-01	k: 6137	n:20000
KS ci ratio: 1.094202e-01	ci left: 5.699136e-02	ci right 6.363718e-02	k: 1205	n:20000
COL16A1   20000 perm   4 sec   (4527 perm/sec)   p_kst 6.025000e-02   p_cons 3.068500e-01   p_joint 1.133000e-01

Joint ci ratio: 5.490492e-02	ci left: 1.412312e-01	ci right 1.492376e-01	k: 4356	n:30000
Cons ci ratio: 3.414239e-02	ci left: 3.000247e-01	ci right 3.104797e-01	k: 9157	n:30000
KS ci ratio: 8.892414e-02	ci left: 5.812189e-02	ci right 6.356354e-02	k: 1824	n:30000
COL16A1   30000 perm   7 sec   (4388 perm/sec)   p_kst 6.080000e-02   p_cons 3.052333e-01   p_joint 1.452000e-01

Outputting figure to mutsig2_images.part000000000041/COL16A1.2_5095_30000_0.0608_0.30523_0.1452.png
                gene_name: COL16A1
               theta_stop: 0.089 
                    nperm: 30000 
                     p_ks: 0.061 
        ci_ks_bounds_left: 0.058 
       ci_ks_bounds_right: 0.064 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.15 

Current progress: 50 percent done.
COL1A2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.284443e-02	ci left: 8.971340e-01	ci right 9.088300e-01	k: 9031	n:10000
Cons ci ratio: 5.521756e-02	ci left: 3.257483e-01	ci right 3.443479e-01	k: 3350	n:10000
KS ci ratio: 5.305884e-02	ci left: 3.436272e-01	ci right 3.624585e-01	k: 3530	n:10000
COL1A2   10000 perm   2 sec   (5429 perm/sec)   p_kst 3.530000e-01   p_cons 3.350000e-01   p_joint 9.031000e-01

Outputting figure to mutsig2_images.part000000000041/COL1A2.2_4309_10000_0.353_0.335_0.9031.png
                gene_name: COL1A2
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.91 

Current progress: 62 percent done.
COL4A5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.025994e-02	ci left: 7.810721e-01	ci right 7.971591e-01	k: 7892	n:10000
Cons ci ratio: 4.687951e-02	ci left: 4.017322e-01	ci right 4.211194e-01	k: 4114	n:10000
KS ci ratio: 4.552242e-02	ci left: 4.159818e-01	ci right 4.354615e-01	k: 4257	n:10000
COL4A5   10000 perm   2 sec   (5054 perm/sec)   p_kst 4.257000e-01   p_cons 4.114000e-01   p_joint 7.892000e-01

Outputting figure to mutsig2_images.part000000000041/COL4A5.2_5273_10000_0.4257_0.4114_0.7892.png
                gene_name: COL4A5
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 75 percent done.
COL5A3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.124198e-02	ci left: 6.018656e-01	ci right 6.210694e-01	k: 6115	n:10000
Cons ci ratio: 9.988650e-03	ci left: 9.342335e-01	ci right 9.437088e-01	k: 9391	n:10000
KS ci ratio: 7.557379e-02	ci left: 2.039253e-01	ci right 2.200428e-01	k: 2119	n:10000
COL5A3   10000 perm   2 sec   (5004 perm/sec)   p_kst 2.119000e-01   p_cons 9.391000e-01   p_joint 6.115000e-01

Outputting figure to mutsig2_images.part000000000041/COL5A3.2_5506_10000_0.2119_0.9391_0.6115.png
                gene_name: COL5A3
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 88 percent done.
COLEC12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.570431e-02	ci left: 3.218765e-01	ci right 3.404219e-01	k: 3311	n:10000
Cons ci ratio: 3.767188e-02	ci left: 5.099533e-01	ci right 5.296352e-01	k: 5198	n:10000
KS ci ratio: 1.365803e-01	ci left: 7.088017e-02	ci right 8.136835e-02	k: 760	n:10000
COLEC12   10000 perm   2 sec   (6066 perm/sec)   p_kst 7.600000e-02   p_cons 5.198000e-01   p_joint 3.311000e-01

Joint ci ratio: 4.987901e-02	ci left: 2.300297e-01	ci right 2.418471e-01	k: 4718	n:20000
Cons ci ratio: 2.668265e-02	ci left: 5.120481e-01	ci right 5.259463e-01	k: 10380	n:20000
KS ci ratio: 9.695863e-02	ci left: 7.187539e-02	ci right 7.924857e-02	k: 1510	n:20000
COLEC12   20000 perm   4 sec   (5407 perm/sec)   p_kst 7.550000e-02   p_cons 5.190000e-01   p_joint 2.359000e-01

Outputting figure to mutsig2_images.part000000000041/COLEC12.2_2269_20000_0.0755_0.519_0.2359.png
                gene_name: COLEC12
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.075 
        ci_ks_bounds_left: 0.072 
       ci_ks_bounds_right: 0.079 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000041
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 41 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1431>
Subject: Job 4397922: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1431>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000042> was used as the working directory.
Started at Wed Oct 24 16:10:44 2012
Results reported at Wed Oct 24 19:07:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000042.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000042.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 42  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000042.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :  11366.92 sec.
    Max Memory :      1559 MB
    Max Swap   :      4068 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
42
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 42
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 42: processing genes 3679 - 3768
Calculating significance of each gene.
Using projection method.
3679	COQ6	7.535907e-02
3680	COQ7	1
3681	COQ9	1
3682	CORIN	3.437957e-01
3683	CORO1A	1
3684	CORO1B	2.040521e-01
3685	CORO1C	1
3686	CORO2A	1
3687	CORO2B	5.677414e-02
3688	CORO6	1.923327e-01
3689	CORO7	3.495246e-01
3690	CORT	1
3691	COTL1	1
3692	COX10	1
3693	COX11	1
3694	COX15	1
3695	COX16	1
3696	COX17	1
3697	COX18	1
3698	COX19	1
3699	COX4I1	1
3700	COX4I2	2.384139e-02
3701	COX4NB	1
3702	COX5A	1
3703	COX5B	1
3704	COX6A1	1
3705	COX6A2	1
3706	COX6B1	1
3707	COX6B2	1
3708	COX6C	1
3709	COX7A1	1
3710	COX7A2	1
3711	COX7A2L	1
3712	COX7B	1
3713	COX7B2	1
3714	COX7C	1
3715	COX8A	1
3716	COX8C	1
3717	CP	8.970320e-02
3718	CP110	1
3719	CPA1	1
3720	CPA2	1
3721	CPA3	1.699225e-01
3722	CPA4	1
3723	CPA5	1
3724	CPA6	5.507122e-02
3725	CPAMD8	1
3726	CPB1	1
3727	CPB2	2.605075e-03
3728	CPD	1
3729	CPE	1
3730	CPEB1	1
3731	CPEB2	2.358080e-01
3732	CPEB3	1
3733	CPEB4	1.761130e-01
3734	CPLX1	1
3735	CPLX2	1
3736	CPLX3	1
3737	CPLX4	1.006491e-02
3738	CPM	1
3739	CPN1	2.561582e-02
3740	CPN2	1
3741	CPNE1	1
3742	CPNE2	1
3743	CPNE3	2.964186e-02
3744	CPNE4	1
3745	CPNE5	1
3746	CPNE6	1
3747	CPNE7	1.010271e-01
3748	CPNE8	1
3749	CPNE9	1
3750	CPO	1
3751	CPOX	1
3752	CPPED1	1.685939e-01
3753	CPS1	3.816443e-01
3754	CPSF1	4.213998e-02
3755	CPSF2	1
3756	CPSF3	1
3757	CPSF3L	1
3758	CPSF4	2.487476e-02
3759	CPSF6	1
3760	CPSF7	2.351361e-02
3761	CPT1A	1
3762	CPT1B	1
3763	CPT1C	1
3764	CPT2	1
3765	CPVL	1
3766	CPXCR1	6.447470e-02
3767	CPXM1	1
3768	CPXM2	1
Done

Running MutSig 2:
Scatter job 42: processing genes 3679 - 3768
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CPNE3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.533478e-01	ci left: 1.699088e-03	ci right 3.807298e-03	k: 26	n:10000
Cons ci ratio: 6.553133e-03	ci left: 9.695265e-01	ci right 9.759942e-01	k: 9729	n:10000
KS ci ratio: 1.959510e+00	ci left: 6.187149e-05	ci right 8.764745e-04	k: 3	n:10000
CPNE3   10000 perm   2 sec   (5491 perm/sec)   p_kst 3.000000e-04   p_cons 9.729000e-01   p_joint 2.600000e-03

Joint ci ratio: 9.503118e-01	ci left: 4.573361e-04	ci right 1.298826e-03	k: 16	n:20000
Cons ci ratio: 4.581538e-03	ci left: 9.711270e-01	ci right 9.756340e-01	k: 19469	n:20000
KS ci ratio: 1.959755e+00	ci left: 3.093467e-05	ci right 4.383005e-04	k: 3	n:20000
CPNE3   20000 perm   7 sec   (2840 perm/sec)   p_kst 1.500000e-04   p_cons 9.734500e-01   p_joint 8.000000e-04

Joint ci ratio: 6.440358e-01	ci left: 8.406024e-04	ci right 1.660923e-03	k: 36	n:30000
Cons ci ratio: 3.769765e-03	ci left: 9.711372e-01	ci right 9.748371e-01	k: 29191	n:30000
KS ci ratio: 1.481423e+00	ci left: 7.339990e-05	ci right 4.352646e-04	k: 6	n:30000
CPNE3   30000 perm   9 sec   (3224 perm/sec)   p_kst 2.000000e-04   p_cons 9.730333e-01   p_joint 1.200000e-03

Joint ci ratio: 5.380899e-01	ci left: 9.710499e-04	ci right 1.704432e-03	k: 52	n:40000
Cons ci ratio: 3.263228e-03	ci left: 9.714158e-01	ci right 9.746150e-01	k: 38922	n:40000
KS ci ratio: 1.239442e+00	ci left: 1.028893e-04	ci right 4.270769e-04	k: 9	n:40000
CPNE3   40000 perm   12 sec   (3372 perm/sec)   p_kst 2.250000e-04   p_cons 9.730500e-01   p_joint 1.300000e-03

Joint ci ratio: 4.648834e-01	ci left: 1.091526e-03	ci right 1.768490e-03	k: 70	n:50000
Cons ci ratio: 2.924589e-03	ci left: 9.714800e-01	ci right 9.743447e-01	k: 48647	n:50000
KS ci ratio: 1.087060e+00	ci left: 1.240175e-04	ci right 4.191941e-04	k: 12	n:50000
CPNE3   50000 perm   14 sec   (3519 perm/sec)   p_kst 2.400000e-04   p_cons 9.729400e-01   p_joint 1.400000e-03

Joint ci ratio: 1.012005e+00	ci left: 1.275712e-04	ci right 3.914627e-04	k: 14	n:60000
Cons ci ratio: 2.634286e-03	ci left: 9.723198e-01	ci right 9.749007e-01	k: 58418	n:60000
KS ci ratio: 1.012005e+00	ci left: 1.275712e-04	ci right 3.914627e-04	k: 14	n:60000
CPNE3   60000 perm   17 sec   (3601 perm/sec)   p_kst 2.333333e-04   p_cons 9.736333e-01   p_joint 2.333333e-04

Joint ci ratio: 9.506174e-01	ci left: 1.306538e-04	ci right 3.711592e-04	k: 16	n:70000
Cons ci ratio: 2.428131e-03	ci left: 9.726482e-01	ci right 9.750266e-01	k: 68170	n:70000
KS ci ratio: 9.506174e-01	ci left: 1.306538e-04	ci right 3.711592e-04	k: 16	n:70000
CPNE3   70000 perm   19 sec   (3642 perm/sec)   p_kst 2.285714e-04   p_cons 9.738571e-01   p_joint 2.285714e-04

Joint ci ratio: 3.517513e-01	ci left: 1.277971e-03	ci right 1.834183e-03	k: 123	n:80000
Cons ci ratio: 2.277124e-03	ci left: 9.725930e-01	ci right 9.748224e-01	k: 77898	n:80000
KS ci ratio: 9.506327e-01	ci left: 1.143215e-04	ci right 3.247672e-04	k: 16	n:80000
CPNE3   80000 perm   22 sec   (3665 perm/sec)   p_kst 2.000000e-04   p_cons 9.737250e-01   p_joint 1.537500e-03

Joint ci ratio: 3.358813e-01	ci left: 1.257798e-03	ci right 1.775187e-03	k: 135	n:90000
Cons ci ratio: 2.148822e-03	ci left: 9.726109e-01	ci right 9.747140e-01	k: 87631	n:90000
KS ci ratio: 9.238553e-01	ci left: 1.100385e-04	ci right 3.024122e-04	k: 17	n:90000
CPNE3   90000 perm   25 sec   (3669 perm/sec)   p_kst 1.888889e-04   p_cons 9.736778e-01   p_joint 1.500000e-03

Joint ci ratio: 3.435815e-01	ci left: 1.077118e-03	ci right 1.532600e-03	k: 129	n:100000
Cons ci ratio: 2.030459e-03	ci left: 9.728726e-01	ci right 9.748598e-01	k: 97388	n:100000
KS ci ratio: 5.716535e-01	ci left: 3.367969e-04	ci right 6.135284e-04	k: 46	n:100000
CPNE3   100000 perm   27 sec   (3666 perm/sec)   p_kst 4.600000e-04   p_cons 9.738800e-01   p_joint 1.290000e-03

Joint ci ratio: 5.542432e-01	ci left: 3.295673e-04	ci right 5.888723e-04	k: 49	n:110000
Cons ci ratio: 1.938287e-03	ci left: 9.728574e-01	ci right 9.747538e-01	k: 107120	n:110000
KS ci ratio: 5.542432e-01	ci left: 3.295673e-04	ci right 5.888723e-04	k: 49	n:110000
CPNE3   110000 perm   30 sec   (3650 perm/sec)   p_kst 4.454545e-04   p_cons 9.738182e-01   p_joint 4.454545e-04

Joint ci ratio: 5.284493e-01	ci left: 3.380714e-04	ci right 5.871121e-04	k: 54	n:120000
Cons ci ratio: 1.857012e-03	ci left: 9.728636e-01	ci right 9.746801e-01	k: 116854	n:120000
KS ci ratio: 5.284493e-01	ci left: 3.380714e-04	ci right 5.871121e-04	k: 54	n:120000
CPNE3   120000 perm   33 sec   (3629 perm/sec)   p_kst 4.500000e-04   p_cons 9.737833e-01   p_joint 4.500000e-04

Joint ci ratio: 5.146044e-01	ci left: 3.321029e-04	ci right 5.680410e-04	k: 57	n:130000
Cons ci ratio: 1.782751e-03	ci left: 9.729407e-01	ci right 9.746843e-01	k: 126597	n:130000
KS ci ratio: 5.146044e-01	ci left: 3.321029e-04	ci right 5.680410e-04	k: 57	n:130000
CPNE3   130000 perm   36 sec   (3599 perm/sec)   p_kst 4.384615e-04   p_cons 9.738231e-01   p_joint 4.384615e-04

Joint ci ratio: 4.977285e-01	ci left: 3.333028e-04	ci right 5.596585e-04	k: 61	n:140000
Cons ci ratio: 1.722748e-03	ci left: 9.728265e-01	ci right 9.745109e-01	k: 136315	n:140000
KS ci ratio: 4.977285e-01	ci left: 3.333028e-04	ci right 5.596585e-04	k: 61	n:140000
CPNE3   140000 perm   40 sec   (3520 perm/sec)   p_kst 4.357143e-04   p_cons 9.736786e-01   p_joint 4.357143e-04

Joint ci ratio: 4.898938e-01	ci left: 3.227542e-04	ci right 5.373309e-04	k: 63	n:150000
Cons ci ratio: 1.660156e-03	ci left: 9.729859e-01	ci right 9.746091e-01	k: 146071	n:150000
KS ci ratio: 4.898938e-01	ci left: 3.227542e-04	ci right 5.373309e-04	k: 63	n:150000
CPNE3   150000 perm   43 sec   (3457 perm/sec)   p_kst 4.200000e-04   p_cons 9.738067e-01   p_joint 4.200000e-04

Joint ci ratio: 4.824176e-01	ci left: 3.135487e-04	ci right 5.177701e-04	k: 65	n:160000
Cons ci ratio: 1.601722e-03	ci left: 9.731958e-01	ci right 9.747620e-01	k: 155838	n:160000
KS ci ratio: 4.824176e-01	ci left: 3.135487e-04	ci right 5.177701e-04	k: 65	n:160000
CPNE3   160000 perm   47 sec   (3429 perm/sec)   p_kst 4.062500e-04   p_cons 9.739875e-01   p_joint 4.062500e-04

Joint ci ratio: 4.555902e-01	ci left: 3.366049e-04	ci right 5.398910e-04	k: 73	n:170000
Cons ci ratio: 1.557109e-03	ci left: 9.731132e-01	ci right 9.746353e-01	k: 165560	n:170000
KS ci ratio: 4.555902e-01	ci left: 3.366049e-04	ci right 5.398910e-04	k: 73	n:170000
CPNE3   170000 perm   50 sec   (3398 perm/sec)   p_kst 4.294118e-04   p_cons 9.738824e-01   p_joint 4.294118e-04

Joint ci ratio: 4.437552e-01	ci left: 3.376098e-04	ci right 5.346203e-04	k: 77	n:180000
Cons ci ratio: 1.511217e-03	ci left: 9.732037e-01	ci right 9.746810e-01	k: 175311	n:180000
KS ci ratio: 4.437552e-01	ci left: 3.376098e-04	ci right 5.346203e-04	k: 77	n:180000
CPNE3   180000 perm   53 sec   (3370 perm/sec)   p_kst 4.277778e-04   p_cons 9.739500e-01   p_joint 4.277778e-04

Joint ci ratio: 4.276114e-01	ci left: 3.479569e-04	ci right 5.415032e-04	k: 83	n:190000
Cons ci ratio: 1.473113e-03	ci left: 9.731465e-01	ci right 9.745863e-01	k: 185036	n:190000
KS ci ratio: 4.276114e-01	ci left: 3.479569e-04	ci right 5.415032e-04	k: 83	n:190000
CPNE3   190000 perm   57 sec   (3335 perm/sec)   p_kst 4.368421e-04   p_cons 9.738737e-01   p_joint 4.368421e-04

Joint ci ratio: 4.177804e-01	ci left: 3.484314e-04	ci right 5.365436e-04	k: 87	n:200000
Cons ci ratio: 1.432805e-03	ci left: 9.732729e-01	ci right 9.746733e-01	k: 194796	n:200000
KS ci ratio: 4.177804e-01	ci left: 3.484314e-04	ci right 5.365436e-04	k: 87	n:200000
CPNE3   200000 perm   61 sec   (3305 perm/sec)   p_kst 4.350000e-04   p_cons 9.739800e-01   p_joint 4.350000e-04

Joint ci ratio: 4.063941e-01	ci left: 3.531808e-04	ci right 5.372583e-04	k: 92	n:210000
Cons ci ratio: 1.398242e-03	ci left: 9.732911e-01	ci right 9.746576e-01	k: 204536	n:210000
KS ci ratio: 4.063941e-01	ci left: 3.531808e-04	ci right 5.372583e-04	k: 92	n:210000
CPNE3   210000 perm   64 sec   (3269 perm/sec)   p_kst 4.380952e-04   p_cons 9.739810e-01   p_joint 4.380952e-04

Joint ci ratio: 3.958907e-01	ci left: 3.575617e-04	ci right 5.378456e-04	k: 97	n:220000
Cons ci ratio: 1.365944e-03	ci left: 9.733127e-01	ci right 9.746475e-01	k: 214277	n:220000
KS ci ratio: 3.958907e-01	ci left: 3.575617e-04	ci right 5.378456e-04	k: 97	n:220000
CPNE3   220000 perm   68 sec   (3235 perm/sec)   p_kst 4.409091e-04   p_cons 9.739864e-01   p_joint 4.409091e-04

Joint ci ratio: 3.958946e-01	ci left: 3.420149e-04	ci right 5.144621e-04	k: 97	n:230000
Cons ci ratio: 1.336930e-03	ci left: 9.732887e-01	ci right 9.745950e-01	k: 224008	n:230000
KS ci ratio: 3.958946e-01	ci left: 3.420149e-04	ci right 5.144621e-04	k: 97	n:230000
CPNE3   230000 perm   72 sec   (3203 perm/sec)   p_kst 4.217391e-04   p_cons 9.739478e-01   p_joint 4.217391e-04

Joint ci ratio: 3.919175e-01	ci left: 3.352719e-04	ci right 5.021814e-04	k: 99	n:240000
Cons ci ratio: 1.310761e-03	ci left: 9.732248e-01	ci right 9.745054e-01	k: 233729	n:240000
KS ci ratio: 3.919175e-01	ci left: 3.352719e-04	ci right 5.021814e-04	k: 99	n:240000
CPNE3   240000 perm   76 sec   (3167 perm/sec)   p_kst 4.125000e-04   p_cons 9.738708e-01   p_joint 4.125000e-04

Joint ci ratio: 3.919208e-01	ci left: 3.218605e-04	ci right 4.820950e-04	k: 99	n:250000
Cons ci ratio: 1.335317e-03	ci left: 9.711557e-01	ci right 9.724573e-01	k: 242953	n:250000
KS ci ratio: 3.919208e-01	ci left: 3.218605e-04	ci right 4.820950e-04	k: 99	n:250000
CPNE3   250000 perm   80 sec   (3131 perm/sec)   p_kst 3.960000e-04   p_cons 9.718120e-01   p_joint 3.960000e-04

Joint ci ratio: 3.824748e-01	ci left: 3.268403e-04	ci right 4.846464e-04	k: 104	n:260000
Cons ci ratio: 1.310129e-03	ci left: 9.711370e-01	ci right 9.724140e-01	k: 252663	n:260000
KS ci ratio: 3.824748e-01	ci left: 3.268403e-04	ci right 4.846464e-04	k: 104	n:260000
CPNE3   260000 perm   84 sec   (3092 perm/sec)   p_kst 4.000000e-04   p_cons 9.717808e-01   p_joint 4.000000e-04

Joint ci ratio: 3.736805e-01	ci left: 3.314941e-04	ci right 4.869665e-04	k: 109	n:270000
Cons ci ratio: 1.284055e-03	ci left: 9.712173e-01	ci right 9.724688e-01	k: 262399	n:270000
KS ci ratio: 3.736805e-01	ci left: 3.314941e-04	ci right 4.869665e-04	k: 109	n:270000
CPNE3   270000 perm   88 sec   (3059 perm/sec)   p_kst 4.037037e-04   p_cons 9.718481e-01   p_joint 4.037037e-04

Joint ci ratio: 3.670662e-01	ci left: 3.326112e-04	ci right 4.851844e-04	k: 113	n:280000
Cons ci ratio: 1.261448e-03	ci left: 9.712054e-01	ci right 9.724348e-01	k: 272111	n:280000
KS ci ratio: 3.670662e-01	ci left: 3.326112e-04	ci right 4.851844e-04	k: 113	n:280000
CPNE3   280000 perm   93 sec   (3025 perm/sec)   p_kst 4.035714e-04   p_cons 9.718250e-01   p_joint 4.035714e-04

Joint ci ratio: 3.577707e-01	ci left: 3.399480e-04	ci right 4.910190e-04	k: 119	n:290000
Cons ci ratio: 1.240695e-03	ci left: 9.711632e-01	ci right 9.723722e-01	k: 281814	n:290000
KS ci ratio: 3.577707e-01	ci left: 3.399480e-04	ci right 4.910190e-04	k: 119	n:290000
CPNE3   290000 perm   97 sec   (2993 perm/sec)   p_kst 4.103448e-04   p_cons 9.717724e-01   p_joint 4.103448e-04

Joint ci ratio: 3.533814e-01	ci left: 3.377232e-04	ci right 4.855414e-04	k: 122	n:300000
Cons ci ratio: 1.221004e-03	ci left: 9.711206e-01	ci right 9.723103e-01	k: 291516	n:300000
KS ci ratio: 3.533814e-01	ci left: 3.377232e-04	ci right 4.855414e-04	k: 122	n:300000
CPNE3   300000 perm   101 sec   (2959 perm/sec)   p_kst 4.066667e-04   p_cons 9.717200e-01   p_joint 4.066667e-04

Joint ci ratio: 3.464102e-01	ci left: 3.415407e-04	ci right 4.874195e-04	k: 127	n:310000
Cons ci ratio: 1.201443e-03	ci left: 9.711167e-01	ci right 9.722873e-01	k: 301229	n:310000
KS ci ratio: 3.464102e-01	ci left: 3.415407e-04	ci right 4.874195e-04	k: 127	n:310000
CPNE3   310000 perm   106 sec   (2927 perm/sec)   p_kst 4.096774e-04   p_cons 9.717065e-01   p_joint 4.096774e-04

Joint ci ratio: 3.437364e-01	ci left: 3.365758e-04	ci right 4.789774e-04	k: 129	n:320000
Cons ci ratio: 1.182457e-03	ci left: 9.711291e-01	ci right 9.722811e-01	k: 310947	n:320000
KS ci ratio: 3.437364e-01	ci left: 3.365758e-04	ci right 4.789774e-04	k: 129	n:320000
CPNE3   320000 perm   111 sec   (2894 perm/sec)   p_kst 4.031250e-04   p_cons 9.717094e-01   p_joint 4.031250e-04

Joint ci ratio: 3.373104e-01	ci left: 3.402327e-04	ci right 4.809050e-04	k: 134	n:330000
Cons ci ratio: 1.163316e-03	ci left: 9.711897e-01	ci right 9.723232e-01	k: 320681	n:330000
KS ci ratio: 3.373104e-01	ci left: 3.402327e-04	ci right 4.809050e-04	k: 134	n:330000
CPNE3   330000 perm   115 sec   (2862 perm/sec)   p_kst 4.060606e-04   p_cons 9.717606e-01   p_joint 4.060606e-04

Joint ci ratio: 3.312318e-01	ci left: 3.436977e-04	ci right 4.826962e-04	k: 139	n:340000
Cons ci ratio: 1.144888e-03	ci left: 9.712559e-01	ci right 9.723714e-01	k: 330418	n:340000
KS ci ratio: 3.312318e-01	ci left: 3.436977e-04	ci right 4.826962e-04	k: 139	n:340000
CPNE3   340000 perm   120 sec   (2832 perm/sec)   p_kst 4.088235e-04   p_cons 9.718176e-01   p_joint 4.088235e-04

Joint ci ratio: 3.265990e-01	ci left: 3.443628e-04	ci right 4.812737e-04	k: 143	n:350000
Cons ci ratio: 1.128835e-03	ci left: 9.712433e-01	ci right 9.723431e-01	k: 340129	n:350000
KS ci ratio: 3.265990e-01	ci left: 3.443628e-04	ci right 4.812737e-04	k: 143	n:350000
CPNE3   350000 perm   125 sec   (2801 perm/sec)   p_kst 4.085714e-04   p_cons 9.717971e-01   p_joint 4.085714e-04

Joint ci ratio: 3.210720e-01	ci left: 3.475573e-04	ci right 4.829189e-04	k: 148	n:360000
Cons ci ratio: 1.113438e-03	ci left: 9.712316e-01	ci right 9.723163e-01	k: 349840	n:360000
KS ci ratio: 3.210720e-01	ci left: 3.475573e-04	ci right 4.829189e-04	k: 148	n:360000
CPNE3   360000 perm   130 sec   (2770 perm/sec)   p_kst 4.111111e-04   p_cons 9.717778e-01   p_joint 4.111111e-04

Joint ci ratio: 3.178882e-01	ci left: 3.456218e-04	ci right 4.786232e-04	k: 151	n:370000
Cons ci ratio: 1.098383e-03	ci left: 9.712343e-01	ci right 9.723043e-01	k: 359556	n:370000
KS ci ratio: 3.178882e-01	ci left: 3.456218e-04	ci right 4.786232e-04	k: 151	n:370000
CPNE3   370000 perm   135 sec   (2740 perm/sec)   p_kst 4.081081e-04   p_cons 9.717730e-01   p_joint 4.081081e-04

Joint ci ratio: 3.147973e-01	ci left: 3.437944e-04	ci right 4.745474e-04	k: 154	n:380000
Cons ci ratio: 1.082415e-03	ci left: 9.713139e-01	ci right 9.723684e-01	k: 369301	n:380000
KS ci ratio: 3.147973e-01	ci left: 3.437944e-04	ci right 4.745474e-04	k: 154	n:380000
CPNE3   380000 perm   140 sec   (2713 perm/sec)   p_kst 4.052632e-04   p_cons 9.718447e-01   p_joint 4.052632e-04

Joint ci ratio: 3.108124e-01	ci left: 3.444306e-04	ci right 4.734385e-04	k: 158	n:390000
Cons ci ratio: 1.068218e-03	ci left: 9.713326e-01	ci right 9.723732e-01	k: 379024	n:390000
KS ci ratio: 3.108124e-01	ci left: 3.444306e-04	ci right 4.734385e-04	k: 158	n:390000
CPNE3   390000 perm   145 sec   (2683 perm/sec)   p_kst 4.051282e-04   p_cons 9.718564e-01   p_joint 4.051282e-04

Joint ci ratio: 3.060374e-01	ci left: 3.473526e-04	ci right 4.750667e-04	k: 163	n:400000
Cons ci ratio: 1.056782e-03	ci left: 9.712344e-01	ci right 9.722638e-01	k: 388701	n:400000
KS ci ratio: 3.060374e-01	ci left: 3.473526e-04	ci right 4.750667e-04	k: 163	n:400000
CPNE3   400000 perm   151 sec   (2654 perm/sec)   p_kst 4.075000e-04   p_cons 9.717525e-01   p_joint 4.075000e-04

Joint ci ratio: 3.014759e-01	ci left: 3.501465e-04	ci right 4.766013e-04	k: 168	n:410000
Cons ci ratio: 1.043049e-03	ci left: 9.712813e-01	ci right 9.722974e-01	k: 398435	n:410000
KS ci ratio: 3.014759e-01	ci left: 3.501465e-04	ci right 4.766013e-04	k: 168	n:410000
CPNE3   410000 perm   156 sec   (2627 perm/sec)   p_kst 4.097561e-04   p_cons 9.717927e-01   p_joint 4.097561e-04

Joint ci ratio: 3.266103e-01	ci left: 2.869675e-04	ci right 4.010639e-04	k: 143	n:420000
Cons ci ratio: 1.031090e-03	ci left: 9.712589e-01	ci right 9.722632e-01	k: 408141	n:420000
KS ci ratio: 3.266103e-01	ci left: 2.869675e-04	ci right 4.010639e-04	k: 143	n:420000
CPNE3   420000 perm   162 sec   (2599 perm/sec)   p_kst 3.404762e-04   p_cons 9.717643e-01   p_joint 3.404762e-04

Joint ci ratio: 3.210829e-01	ci left: 2.909767e-04	ci right 4.043065e-04	k: 148	n:430000
Cons ci ratio: 1.020179e-03	ci left: 9.712023e-01	ci right 9.721959e-01	k: 417832	n:430000
KS ci ratio: 3.210829e-01	ci left: 2.909767e-04	ci right 4.043065e-04	k: 148	n:430000
CPNE3   430000 perm   167 sec   (2573 perm/sec)   p_kst 3.441860e-04   p_cons 9.717023e-01   p_joint 3.441860e-04

Joint ci ratio: 3.189500e-01	ci left: 2.885440e-04	ci right 4.000272e-04	k: 150	n:440000
Cons ci ratio: 1.008770e-03	ci left: 9.711943e-01	ci right 9.721767e-01	k: 427543	n:440000
KS ci ratio: 3.189500e-01	ci left: 2.885440e-04	ci right 4.000272e-04	k: 150	n:440000
CPNE3   440000 perm   173 sec   (2546 perm/sec)   p_kst 3.409091e-04   p_cons 9.716886e-01   p_joint 3.409091e-04

Joint ci ratio: 3.168590e-01	ci left: 2.862217e-04	ci right 3.959357e-04	k: 152	n:450000
Cons ci ratio: 9.965658e-04	ci left: 9.712517e-01	ci right 9.722222e-01	k: 437283	n:450000
KS ci ratio: 3.168590e-01	ci left: 2.862217e-04	ci right 3.959357e-04	k: 152	n:450000
CPNE3   450000 perm   179 sec   (2520 perm/sec)   p_kst 3.377778e-04   p_cons 9.717400e-01   p_joint 3.377778e-04

Joint ci ratio: 3.158294e-01	ci left: 2.820007e-04	ci right 3.896745e-04	k: 153	n:460000
Cons ci ratio: 9.856109e-04	ci left: 9.712606e-01	ci right 9.722204e-01	k: 447002	n:460000
KS ci ratio: 3.158294e-01	ci left: 2.820007e-04	ci right 3.896745e-04	k: 153	n:460000
CPNE3   460000 perm   184 sec   (2494 perm/sec)   p_kst 3.326087e-04   p_cons 9.717435e-01   p_joint 3.326087e-04

Joint ci ratio: 3.137988e-01	ci left: 2.799198e-04	ci right 3.859741e-04	k: 155	n:470000
Cons ci ratio: 9.751605e-04	ci left: 9.712605e-01	ci right 9.722102e-01	k: 456717	n:470000
KS ci ratio: 3.137988e-01	ci left: 2.799198e-04	ci right 3.859741e-04	k: 155	n:470000
CPNE3   470000 perm   190 sec   (2470 perm/sec)   p_kst 3.297872e-04   p_cons 9.717383e-01   p_joint 3.297872e-04

Joint ci ratio: 3.118068e-01	ci left: 2.779277e-04	ci right 3.824257e-04	k: 157	n:480000
Cons ci ratio: 9.643402e-04	ci left: 9.713005e-01	ci right 9.722396e-01	k: 466451	n:480000
KS ci ratio: 3.118068e-01	ci left: 2.779277e-04	ci right 3.824257e-04	k: 157	n:480000
CPNE3   480000 perm   196 sec   (2446 perm/sec)   p_kst 3.270833e-04   p_cons 9.717729e-01   p_joint 3.270833e-04

Joint ci ratio: 3.108255e-01	ci left: 2.741370e-04	ci right 3.768210e-04	k: 158	n:490000
Cons ci ratio: 9.556100e-04	ci left: 9.712380e-01	ci right 9.721686e-01	k: 476136	n:490000
KS ci ratio: 3.108255e-01	ci left: 2.741370e-04	ci right 3.768210e-04	k: 158	n:490000
CPNE3   490000 perm   202 sec   (2421 perm/sec)   p_kst 3.224490e-04   p_cons 9.717061e-01   p_joint 3.224490e-04

Joint ci ratio: 3.098533e-01	ci left: 2.704984e-04	ci right 3.714400e-04	k: 159	n:500000
Cons ci ratio: 9.470732e-04	ci left: 9.711802e-01	ci right 9.721024e-01	k: 485822	n:500000
KS ci ratio: 3.098533e-01	ci left: 2.704984e-04	ci right 3.714400e-04	k: 159	n:500000
CPNE3   500000 perm   209 sec   (2395 perm/sec)   p_kst 3.180000e-04   p_cons 9.716440e-01   p_joint 3.180000e-04

Joint ci ratio: 3.079351e-01	ci left: 2.688121e-04	ci right 3.683815e-04	k: 161	n:510000
Cons ci ratio: 9.386901e-04	ci left: 9.711286e-01	ci right 9.720425e-01	k: 495510	n:510000
KS ci ratio: 3.079351e-01	ci left: 2.688121e-04	ci right 3.683815e-04	k: 161	n:510000
CPNE3   510000 perm   215 sec   (2371 perm/sec)   p_kst 3.156863e-04   p_cons 9.715882e-01   p_joint 3.156863e-04

Joint ci ratio: 3.069897e-01	ci left: 2.654173e-04	ci right 3.633683e-04	k: 162	n:520000
Cons ci ratio: 9.301987e-04	ci left: 9.710984e-01	ci right 9.720040e-01	k: 505208	n:520000
KS ci ratio: 3.069897e-01	ci left: 2.654173e-04	ci right 3.633683e-04	k: 162	n:520000
CPNE3   520000 perm   222 sec   (2347 perm/sec)   p_kst 3.115385e-04   p_cons 9.715538e-01   p_joint 3.115385e-04

Joint ci ratio: 3.023863e-01	ci left: 2.691224e-04	ci right 3.666651e-04	k: 167	n:530000
Cons ci ratio: 9.209575e-04	ci left: 9.711283e-01	ci right 9.720250e-01	k: 514937	n:530000
KS ci ratio: 3.023863e-01	ci left: 2.691224e-04	ci right 3.666651e-04	k: 167	n:530000
CPNE3   530000 perm   228 sec   (2324 perm/sec)   p_kst 3.150943e-04   p_cons 9.715792e-01   p_joint 3.150943e-04

Joint ci ratio: 2.997221e-01	ci left: 2.692746e-04	ci right 3.658489e-04	k: 170	n:540000
Cons ci ratio: 9.125364e-04	ci left: 9.711236e-01	ci right 9.720120e-01	k: 524648	n:540000
KS ci ratio: 2.997221e-01	ci left: 2.692746e-04	ci right 3.658489e-04	k: 170	n:540000
CPNE3   540000 perm   235 sec   (2302 perm/sec)   p_kst 3.148148e-04   p_cons 9.715704e-01   p_joint 3.148148e-04

Joint ci ratio: 2.945976e-01	ci left: 2.744748e-04	ci right 3.709169e-04	k: 176	n:550000
Cons ci ratio: 9.042825e-04	ci left: 9.711228e-01	ci right 9.720031e-01	k: 534361	n:550000
KS ci ratio: 2.945976e-01	ci left: 2.744748e-04	ci right 3.709169e-04	k: 176	n:550000
CPNE3   550000 perm   241 sec   (2279 perm/sec)   p_kst 3.200000e-04   p_cons 9.715655e-01   p_joint 3.200000e-04

Joint ci ratio: 2.913240e-01	ci left: 2.761915e-04	ci right 3.719596e-04	k: 180	n:560000
Cons ci ratio: 8.965961e-04	ci left: 9.711004e-01	ci right 9.719733e-01	k: 544062	n:560000
KS ci ratio: 2.913240e-01	ci left: 2.761915e-04	ci right 3.719596e-04	k: 180	n:560000
CPNE3   560000 perm   248 sec   (2258 perm/sec)   p_kst 3.214286e-04   p_cons 9.715393e-01   p_joint 3.214286e-04

Joint ci ratio: 2.881571e-01	ci left: 2.778537e-04	ci right 3.729600e-04	k: 184	n:570000
Cons ci ratio: 8.893552e-04	ci left: 9.710630e-01	ci right 9.719287e-01	k: 553754	n:570000
KS ci ratio: 2.881571e-01	ci left: 2.778537e-04	ci right 3.729600e-04	k: 184	n:570000
CPNE3   570000 perm   255 sec   (2237 perm/sec)   p_kst 3.228070e-04   p_cons 9.714982e-01   p_joint 3.228070e-04

Joint ci ratio: 2.858488e-01	ci left: 2.778633e-04	ci right 3.720734e-04	k: 187	n:580000
Cons ci ratio: 8.819834e-04	ci left: 9.710460e-01	ci right 9.719045e-01	k: 563457	n:580000
KS ci ratio: 2.858488e-01	ci left: 2.778633e-04	ci right 3.720734e-04	k: 187	n:580000
CPNE3   580000 perm   262 sec   (2217 perm/sec)   p_kst 3.224138e-04   p_cons 9.714776e-01   p_joint 3.224138e-04

Joint ci ratio: 2.858496e-01	ci left: 2.731536e-04	ci right 3.657672e-04	k: 187	n:590000
Cons ci ratio: 8.738821e-04	ci left: 9.710876e-01	ci right 9.719383e-01	k: 573194	n:590000
KS ci ratio: 2.858496e-01	ci left: 2.731536e-04	ci right 3.657672e-04	k: 187	n:590000
CPNE3   590000 perm   269 sec   (2197 perm/sec)   p_kst 3.169492e-04   p_cons 9.715153e-01   p_joint 3.169492e-04

Joint ci ratio: 2.828561e-01	ci left: 2.747924e-04	ci right 3.668119e-04	k: 191	n:600000
Cons ci ratio: 8.671728e-04	ci left: 9.710523e-01	ci right 9.718964e-01	k: 582886	n:600000
KS ci ratio: 2.828561e-01	ci left: 2.747924e-04	ci right 3.668119e-04	k: 191	n:600000
CPNE3   600000 perm   276 sec   (2178 perm/sec)   p_kst 3.183333e-04   p_cons 9.714767e-01   p_joint 3.183333e-04

Joint ci ratio: 2.813946e-01	ci left: 2.733343e-04	ci right 3.643087e-04	k: 193	n:610000
Cons ci ratio: 8.603852e-04	ci left: 9.710331e-01	ci right 9.718706e-01	k: 592587	n:610000
KS ci ratio: 2.813946e-01	ci left: 2.733343e-04	ci right 3.643087e-04	k: 193	n:610000
CPNE3   610000 perm   284 sec   (2149 perm/sec)   p_kst 3.163934e-04   p_cons 9.714541e-01   p_joint 3.163934e-04

Joint ci ratio: 2.799555e-01	ci left: 2.719244e-04	ci right 3.618850e-04	k: 195	n:620000
Cons ci ratio: 8.532329e-04	ci left: 9.710487e-01	ci right 9.718792e-01	k: 602309	n:620000
KS ci ratio: 2.799555e-01	ci left: 2.719244e-04	ci right 3.618850e-04	k: 195	n:620000
CPNE3   620000 perm   291 sec   (2130 perm/sec)   p_kst 3.145161e-04   p_cons 9.714661e-01   p_joint 3.145161e-04

Joint ci ratio: 2.771416e-01	ci left: 2.735140e-04	ci right 3.629323e-04	k: 199	n:630000
Cons ci ratio: 8.467648e-04	ci left: 9.710302e-01	ci right 9.718543e-01	k: 612010	n:630000
KS ci ratio: 2.771416e-01	ci left: 2.735140e-04	ci right 3.629323e-04	k: 199	n:630000
CPNE3   630000 perm   298 sec   (2111 perm/sec)   p_kst 3.158730e-04   p_cons 9.714444e-01   p_joint 3.158730e-04

Joint ci ratio: 2.757665e-01	ci left: 2.721487e-04	ci right 3.606026e-04	k: 201	n:640000
Cons ci ratio: 8.406067e-04	ci left: 9.710013e-01	ci right 9.718194e-01	k: 621704	n:640000
KS ci ratio: 2.757665e-01	ci left: 2.721487e-04	ci right 3.606026e-04	k: 201	n:640000
CPNE3   640000 perm   306 sec   (2093 perm/sec)   p_kst 3.140625e-04   p_cons 9.714125e-01   p_joint 3.140625e-04

Joint ci ratio: 2.744116e-01	ci left: 2.708265e-04	ci right 3.583436e-04	k: 203	n:650000
Cons ci ratio: 8.343952e-04	ci left: 9.709857e-01	ci right 9.717978e-01	k: 631406	n:650000
KS ci ratio: 2.744116e-01	ci left: 2.708265e-04	ci right 3.583436e-04	k: 203	n:650000
CPNE3   650000 perm   313 sec   (2077 perm/sec)   p_kst 3.123077e-04   p_cons 9.713938e-01   p_joint 3.123077e-04

Joint ci ratio: 2.724159e-01	ci left: 2.709569e-04	ci right 3.577704e-04	k: 206	n:660000
Cons ci ratio: 8.277998e-04	ci left: 9.710057e-01	ci right 9.718113e-01	k: 641131	n:660000
KS ci ratio: 2.724159e-01	ci left: 2.709569e-04	ci right 3.577704e-04	k: 206	n:660000
CPNE3   660000 perm   321 sec   (2059 perm/sec)   p_kst 3.121212e-04   p_cons 9.714106e-01   p_joint 3.121212e-04

Joint ci ratio: 2.717607e-01	ci left: 2.683035e-04	ci right 3.540247e-04	k: 207	n:670000
Cons ci ratio: 8.210269e-04	ci left: 9.710477e-01	ci right 9.718467e-01	k: 650871	n:670000
KS ci ratio: 2.717607e-01	ci left: 2.683035e-04	ci right 3.540247e-04	k: 207	n:670000
CPNE3   670000 perm   328 sec   (2042 perm/sec)   p_kst 3.089552e-04   p_cons 9.714493e-01   p_joint 3.089552e-04

Joint ci ratio: 2.704637e-01	ci left: 2.670991e-04	ci right 3.519591e-04	k: 209	n:680000
Cons ci ratio: 8.147187e-04	ci left: 9.710677e-01	ci right 9.718606e-01	k: 660597	n:680000
KS ci ratio: 2.704637e-01	ci left: 2.670991e-04	ci right 3.519591e-04	k: 209	n:680000
CPNE3   680000 perm   336 sec   (2025 perm/sec)   p_kst 3.073529e-04   p_cons 9.714662e-01   p_joint 3.073529e-04

Joint ci ratio: 2.672999e-01	ci left: 2.699861e-04	ci right 3.545919e-04	k: 214	n:690000
Cons ci ratio: 8.083418e-04	ci left: 9.711018e-01	ci right 9.718885e-01	k: 670333	n:690000
KS ci ratio: 2.672999e-01	ci left: 2.699861e-04	ci right 3.545919e-04	k: 214	n:690000
CPNE3   690000 perm   344 sec   (2008 perm/sec)   p_kst 3.101449e-04   p_cons 9.714971e-01   p_joint 3.101449e-04

Joint ci ratio: 2.660655e-01	ci left: 2.687952e-04	ci right 3.525740e-04	k: 216	n:700000
Cons ci ratio: 8.022772e-04	ci left: 9.711233e-01	ci right 9.719042e-01	k: 680061	n:700000
KS ci ratio: 2.660655e-01	ci left: 2.687952e-04	ci right 3.525740e-04	k: 216	n:700000
CPNE3   700000 perm   352 sec   (1991 perm/sec)   p_kst 3.085714e-04   p_cons 9.715157e-01   p_joint 3.085714e-04

Joint ci ratio: 2.654550e-01	ci left: 2.663240e-04	ci right 3.491103e-04	k: 217	n:710000
Cons ci ratio: 7.966508e-04	ci left: 9.711231e-01	ci right 9.718984e-01	k: 689774	n:710000
KS ci ratio: 2.654550e-01	ci left: 2.663240e-04	ci right 3.491103e-04	k: 217	n:710000
CPNE3   710000 perm   360 sec   (1974 perm/sec)   p_kst 3.056338e-04   p_cons 9.715127e-01   p_joint 3.056338e-04

Joint ci ratio: 2.630524e-01	ci left: 2.678126e-04	ci right 3.501843e-04	k: 221	n:720000
Cons ci ratio: 7.910022e-04	ci left: 9.711326e-01	ci right 9.719025e-01	k: 699494	n:720000
KS ci ratio: 2.630524e-01	ci left: 2.678126e-04	ci right 3.501843e-04	k: 221	n:720000
CPNE3   720000 perm   368 sec   (1959 perm/sec)   p_kst 3.069444e-04   p_cons 9.715194e-01   p_joint 3.069444e-04

Joint ci ratio: 2.612929e-01	ci left: 2.679835e-04	ci right 3.497663e-04	k: 224	n:730000
Cons ci ratio: 7.855692e-04	ci left: 9.711350e-01	ci right 9.718996e-01	k: 709209	n:730000
KS ci ratio: 2.612929e-01	ci left: 2.679835e-04	ci right 3.497663e-04	k: 224	n:730000
CPNE3   730000 perm   376 sec   (1943 perm/sec)   p_kst 3.068493e-04   p_cons 9.715192e-01   p_joint 3.068493e-04

Joint ci ratio: 2.595682e-01	ci left: 2.681515e-04	ci right 3.493578e-04	k: 227	n:740000
Cons ci ratio: 7.802086e-04	ci left: 9.711401e-01	ci right 9.718994e-01	k: 718926	n:740000
KS ci ratio: 2.595682e-01	ci left: 2.681515e-04	ci right 3.493578e-04	k: 227	n:740000
CPNE3   740000 perm   384 sec   (1928 perm/sec)   p_kst 3.067568e-04   p_cons 9.715216e-01   p_joint 3.067568e-04

Joint ci ratio: 2.573206e-01	ci left: 2.695641e-04	ci right 3.503777e-04	k: 231	n:750000
Cons ci ratio: 7.748255e-04	ci left: 9.711545e-01	ci right 9.719085e-01	k: 728650	n:750000
KS ci ratio: 2.573206e-01	ci left: 2.695641e-04	ci right 3.503777e-04	k: 231	n:750000
CPNE3   750000 perm   392 sec   (1914 perm/sec)   p_kst 3.080000e-04   p_cons 9.715333e-01   p_joint 3.080000e-04

Joint ci ratio: 2.562188e-01	ci left: 2.684794e-04	ci right 3.485681e-04	k: 233	n:760000
Cons ci ratio: 7.699183e-04	ci left: 9.711420e-01	ci right 9.718913e-01	k: 738354	n:760000
KS ci ratio: 2.562188e-01	ci left: 2.684794e-04	ci right 3.485681e-04	k: 233	n:760000
CPNE3   760000 perm   400 sec   (1899 perm/sec)   p_kst 3.065789e-04   p_cons 9.715184e-01   p_joint 3.065789e-04

Joint ci ratio: 2.551310e-01	ci left: 2.674236e-04	ci right 3.468048e-04	k: 235	n:770000
Cons ci ratio: 7.652466e-04	ci left: 9.711194e-01	ci right 9.718641e-01	k: 748050	n:770000
KS ci ratio: 2.551310e-01	ci left: 2.674236e-04	ci right 3.468048e-04	k: 235	n:770000
CPNE3   770000 perm   408 sec   (1885 perm/sec)   p_kst 3.051948e-04   p_cons 9.714935e-01   p_joint 3.051948e-04

Joint ci ratio: 2.545925e-01	ci left: 2.651952e-04	ci right 3.437224e-04	k: 236	n:780000
Cons ci ratio: 7.597255e-04	ci left: 9.711657e-01	ci right 9.719051e-01	k: 757799	n:780000
KS ci ratio: 2.545925e-01	ci left: 2.651952e-04	ci right 3.437224e-04	k: 236	n:780000
CPNE3   780000 perm   417 sec   (1870 perm/sec)   p_kst 3.025641e-04   p_cons 9.715372e-01   p_joint 3.025641e-04

Joint ci ratio: 2.535252e-01	ci left: 2.642087e-04	ci right 3.420640e-04	k: 238	n:790000
Cons ci ratio: 7.548043e-04	ci left: 9.711753e-01	ci right 9.719099e-01	k: 767520	n:790000
KS ci ratio: 2.535252e-01	ci left: 2.642087e-04	ci right 3.420640e-04	k: 238	n:790000
CPNE3   790000 perm   425 sec   (1857 perm/sec)   p_kst 3.012658e-04   p_cons 9.715443e-01   p_joint 3.012658e-04

Joint ci ratio: 2.524712e-01	ci left: 2.632476e-04	ci right 3.404464e-04	k: 240	n:800000
Cons ci ratio: 7.506048e-04	ci left: 9.711381e-01	ci right 9.718685e-01	k: 777204	n:800000
KS ci ratio: 2.524712e-01	ci left: 2.632476e-04	ci right 3.404464e-04	k: 240	n:800000
CPNE3   800000 perm   434 sec   (1843 perm/sec)   p_kst 3.000000e-04   p_cons 9.715050e-01   p_joint 3.000000e-04

Joint ci ratio: 2.504016e-01	ci left: 2.646248e-04	ci right 3.414921e-04	k: 244	n:810000
Cons ci ratio: 7.459244e-04	ci left: 9.711428e-01	ci right 9.718687e-01	k: 786921	n:810000
KS ci ratio: 2.504016e-01	ci left: 2.646248e-04	ci right 3.414921e-04	k: 244	n:810000
CPNE3   810000 perm   443 sec   (1829 perm/sec)   p_kst 3.012346e-04   p_cons 9.715074e-01   p_joint 3.012346e-04

Joint ci ratio: 2.459244e-01	ci left: 2.716909e-04	ci right 3.489841e-04	k: 253	n:820000
Cons ci ratio: 7.411672e-04	ci left: 9.711597e-01	ci right 9.718809e-01	k: 796648	n:820000
KS ci ratio: 2.459244e-01	ci left: 2.716909e-04	ci right 3.489841e-04	k: 253	n:820000
CPNE3   820000 perm   452 sec   (1815 perm/sec)   p_kst 3.085366e-04   p_cons 9.715220e-01   p_joint 3.085366e-04

Joint ci ratio: 2.444849e-01	ci left: 2.718099e-04	ci right 3.486156e-04	k: 256	n:830000
Cons ci ratio: 7.364355e-04	ci left: 9.711810e-01	ci right 9.718976e-01	k: 806379	n:830000
KS ci ratio: 2.444849e-01	ci left: 2.718099e-04	ci right 3.486156e-04	k: 256	n:830000
CPNE3   830000 perm   461 sec   (1801 perm/sec)   p_kst 3.084337e-04   p_cons 9.715410e-01   p_joint 3.084337e-04

Joint ci ratio: 2.426041e-01	ci left: 2.730454e-04	ci right 3.495173e-04	k: 260	n:840000
Cons ci ratio: 7.324547e-04	ci left: 9.711515e-01	ci right 9.718643e-01	k: 816068	n:840000
KS ci ratio: 2.426041e-01	ci left: 2.730454e-04	ci right 3.495173e-04	k: 260	n:840000
CPNE3   840000 perm   470 sec   (1787 perm/sec)   p_kst 3.095238e-04   p_cons 9.715095e-01   p_joint 3.095238e-04

Joint ci ratio: 2.398623e-01	ci left: 2.764653e-04	ci right 3.528900e-04	k: 266	n:850000
Cons ci ratio: 7.284287e-04	ci left: 9.711310e-01	ci right 9.718399e-01	k: 825764	n:850000
KS ci ratio: 2.398623e-01	ci left: 2.764653e-04	ci right 3.528900e-04	k: 266	n:850000
CPNE3   850000 perm   479 sec   (1773 perm/sec)   p_kst 3.129412e-04   p_cons 9.714871e-01   p_joint 3.129412e-04

Joint ci ratio: 2.389691e-01	ci left: 2.754367e-04	ci right 3.512514e-04	k: 268	n:860000
Cons ci ratio: 7.241031e-04	ci left: 9.711391e-01	ci right 9.718437e-01	k: 835484	n:860000
KS ci ratio: 2.389691e-01	ci left: 2.754367e-04	ci right 3.512514e-04	k: 268	n:860000
CPNE3   860000 perm   489 sec   (1760 perm/sec)   p_kst 3.116279e-04   p_cons 9.714930e-01   p_joint 3.116279e-04

Joint ci ratio: 2.372118e-01	ci left: 2.765942e-04	ci right 3.520855e-04	k: 272	n:870000
Cons ci ratio: 7.200180e-04	ci left: 9.711343e-01	ci right 9.718349e-01	k: 845193	n:870000
KS ci ratio: 2.372118e-01	ci left: 2.765942e-04	ci right 3.520855e-04	k: 272	n:870000
CPNE3   870000 perm   499 sec   (1743 perm/sec)   p_kst 3.126437e-04   p_cons 9.714862e-01   p_joint 3.126437e-04

Joint ci ratio: 2.346469e-01	ci left: 2.798663e-04	ci right 3.553049e-04	k: 278	n:880000
Cons ci ratio: 7.161627e-04	ci left: 9.711171e-01	ci right 9.718139e-01	k: 854891	n:880000
KS ci ratio: 2.346469e-01	ci left: 2.798663e-04	ci right 3.553049e-04	k: 278	n:880000
CPNE3   880000 perm   509 sec   (1729 perm/sec)   p_kst 3.159091e-04   p_cons 9.714670e-01   p_joint 3.159091e-04

Joint ci ratio: 2.321634e-01	ci left: 2.830692e-04	ci right 3.584477e-04	k: 284	n:890000
Cons ci ratio: 7.119787e-04	ci left: 9.711307e-01	ci right 9.718235e-01	k: 864616	n:890000
KS ci ratio: 2.321634e-01	ci left: 2.830692e-04	ci right 3.584477e-04	k: 284	n:890000
CPNE3   890000 perm   518 sec   (1717 perm/sec)   p_kst 3.191011e-04   p_cons 9.714787e-01   p_joint 3.191011e-04

Joint ci ratio: 2.297572e-01	ci left: 2.862050e-04	ci right 3.615166e-04	k: 290	n:900000
Cons ci ratio: 7.077393e-04	ci left: 9.711542e-01	ci right 9.718428e-01	k: 874350	n:900000
KS ci ratio: 2.297572e-01	ci left: 2.862050e-04	ci right 3.615166e-04	k: 290	n:900000
CPNE3   900000 perm   528 sec   (1705 perm/sec)   p_kst 3.222222e-04   p_cons 9.715000e-01   p_joint 3.222222e-04

Joint ci ratio: 2.285820e-01	ci left: 2.861674e-04	ci right 3.610295e-04	k: 293	n:910000
Cons ci ratio: 7.038817e-04	ci left: 9.711528e-01	ci right 9.718376e-01	k: 884062	n:910000
KS ci ratio: 2.285820e-01	ci left: 2.861674e-04	ci right 3.610295e-04	k: 293	n:910000
CPNE3   910000 perm   538 sec   (1693 perm/sec)   p_kst 3.219780e-04   p_cons 9.714967e-01   p_joint 3.219780e-04

Joint ci ratio: 2.278086e-01	ci left: 2.851065e-04	ci right 3.594033e-04	k: 295	n:920000
Cons ci ratio: 7.001139e-04	ci left: 9.711492e-01	ci right 9.718304e-01	k: 893772	n:920000
KS ci ratio: 2.278086e-01	ci left: 2.851065e-04	ci right 3.594033e-04	k: 295	n:920000
CPNE3   920000 perm   547 sec   (1680 perm/sec)   p_kst 3.206522e-04   p_cons 9.714913e-01   p_joint 3.206522e-04

Joint ci ratio: 2.262847e-01	ci left: 2.860973e-04	ci right 3.600840e-04	k: 299	n:930000
Cons ci ratio: 6.965816e-04	ci left: 9.711317e-01	ci right 9.718095e-01	k: 903469	n:930000
KS ci ratio: 2.262847e-01	ci left: 2.860973e-04	ci right 3.600840e-04	k: 299	n:930000
CPNE3   930000 perm   557 sec   (1669 perm/sec)   p_kst 3.215054e-04   p_cons 9.714720e-01   p_joint 3.215054e-04

Joint ci ratio: 2.240549e-01	ci left: 2.890767e-04	ci right 3.629956e-04	k: 305	n:940000
Cons ci ratio: 6.929424e-04	ci left: 9.711274e-01	ci right 9.718016e-01	k: 913178	n:940000
KS ci ratio: 2.240549e-01	ci left: 2.890767e-04	ci right 3.629956e-04	k: 305	n:940000
CPNE3   940000 perm   567 sec   (1657 perm/sec)   p_kst 3.244681e-04   p_cons 9.714660e-01   p_joint 3.244681e-04

Joint ci ratio: 2.233264e-01	ci left: 2.880211e-04	ci right 3.613977e-04	k: 307	n:950000
Cons ci ratio: 6.893858e-04	ci left: 9.711211e-01	ci right 9.717918e-01	k: 922885	n:950000
KS ci ratio: 2.233264e-01	ci left: 2.880211e-04	ci right 3.613977e-04	k: 307	n:950000
CPNE3   950000 perm   577 sec   (1646 perm/sec)   p_kst 3.231579e-04   p_cons 9.714579e-01   p_joint 3.231579e-04

Joint ci ratio: 2.215353e-01	ci left: 2.899391e-04	ci right 3.631311e-04	k: 312	n:960000
Cons ci ratio: 6.857804e-04	ci left: 9.711233e-01	ci right 9.717905e-01	k: 932600	n:960000
KS ci ratio: 2.215353e-01	ci left: 2.899391e-04	ci right 3.631311e-04	k: 312	n:960000
CPNE3   960000 perm   587 sec   (1635 perm/sec)   p_kst 3.250000e-04   p_cons 9.714583e-01   p_joint 3.250000e-04

Joint ci ratio: 2.201330e-01	ci left: 2.908457e-04	ci right 3.637389e-04	k: 316	n:970000
Cons ci ratio: 6.824464e-04	ci left: 9.711078e-01	ci right 9.717718e-01	k: 942298	n:970000
KS ci ratio: 2.201330e-01	ci left: 2.908457e-04	ci right 3.637389e-04	k: 316	n:970000
CPNE3   970000 perm   597 sec   (1624 perm/sec)   p_kst 3.257732e-04   p_cons 9.714412e-01   p_joint 3.257732e-04

Joint ci ratio: 2.194420e-01	ci left: 2.898063e-04	ci right 3.621803e-04	k: 318	n:980000
Cons ci ratio: 6.788608e-04	ci left: 9.711173e-01	ci right 9.717778e-01	k: 952020	n:980000
KS ci ratio: 2.194420e-01	ci left: 2.898063e-04	ci right 3.621803e-04	k: 318	n:980000
CPNE3   980000 perm   608 sec   (1613 perm/sec)   p_kst 3.244898e-04   p_cons 9.714490e-01   p_joint 3.244898e-04

Joint ci ratio: 2.180789e-01	ci left: 2.906980e-04	ci right 3.627833e-04	k: 322	n:990000
Cons ci ratio: 6.753556e-04	ci left: 9.711246e-01	ci right 9.717817e-01	k: 961740	n:990000
KS ci ratio: 2.180789e-01	ci left: 2.906980e-04	ci right 3.627833e-04	k: 322	n:990000
CPNE3   990000 perm   618 sec   (1602 perm/sec)   p_kst 3.252525e-04   p_cons 9.714545e-01   p_joint 3.252525e-04

Joint ci ratio: 2.167409e-01	ci left: 2.915733e-04	ci right 3.633730e-04	k: 326	n:1000000
Cons ci ratio: 6.719890e-04	ci left: 9.711247e-01	ci right 9.717785e-01	k: 971453	n:1000000
KS ci ratio: 2.167409e-01	ci left: 2.915733e-04	ci right 3.633730e-04	k: 326	n:1000000
CPNE3   1000000 perm   628 sec   (1592 perm/sec)   p_kst 3.260000e-04   p_cons 9.714530e-01   p_joint 3.260000e-04

Joint ci ratio: 2.147792e-01	ci left: 2.943060e-04	ci right 3.660363e-04	k: 332	n:1010000
Cons ci ratio: 6.686244e-04	ci left: 9.711288e-01	ci right 9.717793e-01	k: 981170	n:1010000
KS ci ratio: 2.147792e-01	ci left: 2.943060e-04	ci right 3.660363e-04	k: 332	n:1010000
CPNE3   1010000 perm   639 sec   (1581 perm/sec)   p_kst 3.287129e-04   p_cons 9.714554e-01   p_joint 3.287129e-04

Joint ci ratio: 2.141372e-01	ci left: 2.932761e-04	ci right 3.645136e-04	k: 334	n:1020000
Cons ci ratio: 6.653570e-04	ci left: 9.711289e-01	ci right 9.717762e-01	k: 990883	n:1020000
KS ci ratio: 2.141372e-01	ci left: 2.932761e-04	ci right 3.645136e-04	k: 334	n:1020000
CPNE3   1020000 perm   649 sec   (1571 perm/sec)   p_kst 3.274510e-04   p_cons 9.714539e-01   p_joint 3.274510e-04

Joint ci ratio: 2.119340e-01	ci left: 2.968624e-04	ci right 3.681327e-04	k: 341	n:1030000
Cons ci ratio: 6.622297e-04	ci left: 9.711212e-01	ci right 9.717655e-01	k: 1000588	n:1030000
KS ci ratio: 2.119340e-01	ci left: 2.968624e-04	ci right 3.681327e-04	k: 341	n:1030000
CPNE3   1030000 perm   660 sec   (1560 perm/sec)   p_kst 3.310680e-04   p_cons 9.714447e-01   p_joint 3.310680e-04

Joint ci ratio: 2.110106e-01	ci left: 2.967398e-04	ci right 3.676302e-04	k: 344	n:1040000
Cons ci ratio: 6.588261e-04	ci left: 9.711407e-01	ci right 9.717817e-01	k: 1010321	n:1040000
KS ci ratio: 2.110106e-01	ci left: 2.967398e-04	ci right 3.676302e-04	k: 344	n:1040000
CPNE3   1040000 perm   671 sec   (1549 perm/sec)   p_kst 3.307692e-04   p_cons 9.714625e-01   p_joint 3.307692e-04

Joint ci ratio: 2.100991e-01	ci left: 2.966202e-04	ci right 3.671365e-04	k: 347	n:1050000
Cons ci ratio: 6.557559e-04	ci left: 9.711359e-01	ci right 9.717739e-01	k: 1020029	n:1050000
KS ci ratio: 2.100991e-01	ci left: 2.966202e-04	ci right 3.671365e-04	k: 347	n:1050000
CPNE3   1050000 perm   682 sec   (1540 perm/sec)   p_kst 3.304762e-04   p_cons 9.714562e-01   p_joint 3.304762e-04

Joint ci ratio: 2.091994e-01	ci left: 2.965035e-04	ci right 3.666515e-04	k: 350	n:1060000
Cons ci ratio: 6.524838e-04	ci left: 9.711521e-01	ci right 9.717869e-01	k: 1029759	n:1060000
KS ci ratio: 2.091994e-01	ci left: 2.965035e-04	ci right 3.666515e-04	k: 350	n:1060000
CPNE3   1060000 perm   693 sec   (1530 perm/sec)   p_kst 3.301887e-04   p_cons 9.714708e-01   p_joint 3.301887e-04

Joint ci ratio: 2.089022e-01	ci left: 2.946181e-04	ci right 3.642083e-04	k: 351	n:1070000
Cons ci ratio: 6.496215e-04	ci left: 9.711369e-01	ci right 9.717689e-01	k: 1039456	n:1070000
KS ci ratio: 2.089022e-01	ci left: 2.946181e-04	ci right 3.642083e-04	k: 351	n:1070000
CPNE3   1070000 perm   704 sec   (1520 perm/sec)   p_kst 3.280374e-04   p_cons 9.714542e-01   p_joint 3.280374e-04

Joint ci ratio: 2.074340e-01	ci left: 2.962785e-04	ci right 3.657066e-04	k: 356	n:1080000
Cons ci ratio: 6.465588e-04	ci left: 9.711426e-01	ci right 9.717716e-01	k: 1049175	n:1080000
KS ci ratio: 2.074340e-01	ci left: 2.962785e-04	ci right 3.657066e-04	k: 356	n:1080000
CPNE3   1080000 perm   715 sec   (1511 perm/sec)   p_kst 3.296296e-04   p_cons 9.714583e-01   p_joint 3.296296e-04

Joint ci ratio: 2.068555e-01	ci left: 2.953000e-04	ci right 3.642815e-04	k: 358	n:1090000
Cons ci ratio: 6.435070e-04	ci left: 9.711509e-01	ci right 9.717769e-01	k: 1058897	n:1090000
KS ci ratio: 2.068555e-01	ci left: 2.953000e-04	ci right 3.642815e-04	k: 358	n:1090000
CPNE3   1090000 perm   726 sec   (1501 perm/sec)   p_kst 3.284404e-04   p_cons 9.714651e-01   p_joint 3.284404e-04

Joint ci ratio: 2.065682e-01	ci left: 2.934774e-04	ci right 3.619259e-04	k: 359	n:1100000
Cons ci ratio: 6.406976e-04	ci left: 9.711417e-01	ci right 9.717650e-01	k: 1068600	n:1100000
KS ci ratio: 2.065682e-01	ci left: 2.934774e-04	ci right 3.619259e-04	k: 359	n:1100000
CPNE3   1100000 perm   738 sec   (1491 perm/sec)   p_kst 3.263636e-04   p_cons 9.714545e-01   p_joint 3.263636e-04

Joint ci ratio: 2.051483e-01	ci left: 2.951058e-04	ci right 3.634017e-04	k: 364	n:1110000
Cons ci ratio: 6.377070e-04	ci left: 9.711516e-01	ci right 9.717720e-01	k: 1078324	n:1110000
KS ci ratio: 2.051483e-01	ci left: 2.951058e-04	ci right 3.634017e-04	k: 364	n:1110000
CPNE3   1110000 perm   749 sec   (1482 perm/sec)   p_kst 3.279279e-04   p_cons 9.714631e-01   p_joint 3.279279e-04

Joint ci ratio: 2.043105e-01	ci left: 2.950122e-04	ci right 3.629727e-04	k: 367	n:1120000
Cons ci ratio: 6.350134e-04	ci left: 9.711390e-01	ci right 9.717568e-01	k: 1088023	n:1120000
KS ci ratio: 2.043105e-01	ci left: 2.950122e-04	ci right 3.629727e-04	k: 367	n:1120000
CPNE3   1120000 perm   761 sec   (1472 perm/sec)   p_kst 3.276786e-04   p_cons 9.714491e-01   p_joint 3.276786e-04

Joint ci ratio: 2.034828e-01	ci left: 2.949208e-04	ci right 3.625508e-04	k: 370	n:1130000
Cons ci ratio: 6.322627e-04	ci left: 9.711346e-01	ci right 9.717497e-01	k: 1097731	n:1130000
KS ci ratio: 2.034828e-01	ci left: 2.949208e-04	ci right 3.625508e-04	k: 370	n:1130000
CPNE3   1130000 perm   772 sec   (1464 perm/sec)   p_kst 3.274336e-04   p_cons 9.714434e-01   p_joint 3.274336e-04

Joint ci ratio: 2.023945e-01	ci left: 2.956643e-04	ci right 3.630574e-04	k: 374	n:1140000
Cons ci ratio: 6.296371e-04	ci left: 9.711224e-01	ci right 9.717349e-01	k: 1107430	n:1140000
KS ci ratio: 2.023945e-01	ci left: 2.956643e-04	ci right 3.630574e-04	k: 374	n:1140000
CPNE3   1140000 perm   784 sec   (1454 perm/sec)   p_kst 3.280702e-04   p_cons 9.714298e-01   p_joint 3.280702e-04

Joint ci ratio: 2.015898e-01	ci left: 2.955700e-04	ci right 3.626408e-04	k: 377	n:1150000
Cons ci ratio: 6.269848e-04	ci left: 9.711156e-01	ci right 9.717255e-01	k: 1117135	n:1150000
KS ci ratio: 2.015898e-01	ci left: 2.955700e-04	ci right 3.626408e-04	k: 377	n:1150000
CPNE3   1150000 perm   796 sec   (1445 perm/sec)   p_kst 3.278261e-04   p_cons 9.714217e-01   p_joint 3.278261e-04

Joint ci ratio: 2.002695e-01	ci left: 2.971155e-04	ci right 3.640415e-04	k: 382	n:1160000
Cons ci ratio: 6.240264e-04	ci left: 9.711393e-01	ci right 9.717463e-01	k: 1126875	n:1160000
KS ci ratio: 2.002695e-01	ci left: 2.971155e-04	ci right 3.640415e-04	k: 382	n:1160000
CPNE3   1160000 perm   808 sec   (1436 perm/sec)   p_kst 3.293103e-04   p_cons 9.714440e-01   p_joint 3.293103e-04

Joint ci ratio: 1.997487e-01	ci left: 2.961999e-04	ci right 3.627249e-04	k: 384	n:1170000
Cons ci ratio: 6.213293e-04	ci left: 9.711428e-01	ci right 9.717472e-01	k: 1136592	n:1170000
KS ci ratio: 1.997487e-01	ci left: 2.961999e-04	ci right 3.627249e-04	k: 384	n:1170000
CPNE3   1170000 perm   820 sec   (1427 perm/sec)   p_kst 3.282051e-04   p_cons 9.714462e-01   p_joint 3.282051e-04

Joint ci ratio: 1.989750e-01	ci left: 2.961052e-04	ci right 3.623201e-04	k: 387	n:1180000
Cons ci ratio: 6.187330e-04	ci left: 9.711403e-01	ci right 9.717422e-01	k: 1146302	n:1180000
KS ci ratio: 1.989750e-01	ci left: 2.961052e-04	ci right 3.623201e-04	k: 387	n:1180000
CPNE3   1180000 perm   832 sec   (1419 perm/sec)   p_kst 3.279661e-04   p_cons 9.714424e-01   p_joint 3.279661e-04

Joint ci ratio: 1.987193e-01	ci left: 2.944154e-04	ci right 3.601576e-04	k: 388	n:1190000
Cons ci ratio: 6.161317e-04	ci left: 9.711412e-01	ci right 9.717405e-01	k: 1156016	n:1190000
KS ci ratio: 1.987193e-01	ci left: 2.944154e-04	ci right 3.601576e-04	k: 388	n:1190000
CPNE3   1190000 perm   844 sec   (1410 perm/sec)   p_kst 3.260504e-04   p_cons 9.714420e-01   p_joint 3.260504e-04

Joint ci ratio: 1.984646e-01	ci left: 2.927538e-04	ci right 3.580310e-04	k: 389	n:1200000
Cons ci ratio: 6.139591e-04	ci left: 9.711061e-01	ci right 9.717033e-01	k: 1165687	n:1200000
KS ci ratio: 1.984646e-01	ci left: 2.927538e-04	ci right 3.580310e-04	k: 389	n:1200000
CPNE3   1200000 perm   856 sec   (1402 perm/sec)   p_kst 3.241667e-04   p_cons 9.714058e-01   p_joint 3.241667e-04

Joint ci ratio: 1.974545e-01	ci left: 2.934763e-04	ci right 3.585415e-04	k: 393	n:1210000
Cons ci ratio: 6.112353e-04	ci left: 9.711239e-01	ci right 9.717185e-01	k: 1175421	n:1210000
KS ci ratio: 1.974545e-01	ci left: 2.934763e-04	ci right 3.585415e-04	k: 393	n:1210000
CPNE3   1210000 perm   868 sec   (1394 perm/sec)   p_kst 3.247934e-04   p_cons 9.714223e-01   p_joint 3.247934e-04

Joint ci ratio: 1.969554e-01	ci left: 2.926291e-04	ci right 3.573228e-04	k: 395	n:1220000
Cons ci ratio: 6.084754e-04	ci left: 9.711480e-01	ci right 9.717399e-01	k: 1185163	n:1220000
KS ci ratio: 1.969554e-01	ci left: 2.926291e-04	ci right 3.573228e-04	k: 395	n:1220000
CPNE3   1220000 perm   880 sec   (1386 perm/sec)   p_kst 3.237705e-04   p_cons 9.714451e-01   p_joint 3.237705e-04

Joint ci ratio: 1.964600e-01	ci left: 2.917959e-04	ci right 3.561238e-04	k: 397	n:1230000
Cons ci ratio: 6.059919e-04	ci left: 9.711497e-01	ci right 9.717392e-01	k: 1194878	n:1230000
KS ci ratio: 1.964600e-01	ci left: 2.917959e-04	ci right 3.561238e-04	k: 397	n:1230000
CPNE3   1230000 perm   893 sec   (1378 perm/sec)   p_kst 3.227642e-04   p_cons 9.714455e-01   p_joint 3.227642e-04

Joint ci ratio: 1.957237e-01	ci left: 2.917433e-04	ci right 3.557898e-04	k: 400	n:1240000
Cons ci ratio: 6.034684e-04	ci left: 9.711578e-01	ci right 9.717448e-01	k: 1204601	n:1240000
KS ci ratio: 1.957237e-01	ci left: 2.917433e-04	ci right 3.557898e-04	k: 400	n:1240000
CPNE3   1240000 perm   905 sec   (1370 perm/sec)   p_kst 3.225806e-04   p_cons 9.714524e-01   p_joint 3.225806e-04

Joint ci ratio: 1.942755e-01	ci left: 2.939751e-04	ci right 3.579775e-04	k: 406	n:1250000
Cons ci ratio: 6.010628e-04	ci left: 9.711578e-01	ci right 9.717424e-01	k: 1214314	n:1250000
KS ci ratio: 1.942755e-01	ci left: 2.939751e-04	ci right 3.579775e-04	k: 406	n:1250000
CPNE3   1250000 perm   918 sec   (1362 perm/sec)   p_kst 3.248000e-04   p_cons 9.714512e-01   p_joint 3.248000e-04

Joint ci ratio: 1.935634e-01	ci left: 2.939073e-04	ci right 3.576328e-04	k: 409	n:1260000
Cons ci ratio: 5.989085e-04	ci left: 9.711370e-01	ci right 9.717196e-01	k: 1224001	n:1260000
KS ci ratio: 1.935634e-01	ci left: 2.939073e-04	ci right 3.576328e-04	k: 409	n:1260000
CPNE3   1260000 perm   930 sec   (1355 perm/sec)   p_kst 3.246032e-04   p_cons 9.714294e-01   p_joint 3.246032e-04

Joint ci ratio: 1.919316e-01	ci left: 2.968390e-04	ci right 3.605942e-04	k: 416	n:1270000
Cons ci ratio: 5.966837e-04	ci left: 9.711253e-01	ci right 9.717057e-01	k: 1233699	n:1270000
KS ci ratio: 1.919316e-01	ci left: 2.968390e-04	ci right 3.605942e-04	k: 416	n:1270000
CPNE3   1270000 perm   943 sec   (1347 perm/sec)   p_kst 3.275591e-04   p_cons 9.714165e-01   p_joint 3.275591e-04

Joint ci ratio: 1.914731e-01	ci left: 2.960074e-04	ci right 3.594145e-04	k: 418	n:1280000
Cons ci ratio: 5.943831e-04	ci left: 9.711231e-01	ci right 9.717013e-01	k: 1243409	n:1280000
KS ci ratio: 1.914731e-01	ci left: 2.960074e-04	ci right 3.594145e-04	k: 418	n:1280000
CPNE3   1280000 perm   956 sec   (1340 perm/sec)   p_kst 3.265625e-04   p_cons 9.714133e-01   p_joint 3.265625e-04

Joint ci ratio: 1.905656e-01	ci left: 2.966653e-04	ci right 3.598772e-04	k: 422	n:1290000
Cons ci ratio: 5.920015e-04	ci left: 9.711312e-01	ci right 9.717070e-01	k: 1253132	n:1290000
KS ci ratio: 1.905656e-01	ci left: 2.966653e-04	ci right 3.598772e-04	k: 422	n:1290000
CPNE3   1290000 perm   968 sec   (1332 perm/sec)   p_kst 3.271318e-04   p_cons 9.714202e-01   p_joint 3.271318e-04

Joint ci ratio: 1.896709e-01	ci left: 2.973137e-04	ci right 3.603321e-04	k: 426	n:1300000
Cons ci ratio: 5.899586e-04	ci left: 9.711097e-01	ci right 9.716836e-01	k: 1262817	n:1300000
KS ci ratio: 1.896709e-01	ci left: 2.973137e-04	ci right 3.603321e-04	k: 426	n:1300000
CPNE3   1300000 perm   982 sec   (1324 perm/sec)   p_kst 3.276923e-04   p_cons 9.713977e-01   p_joint 3.276923e-04

Joint ci ratio: 1.885699e-01	ci left: 2.986803e-04	ci right 3.615787e-04	k: 431	n:1310000
Cons ci ratio: 5.877911e-04	ci left: 9.711024e-01	ci right 9.716741e-01	k: 1272520	n:1310000
KS ci ratio: 1.885699e-01	ci left: 2.986803e-04	ci right 3.615787e-04	k: 431	n:1310000
CPNE3   1310000 perm   995 sec   (1317 perm/sec)   p_kst 3.290076e-04   p_cons 9.713893e-01   p_joint 3.290076e-04

Joint ci ratio: 1.879186e-01	ci left: 2.985832e-04	ci right 3.612192e-04	k: 434	n:1320000
Cons ci ratio: 5.854318e-04	ci left: 9.711158e-01	ci right 9.716852e-01	k: 1282250	n:1320000
KS ci ratio: 1.879186e-01	ci left: 2.985832e-04	ci right 3.612192e-04	k: 434	n:1320000
CPNE3   1320000 perm   1008 sec   (1310 perm/sec)   p_kst 3.287879e-04   p_cons 9.714015e-01   p_joint 3.287879e-04

Joint ci ratio: 1.872739e-01	ci left: 2.984879e-04	ci right 3.608647e-04	k: 437	n:1330000
Cons ci ratio: 5.832663e-04	ci left: 9.711131e-01	ci right 9.716804e-01	k: 1291959	n:1330000
KS ci ratio: 1.872739e-01	ci left: 2.984879e-04	ci right 3.608647e-04	k: 437	n:1330000
CPNE3   1330000 perm   1021 sec   (1303 perm/sec)   p_kst 3.285714e-04   p_cons 9.713977e-01   p_joint 3.285714e-04

Joint ci ratio: 1.862140e-01	ci left: 2.998173e-04	ci right 3.620772e-04	k: 442	n:1340000
Cons ci ratio: 5.811403e-04	ci left: 9.711089e-01	ci right 9.716741e-01	k: 1301666	n:1340000
KS ci ratio: 1.862140e-01	ci left: 2.998173e-04	ci right 3.620772e-04	k: 442	n:1340000
CPNE3   1340000 perm   1034 sec   (1295 perm/sec)   p_kst 3.298507e-04   p_cons 9.713925e-01   p_joint 3.298507e-04

Joint ci ratio: 1.857951e-01	ci left: 2.990089e-04	ci right 3.609456e-04	k: 444	n:1350000
Cons ci ratio: 5.788829e-04	ci left: 9.711197e-01	ci right 9.716827e-01	k: 1311393	n:1350000
KS ci ratio: 1.857951e-01	ci left: 2.990089e-04	ci right 3.609456e-04	k: 444	n:1350000
CPNE3   1350000 perm   1048 sec   (1289 perm/sec)   p_kst 3.288889e-04   p_cons 9.714022e-01   p_joint 3.288889e-04

Joint ci ratio: 1.851720e-01	ci left: 2.989138e-04	ci right 3.605998e-04	k: 447	n:1360000
Cons ci ratio: 5.768120e-04	ci left: 9.711148e-01	ci right 9.716758e-01	k: 1321099	n:1360000
KS ci ratio: 1.851720e-01	ci left: 2.989138e-04	ci right 3.605998e-04	k: 447	n:1360000
CPNE3   1360000 perm   1061 sec   (1281 perm/sec)   p_kst 3.286765e-04   p_cons 9.713963e-01   p_joint 3.286765e-04

Joint ci ratio: 1.839442e-01	ci left: 3.009092e-04	ci right 3.625493e-04	k: 453	n:1370000
Cons ci ratio: 5.748838e-04	ci left: 9.710983e-01	ci right 9.716574e-01	k: 1330789	n:1370000
KS ci ratio: 1.839442e-01	ci left: 3.009092e-04	ci right 3.625493e-04	k: 453	n:1370000
CPNE3   1370000 perm   1075 sec   (1274 perm/sec)   p_kst 3.306569e-04   p_cons 9.713788e-01   p_joint 3.306569e-04

Joint ci ratio: 1.829394e-01	ci left: 3.021855e-04	ci right 3.637115e-04	k: 458	n:1380000
Cons ci ratio: 5.728104e-04	ci left: 9.710980e-01	ci right 9.716551e-01	k: 1340501	n:1380000
KS ci ratio: 1.829394e-01	ci left: 3.021855e-04	ci right 3.637115e-04	k: 458	n:1380000
CPNE3   1380000 perm   1089 sec   (1267 perm/sec)   p_kst 3.318841e-04   p_cons 9.713775e-01   p_joint 3.318841e-04

Joint ci ratio: 1.823445e-01	ci left: 3.020711e-04	ci right 3.633517e-04	k: 461	n:1390000
Cons ci ratio: 5.704417e-04	ci left: 9.711288e-01	ci right 9.716836e-01	k: 1350256	n:1390000
KS ci ratio: 1.823445e-01	ci left: 3.020711e-04	ci right 3.633517e-04	k: 461	n:1390000
CPNE3   1390000 perm   1103 sec   (1260 perm/sec)   p_kst 3.316547e-04   p_cons 9.714072e-01   p_joint 3.316547e-04

Joint ci ratio: 1.817554e-01	ci left: 3.019587e-04	ci right 3.629967e-04	k: 464	n:1400000
Cons ci ratio: 5.683062e-04	ci left: 9.711391e-01	ci right 9.716918e-01	k: 1359983	n:1400000
KS ci ratio: 1.817554e-01	ci left: 3.019587e-04	ci right 3.629967e-04	k: 464	n:1400000
CPNE3   1400000 perm   1117 sec   (1254 perm/sec)   p_kst 3.314286e-04   p_cons 9.714164e-01   p_joint 3.314286e-04

Joint ci ratio: 1.815604e-01	ci left: 3.004941e-04	ci right 3.611637e-04	k: 465	n:1410000
Cons ci ratio: 5.665054e-04	ci left: 9.711186e-01	ci right 9.716696e-01	k: 1369667	n:1410000
KS ci ratio: 1.815604e-01	ci left: 3.004941e-04	ci right 3.611637e-04	k: 465	n:1410000
CPNE3   1410000 perm   1131 sec   (1247 perm/sec)   p_kst 3.297872e-04   p_cons 9.713950e-01   p_joint 3.297872e-04

Joint ci ratio: 1.804026e-01	ci left: 3.024119e-04	ci right 3.630369e-04	k: 471	n:1420000
Cons ci ratio: 5.643923e-04	ci left: 9.711309e-01	ci right 9.716798e-01	k: 1379397	n:1420000
KS ci ratio: 1.804026e-01	ci left: 3.024119e-04	ci right 3.630369e-04	k: 471	n:1420000
CPNE3   1420000 perm   1146 sec   (1240 perm/sec)   p_kst 3.316901e-04   p_cons 9.714063e-01   p_joint 3.316901e-04

Joint ci ratio: 1.796429e-01	ci left: 3.029683e-04	ci right 3.634212e-04	k: 475	n:1430000
Cons ci ratio: 5.625645e-04	ci left: 9.711171e-01	ci right 9.716642e-01	k: 1389090	n:1430000
KS ci ratio: 1.796429e-01	ci left: 3.029683e-04	ci right 3.634212e-04	k: 475	n:1430000
CPNE3   1430000 perm   1160 sec   (1233 perm/sec)   p_kst 3.321678e-04   p_cons 9.713916e-01   p_joint 3.321678e-04

Joint ci ratio: 1.790795e-01	ci left: 3.028541e-04	ci right 3.630743e-04	k: 478	n:1440000
Cons ci ratio: 5.606001e-04	ci left: 9.711188e-01	ci right 9.716640e-01	k: 1398805	n:1440000
KS ci ratio: 1.790795e-01	ci left: 3.028541e-04	ci right 3.630743e-04	k: 478	n:1440000
CPNE3   1440000 perm   1174 sec   (1226 perm/sec)   p_kst 3.319444e-04   p_cons 9.713924e-01   p_joint 3.319444e-04

Joint ci ratio: 1.779682e-01	ci left: 3.047185e-04	ci right 3.648929e-04	k: 484	n:1450000
Cons ci ratio: 5.587670e-04	ci left: 9.711094e-01	ci right 9.716529e-01	k: 1408504	n:1450000
KS ci ratio: 1.779682e-01	ci left: 3.047185e-04	ci right 3.648929e-04	k: 484	n:1450000
CPNE3   1450000 perm   1189 sec   (1220 perm/sec)   p_kst 3.337931e-04   p_cons 9.713821e-01   p_joint 3.337931e-04

Joint ci ratio: 1.776025e-01	ci left: 3.039403e-04	ci right 3.638244e-04	k: 486	n:1460000
Cons ci ratio: 5.567391e-04	ci left: 9.711215e-01	ci right 9.716630e-01	k: 1418234	n:1460000
KS ci ratio: 1.776025e-01	ci left: 3.039403e-04	ci right 3.638244e-04	k: 486	n:1460000
CPNE3   1460000 perm   1203 sec   (1213 perm/sec)   p_kst 3.328767e-04   p_cons 9.713932e-01   p_joint 3.328767e-04

Joint ci ratio: 1.766976e-01	ci left: 3.051233e-04	ci right 3.649014e-04	k: 491	n:1470000
Cons ci ratio: 5.550115e-04	ci left: 9.711054e-01	ci right 9.716452e-01	k: 1427923	n:1470000
KS ci ratio: 1.766976e-01	ci left: 3.051233e-04	ci right 3.649014e-04	k: 491	n:1470000
CPNE3   1470000 perm   1218 sec   (1207 perm/sec)   p_kst 3.340136e-04   p_cons 9.713762e-01   p_joint 3.340136e-04

Joint ci ratio: 1.763396e-01	ci left: 3.043533e-04	ci right 3.638469e-04	k: 493	n:1480000
Cons ci ratio: 5.530846e-04	ci left: 9.711112e-01	ci right 9.716491e-01	k: 1437644	n:1480000
KS ci ratio: 1.763396e-01	ci left: 3.043533e-04	ci right 3.638469e-04	k: 493	n:1480000
CPNE3   1480000 perm   1232 sec   (1201 perm/sec)   p_kst 3.331081e-04   p_cons 9.713811e-01   p_joint 3.331081e-04

Joint ci ratio: 1.763398e-01	ci left: 3.023106e-04	ci right 3.614050e-04	k: 493	n:1490000
Cons ci ratio: 5.513639e-04	ci left: 9.710981e-01	ci right 9.716343e-01	k: 1447337	n:1490000
KS ci ratio: 1.763398e-01	ci left: 3.023106e-04	ci right 3.614050e-04	k: 493	n:1490000
CPNE3   1490000 perm   1246 sec   (1195 perm/sec)   p_kst 3.308725e-04   p_cons 9.713671e-01   p_joint 3.308725e-04

Joint ci ratio: 1.758068e-01	ci left: 3.022070e-04	ci right 3.610837e-04	k: 496	n:1500000
Cons ci ratio: 5.496919e-04	ci left: 9.710818e-01	ci right 9.716164e-01	k: 1457025	n:1500000
KS ci ratio: 1.758068e-01	ci left: 3.022070e-04	ci right 3.610837e-04	k: 496	n:1500000
CPNE3   1500000 perm   1262 sec   (1189 perm/sec)   p_kst 3.306667e-04   p_cons 9.713500e-01   p_joint 3.306667e-04

Joint ci ratio: 1.747550e-01	ci left: 3.040049e-04	ci right 3.628400e-04	k: 502	n:1510000
Cons ci ratio: 5.476763e-04	ci left: 9.711023e-01	ci right 9.716350e-01	k: 1466768	n:1510000
KS ci ratio: 1.747550e-01	ci left: 3.040049e-04	ci right 3.628400e-04	k: 502	n:1510000
CPNE3   1510000 perm   1277 sec   (1183 perm/sec)   p_kst 3.324503e-04   p_cons 9.713695e-01   p_joint 3.324503e-04

Joint ci ratio: 1.738928e-01	ci left: 3.051508e-04	ci right 3.638858e-04	k: 507	n:1520000
Cons ci ratio: 5.458440e-04	ci left: 9.711060e-01	ci right 9.716369e-01	k: 1476486	n:1520000
KS ci ratio: 1.738928e-01	ci left: 3.051508e-04	ci right 3.638858e-04	k: 507	n:1520000
CPNE3   1520000 perm   1292 sec   (1177 perm/sec)   p_kst 3.335526e-04   p_cons 9.713724e-01   p_joint 3.335526e-04

Joint ci ratio: 1.732121e-01	ci left: 3.056572e-04	ci right 3.642352e-04	k: 511	n:1530000
Cons ci ratio: 5.441258e-04	ci left: 9.710999e-01	ci right 9.716291e-01	k: 1486189	n:1530000
KS ci ratio: 1.732121e-01	ci left: 3.056572e-04	ci right 3.642352e-04	k: 511	n:1530000
CPNE3   1530000 perm   1307 sec   (1171 perm/sec)   p_kst 3.339869e-04   p_cons 9.713654e-01   p_joint 3.339869e-04

Joint ci ratio: 1.723724e-01	ci left: 3.067788e-04	ci right 3.652571e-04	k: 516	n:1540000
Cons ci ratio: 5.424363e-04	ci left: 9.710925e-01	ci right 9.716200e-01	k: 1495890	n:1540000
KS ci ratio: 1.723724e-01	ci left: 3.067788e-04	ci right 3.652571e-04	k: 516	n:1540000
CPNE3   1540000 perm   1325 sec   (1163 perm/sec)   p_kst 3.350649e-04   p_cons 9.713571e-01   p_joint 3.350649e-04

Joint ci ratio: 1.718745e-01	ci left: 3.066516e-04	ci right 3.649194e-04	k: 519	n:1550000
Cons ci ratio: 5.404741e-04	ci left: 9.711150e-01	ci right 9.716406e-01	k: 1505637	n:1550000
KS ci ratio: 1.718745e-01	ci left: 3.066516e-04	ci right 3.649194e-04	k: 519	n:1550000
CPNE3   1550000 perm   1340 sec   (1157 perm/sec)   p_kst 3.348387e-04   p_cons 9.713787e-01   p_joint 3.348387e-04

Joint ci ratio: 1.710540e-01	ci left: 3.077535e-04	ci right 3.659227e-04	k: 524	n:1560000
Cons ci ratio: 5.386258e-04	ci left: 9.711276e-01	ci right 9.716514e-01	k: 1515369	n:1560000
KS ci ratio: 1.710540e-01	ci left: 3.077535e-04	ci right 3.659227e-04	k: 524	n:1560000
CPNE3   1560000 perm   1355 sec   (1151 perm/sec)   p_kst 3.358974e-04   p_cons 9.713904e-01   p_joint 3.358974e-04

Joint ci ratio: 1.705674e-01	ci left: 3.076225e-04	ci right 3.655844e-04	k: 527	n:1570000
Cons ci ratio: 5.367348e-04	ci left: 9.711464e-01	ci right 9.716684e-01	k: 1525111	n:1570000
KS ci ratio: 1.705674e-01	ci left: 3.076225e-04	ci right 3.655844e-04	k: 527	n:1570000
CPNE3   1570000 perm   1370 sec   (1146 perm/sec)   p_kst 3.356688e-04   p_cons 9.714083e-01   p_joint 3.356688e-04

Joint ci ratio: 1.699249e-01	ci left: 3.080993e-04	ci right 3.659100e-04	k: 531	n:1580000
Cons ci ratio: 5.350219e-04	ci left: 9.711485e-01	ci right 9.716688e-01	k: 1534827	n:1580000
KS ci ratio: 1.699249e-01	ci left: 3.080993e-04	ci right 3.659100e-04	k: 531	n:1580000
CPNE3   1580000 perm   1386 sec   (1140 perm/sec)   p_kst 3.360759e-04   p_cons 9.714095e-01   p_joint 3.360759e-04

Joint ci ratio: 1.696064e-01	ci left: 3.073659e-04	ci right 3.649199e-04	k: 533	n:1590000
Cons ci ratio: 5.334943e-04	ci left: 9.711328e-01	ci right 9.716516e-01	k: 1544515	n:1590000
KS ci ratio: 1.696064e-01	ci left: 3.073659e-04	ci right 3.649199e-04	k: 533	n:1590000
CPNE3   1590000 perm   1401 sec   (1135 perm/sec)   p_kst 3.352201e-04   p_cons 9.713931e-01   p_joint 3.352201e-04

Joint ci ratio: 1.691320e-01	ci left: 3.072404e-04	ci right 3.645936e-04	k: 536	n:1600000
Cons ci ratio: 5.317822e-04	ci left: 9.711381e-01	ci right 9.716552e-01	k: 1554236	n:1600000
KS ci ratio: 1.691320e-01	ci left: 3.072404e-04	ci right 3.645936e-04	k: 536	n:1600000
CPNE3   1600000 perm   1423 sec   (1125 perm/sec)   p_kst 3.350000e-04   p_cons 9.713975e-01   p_joint 3.350000e-04

Joint ci ratio: 1.683500e-01	ci left: 3.083065e-04	ci right 3.655656e-04	k: 541	n:1610000
Cons ci ratio: 5.301339e-04	ci left: 9.711383e-01	ci right 9.716538e-01	k: 1563949	n:1610000
KS ci ratio: 1.683500e-01	ci left: 3.083065e-04	ci right 3.655656e-04	k: 541	n:1610000
CPNE3   1610000 perm   1439 sec   (1119 perm/sec)   p_kst 3.360248e-04   p_cons 9.713969e-01   p_joint 3.360248e-04

Joint ci ratio: 1.678861e-01	ci left: 3.081774e-04	ci right 3.652387e-04	k: 544	n:1620000
Cons ci ratio: 5.285242e-04	ci left: 9.711360e-01	ci right 9.716500e-01	k: 1573658	n:1620000
KS ci ratio: 1.678861e-01	ci left: 3.081774e-04	ci right 3.652387e-04	k: 544	n:1620000
CPNE3   1620000 perm   1455 sec   (1113 perm/sec)   p_kst 3.358025e-04   p_cons 9.713938e-01   p_joint 3.358025e-04

Joint ci ratio: 1.675789e-01	ci left: 3.074622e-04	ci right 3.642765e-04	k: 546	n:1630000
Cons ci ratio: 5.267663e-04	ci left: 9.711510e-01	ci right 9.716633e-01	k: 1583395	n:1630000
KS ci ratio: 1.675789e-01	ci left: 3.074622e-04	ci right 3.642765e-04	k: 546	n:1630000
CPNE3   1630000 perm   1471 sec   (1108 perm/sec)   p_kst 3.349693e-04   p_cons 9.714080e-01   p_joint 3.349693e-04

Joint ci ratio: 1.672735e-01	ci left: 3.067558e-04	ci right 3.633259e-04	k: 548	n:1640000
Cons ci ratio: 5.252678e-04	ci left: 9.711401e-01	ci right 9.716509e-01	k: 1593090	n:1640000
KS ci ratio: 1.672735e-01	ci left: 3.067558e-04	ci right 3.633259e-04	k: 548	n:1640000
CPNE3   1640000 perm   1487 sec   (1103 perm/sec)   p_kst 3.341463e-04   p_cons 9.713963e-01   p_joint 3.341463e-04

Joint ci ratio: 1.666674e-01	ci left: 3.072196e-04	ci right 3.636493e-04	k: 552	n:1650000
Cons ci ratio: 5.237420e-04	ci left: 9.711336e-01	ci right 9.716429e-01	k: 1602792	n:1650000
KS ci ratio: 1.666674e-01	ci left: 3.072196e-04	ci right 3.636493e-04	k: 552	n:1650000
CPNE3   1650000 perm   1503 sec   (1098 perm/sec)   p_kst 3.345455e-04   p_cons 9.713891e-01   p_joint 3.345455e-04

Joint ci ratio: 1.663669e-01	ci left: 3.065235e-04	ci right 3.627137e-04	k: 554	n:1660000
Cons ci ratio: 5.221727e-04	ci left: 9.711332e-01	ci right 9.716410e-01	k: 1612504	n:1660000
KS ci ratio: 1.663669e-01	ci left: 3.065235e-04	ci right 3.627137e-04	k: 554	n:1660000
CPNE3   1660000 perm   1519 sec   (1093 perm/sec)   p_kst 3.337349e-04   p_cons 9.713880e-01   p_joint 3.337349e-04

Joint ci ratio: 1.656224e-01	ci left: 3.075577e-04	ci right 3.636600e-04	k: 559	n:1670000
Cons ci ratio: 5.206287e-04	ci left: 9.711317e-01	ci right 9.716380e-01	k: 1622214	n:1670000
KS ci ratio: 1.656224e-01	ci left: 3.075577e-04	ci right 3.636600e-04	k: 559	n:1670000
CPNE3   1670000 perm   1535 sec   (1088 perm/sec)   p_kst 3.347305e-04   p_cons 9.713856e-01   p_joint 3.347305e-04

Joint ci ratio: 1.651806e-01	ci left: 3.074388e-04	ci right 3.633549e-04	k: 562	n:1680000
Cons ci ratio: 5.192039e-04	ci left: 9.711187e-01	ci right 9.716237e-01	k: 1631905	n:1680000
KS ci ratio: 1.651806e-01	ci left: 3.074388e-04	ci right 3.633549e-04	k: 562	n:1680000
CPNE3   1680000 perm   1551 sec   (1083 perm/sec)   p_kst 3.345238e-04   p_cons 9.713720e-01   p_joint 3.345238e-04

Joint ci ratio: 1.648880e-01	ci left: 3.067542e-04	ci right 3.624372e-04	k: 564	n:1690000
Cons ci ratio: 5.177631e-04	ci left: 9.711090e-01	ci right 9.716125e-01	k: 1641601	n:1690000
KS ci ratio: 1.648880e-01	ci left: 3.067542e-04	ci right 3.624372e-04	k: 564	n:1690000
CPNE3   1690000 perm   1568 sec   (1078 perm/sec)   p_kst 3.337278e-04   p_cons 9.713615e-01   p_joint 3.337278e-04

Joint ci ratio: 1.647424e-01	ci left: 3.055137e-04	ci right 3.609177e-04	k: 565	n:1700000
Cons ci ratio: 5.161376e-04	ci left: 9.711206e-01	ci right 9.716225e-01	k: 1651333	n:1700000
KS ci ratio: 1.647424e-01	ci left: 3.055137e-04	ci right 3.609177e-04	k: 565	n:1700000
CPNE3   1700000 perm   1584 sec   (1073 perm/sec)   p_kst 3.323529e-04   p_cons 9.713724e-01   p_joint 3.323529e-04

Joint ci ratio: 1.641633e-01	ci left: 3.059700e-04	ci right 3.612424e-04	k: 569	n:1710000
Cons ci ratio: 5.145706e-04	ci left: 9.711274e-01	ci right 9.716278e-01	k: 1661057	n:1710000
KS ci ratio: 1.641633e-01	ci left: 3.059700e-04	ci right 3.612424e-04	k: 569	n:1710000
CPNE3   1710000 perm   1600 sec   (1068 perm/sec)   p_kst 3.327485e-04   p_cons 9.713784e-01   p_joint 3.327485e-04

Joint ci ratio: 1.637330e-01	ci left: 3.058637e-04	ci right 3.609579e-04	k: 572	n:1720000
Cons ci ratio: 5.131518e-04	ci left: 9.711195e-01	ci right 9.716185e-01	k: 1670756	n:1720000
KS ci ratio: 1.637330e-01	ci left: 3.058637e-04	ci right 3.609579e-04	k: 572	n:1720000
CPNE3   1720000 perm   1617 sec   (1064 perm/sec)   p_kst 3.325581e-04   p_cons 9.713698e-01   p_joint 3.325581e-04

Joint ci ratio: 1.634481e-01	ci left: 3.052044e-04	ci right 3.600748e-04	k: 574	n:1730000
Cons ci ratio: 5.116915e-04	ci left: 9.711175e-01	ci right 9.716151e-01	k: 1680465	n:1730000
KS ci ratio: 1.634481e-01	ci left: 3.052044e-04	ci right 3.600748e-04	k: 574	n:1730000
CPNE3   1730000 perm   1633 sec   (1059 perm/sec)   p_kst 3.317919e-04   p_cons 9.713671e-01   p_joint 3.317919e-04

Joint ci ratio: 1.628825e-01	ci left: 3.056554e-04	ci right 3.603980e-04	k: 578	n:1740000
Cons ci ratio: 5.101435e-04	ci left: 9.711265e-01	ci right 9.716226e-01	k: 1690193	n:1740000
KS ci ratio: 1.628825e-01	ci left: 3.056554e-04	ci right 3.603980e-04	k: 578	n:1740000
CPNE3   1740000 perm   1650 sec   (1054 perm/sec)   p_kst 3.321839e-04   p_cons 9.713753e-01   p_joint 3.321839e-04

Joint ci ratio: 1.621836e-01	ci left: 3.066497e-04	ci right 3.613118e-04	k: 583	n:1750000
Cons ci ratio: 5.086721e-04	ci left: 9.711285e-01	ci right 9.716231e-01	k: 1699909	n:1750000
KS ci ratio: 1.621836e-01	ci left: 3.066497e-04	ci right 3.613118e-04	k: 583	n:1750000
CPNE3   1750000 perm   1667 sec   (1050 perm/sec)   p_kst 3.331429e-04   p_cons 9.713766e-01   p_joint 3.331429e-04

Joint ci ratio: 1.616310e-01	ci left: 3.070880e-04	ci right 3.616236e-04	k: 587	n:1760000
Cons ci ratio: 5.074154e-04	ci left: 9.711082e-01	ci right 9.716016e-01	k: 1709586	n:1760000
KS ci ratio: 1.616310e-01	ci left: 3.070880e-04	ci right 3.616236e-04	k: 587	n:1760000
CPNE3   1760000 perm   1687 sec   (1043 perm/sec)   p_kst 3.335227e-04   p_cons 9.713557e-01   p_joint 3.335227e-04

Joint ci ratio: 1.613569e-01	ci left: 3.064374e-04	ci right 3.607561e-04	k: 589	n:1770000
Cons ci ratio: 5.058493e-04	ci left: 9.711233e-01	ci right 9.716152e-01	k: 1719325	n:1770000
KS ci ratio: 1.613569e-01	ci left: 3.064374e-04	ci right 3.607561e-04	k: 589	n:1770000
CPNE3   1770000 perm   1706 sec   (1038 perm/sec)   p_kst 3.327684e-04   p_cons 9.713701e-01   p_joint 3.327684e-04

Joint ci ratio: 1.610842e-01	ci left: 3.057940e-04	ci right 3.598983e-04	k: 591	n:1780000
Cons ci ratio: 5.045165e-04	ci left: 9.711140e-01	ci right 9.716047e-01	k: 1729021	n:1780000
KS ci ratio: 1.610842e-01	ci left: 3.057940e-04	ci right 3.598983e-04	k: 591	n:1780000
CPNE3   1780000 perm   1724 sec   (1032 perm/sec)   p_kst 3.320225e-04   p_cons 9.713601e-01   p_joint 3.320225e-04

Joint ci ratio: 1.608128e-01	ci left: 3.051580e-04	ci right 3.590500e-04	k: 593	n:1790000
Cons ci ratio: 5.031133e-04	ci left: 9.711138e-01	ci right 9.716031e-01	k: 1738733	n:1790000
KS ci ratio: 1.608128e-01	ci left: 3.051580e-04	ci right 3.590500e-04	k: 593	n:1790000
CPNE3   1790000 perm   1742 sec   (1028 perm/sec)   p_kst 3.312849e-04   p_cons 9.713592e-01   p_joint 3.312849e-04

Joint ci ratio: 1.604083e-01	ci left: 3.050624e-04	ci right 3.587889e-04	k: 596	n:1800000
Cons ci ratio: 5.017669e-04	ci left: 9.711086e-01	ci right 9.715965e-01	k: 1748436	n:1800000
KS ci ratio: 1.604083e-01	ci left: 3.050624e-04	ci right 3.587889e-04	k: 596	n:1800000
CPNE3   1800000 perm   1759 sec   (1023 perm/sec)   p_kst 3.311111e-04   p_cons 9.713533e-01   p_joint 3.311111e-04

Joint ci ratio: 1.601403e-01	ci left: 3.044376e-04	ci right 3.579559e-04	k: 598	n:1810000
Cons ci ratio: 5.003467e-04	ci left: 9.711129e-01	ci right 9.715994e-01	k: 1758156	n:1810000
KS ci ratio: 1.601403e-01	ci left: 3.044376e-04	ci right 3.579559e-04	k: 598	n:1810000
CPNE3   1810000 perm   1776 sec   (1019 perm/sec)   p_kst 3.303867e-04   p_cons 9.713569e-01   p_joint 3.303867e-04

Joint ci ratio: 1.593441e-01	ci left: 3.059298e-04	ci right 3.594175e-04	k: 604	n:1820000
Cons ci ratio: 4.989434e-04	ci left: 9.711165e-01	ci right 9.716017e-01	k: 1767875	n:1820000
KS ci ratio: 1.593441e-01	ci left: 3.059298e-04	ci right 3.594175e-04	k: 604	n:1820000
CPNE3   1820000 perm   1794 sec   (1015 perm/sec)   p_kst 3.318681e-04   p_cons 9.713599e-01   p_joint 3.318681e-04

Joint ci ratio: 1.590815e-01	ci left: 3.053074e-04	ci right 3.585898e-04	k: 606	n:1830000
Cons ci ratio: 4.975812e-04	ci left: 9.711169e-01	ci right 9.716007e-01	k: 1777588	n:1830000
KS ci ratio: 1.590815e-01	ci left: 3.053074e-04	ci right 3.585898e-04	k: 606	n:1830000
CPNE3   1830000 perm   1811 sec   (1010 perm/sec)   p_kst 3.311475e-04   p_cons 9.713596e-01   p_joint 3.311475e-04

Joint ci ratio: 1.588201e-01	ci left: 3.046918e-04	ci right 3.577712e-04	k: 608	n:1840000
Cons ci ratio: 4.963125e-04	ci left: 9.711079e-01	ci right 9.715906e-01	k: 1787284	n:1840000
KS ci ratio: 1.588201e-01	ci left: 3.046918e-04	ci right 3.577712e-04	k: 608	n:1840000
CPNE3   1840000 perm   1828 sec   (1006 perm/sec)   p_kst 3.304348e-04   p_cons 9.713500e-01   p_joint 3.304348e-04

Joint ci ratio: 1.577869e-01	ci left: 3.071979e-04	ci right 3.603327e-04	k: 616	n:1850000
Cons ci ratio: 4.950198e-04	ci left: 9.711029e-01	ci right 9.715843e-01	k: 1796987	n:1850000
KS ci ratio: 1.577869e-01	ci left: 3.071979e-04	ci right 3.603327e-04	k: 616	n:1850000
CPNE3   1850000 perm   1846 sec   (1002 perm/sec)   p_kst 3.329730e-04   p_cons 9.713443e-01   p_joint 3.329730e-04

Joint ci ratio: 1.575318e-01	ci left: 3.065791e-04	ci right 3.595131e-04	k: 618	n:1860000
Cons ci ratio: 4.937037e-04	ci left: 9.711017e-01	ci right 9.715818e-01	k: 1806697	n:1860000
KS ci ratio: 1.575318e-01	ci left: 3.065791e-04	ci right 3.595131e-04	k: 618	n:1860000
CPNE3   1860000 perm   1864 sec   (998 perm/sec)   p_kst 3.322581e-04   p_cons 9.713425e-01   p_joint 3.322581e-04

Joint ci ratio: 1.570253e-01	ci left: 3.069945e-04	ci right 3.598137e-04	k: 622	n:1870000
Cons ci ratio: 4.924690e-04	ci left: 9.710925e-01	ci right 9.715713e-01	k: 1816392	n:1870000
KS ci ratio: 1.570253e-01	ci left: 3.069945e-04	ci right 3.598137e-04	k: 622	n:1870000
CPNE3   1870000 perm   1882 sec   (993 perm/sec)   p_kst 3.326203e-04   p_cons 9.713326e-01   p_joint 3.326203e-04

Joint ci ratio: 1.566486e-01	ci left: 3.068947e-04	ci right 3.595581e-04	k: 625	n:1880000
Cons ci ratio: 4.910933e-04	ci left: 9.711004e-01	ci right 9.715779e-01	k: 1826119	n:1880000
KS ci ratio: 1.566486e-01	ci left: 3.068947e-04	ci right 3.595581e-04	k: 625	n:1880000
CPNE3   1880000 perm   1905 sec   (987 perm/sec)   p_kst 3.324468e-04   p_cons 9.713399e-01   p_joint 3.324468e-04

Joint ci ratio: 1.562746e-01	ci left: 3.067961e-04	ci right 3.593051e-04	k: 628	n:1890000
Cons ci ratio: 4.898687e-04	ci left: 9.710923e-01	ci right 9.715687e-01	k: 1835816	n:1890000
KS ci ratio: 1.562746e-01	ci left: 3.067961e-04	ci right 3.593051e-04	k: 628	n:1890000
CPNE3   1890000 perm   1923 sec   (983 perm/sec)   p_kst 3.322751e-04   p_cons 9.713312e-01   p_joint 3.322751e-04

Joint ci ratio: 1.559033e-01	ci left: 3.066986e-04	ci right 3.590546e-04	k: 631	n:1900000
Cons ci ratio: 4.886624e-04	ci left: 9.710833e-01	ci right 9.715584e-01	k: 1845511	n:1900000
KS ci ratio: 1.559033e-01	ci left: 3.066986e-04	ci right 3.590546e-04	k: 631	n:1900000
CPNE3   1900000 perm   1941 sec   (979 perm/sec)   p_kst 3.321053e-04   p_cons 9.713216e-01   p_joint 3.321053e-04

Joint ci ratio: 1.552901e-01	ci left: 3.076088e-04	ci right 3.598944e-04	k: 636	n:1910000
Cons ci ratio: 4.874694e-04	ci left: 9.710738e-01	ci right 9.715478e-01	k: 1855205	n:1910000
KS ci ratio: 1.552901e-01	ci left: 3.076088e-04	ci right 3.598944e-04	k: 636	n:1910000
CPNE3   1910000 perm   1959 sec   (975 perm/sec)   p_kst 3.329843e-04   p_cons 9.713115e-01   p_joint 3.329843e-04

Joint ci ratio: 1.552902e-01	ci left: 3.060066e-04	ci right 3.580199e-04	k: 636	n:1920000
Cons ci ratio: 4.863033e-04	ci left: 9.710623e-01	ci right 9.715352e-01	k: 1864895	n:1920000
KS ci ratio: 1.552902e-01	ci left: 3.060066e-04	ci right 3.580199e-04	k: 636	n:1920000
CPNE3   1920000 perm   1978 sec   (971 perm/sec)   p_kst 3.312500e-04   p_cons 9.712995e-01   p_joint 3.312500e-04

Joint ci ratio: 1.549259e-01	ci left: 3.059152e-04	ci right 3.577796e-04	k: 639	n:1930000
Cons ci ratio: 4.850643e-04	ci left: 9.710604e-01	ci right 9.715320e-01	k: 1874603	n:1930000
KS ci ratio: 1.549259e-01	ci left: 3.059152e-04	ci right 3.577796e-04	k: 639	n:1930000
CPNE3   1930000 perm   1996 sec   (967 perm/sec)   p_kst 3.310881e-04   p_cons 9.712969e-01   p_joint 3.310881e-04

Joint ci ratio: 1.542046e-01	ci left: 3.073115e-04	ci right 3.591477e-04	k: 645	n:1940000
Cons ci ratio: 4.839689e-04	ci left: 9.710429e-01	ci right 9.715134e-01	k: 1884281	n:1940000
KS ci ratio: 1.542046e-01	ci left: 3.073115e-04	ci right 3.591477e-04	k: 645	n:1940000
CPNE3   1940000 perm   2014 sec   (963 perm/sec)   p_kst 3.324742e-04   p_cons 9.712789e-01   p_joint 3.324742e-04

Joint ci ratio: 1.534933e-01	ci left: 3.086940e-04	ci right 3.605011e-04	k: 651	n:1950000
Cons ci ratio: 4.827654e-04	ci left: 9.710390e-01	ci right 9.715084e-01	k: 1893985	n:1950000
KS ci ratio: 1.534933e-01	ci left: 3.086940e-04	ci right 3.605011e-04	k: 651	n:1950000
CPNE3   1950000 perm   2033 sec   (959 perm/sec)   p_kst 3.338462e-04   p_cons 9.712744e-01   p_joint 3.338462e-04

Joint ci ratio: 1.532585e-01	ci left: 3.081003e-04	ci right 3.597214e-04	k: 653	n:1960000
Cons ci ratio: 4.816015e-04	ci left: 9.710315e-01	ci right 9.714998e-01	k: 1903682	n:1960000
KS ci ratio: 1.532585e-01	ci left: 3.081003e-04	ci right 3.597214e-04	k: 653	n:1960000
CPNE3   1960000 perm   2051 sec   (955 perm/sec)   p_kst 3.331633e-04   p_cons 9.712663e-01   p_joint 3.331633e-04

Joint ci ratio: 1.527919e-01	ci left: 3.084890e-04	ci right 3.600035e-04	k: 657	n:1970000
Cons ci ratio: 4.805334e-04	ci left: 9.710139e-01	ci right 9.714811e-01	k: 1913359	n:1970000
KS ci ratio: 1.527919e-01	ci left: 3.084890e-04	ci right 3.600035e-04	k: 657	n:1970000
CPNE3   1970000 perm   2070 sec   (952 perm/sec)   p_kst 3.335025e-04   p_cons 9.712482e-01   p_joint 3.335025e-04

Joint ci ratio: 1.525603e-01	ci left: 3.079025e-04	ci right 3.592340e-04	k: 659	n:1980000
Cons ci ratio: 4.793508e-04	ci left: 9.710107e-01	ci right 9.714768e-01	k: 1923064	n:1980000
KS ci ratio: 1.525603e-01	ci left: 3.079025e-04	ci right 3.592340e-04	k: 659	n:1980000
CPNE3   1980000 perm   2088 sec   (948 perm/sec)   p_kst 3.328283e-04   p_cons 9.712444e-01   p_joint 3.328283e-04

Joint ci ratio: 1.518715e-01	ci left: 3.092555e-04	ci right 3.605586e-04	k: 665	n:1990000
Cons ci ratio: 4.780908e-04	ci left: 9.710176e-01	ci right 9.714825e-01	k: 1932789	n:1990000
KS ci ratio: 1.518715e-01	ci left: 3.092555e-04	ci right 3.605586e-04	k: 665	n:1990000
CPNE3   1990000 perm   2108 sec   (944 perm/sec)   p_kst 3.341709e-04   p_cons 9.712508e-01   p_joint 3.341709e-04

Joint ci ratio: 1.515306e-01	ci left: 3.091523e-04	ci right 3.603127e-04	k: 668	n:2000000
Cons ci ratio: 4.770201e-04	ci left: 9.710034e-01	ci right 9.714672e-01	k: 1942472	n:2000000
KS ci ratio: 1.515306e-01	ci left: 3.091523e-04	ci right 3.603127e-04	k: 668	n:2000000
CPNE3   2000000 perm   2127 sec   (940 perm/sec)   p_kst 3.340000e-04   p_cons 9.712360e-01   p_joint 3.340000e-04

Joint ci ratio: 1.507438e-01	ci left: 3.109651e-04	ci right 3.621343e-04	k: 675	n:2010000
Cons ci ratio: 4.759479e-04	ci left: 9.709903e-01	ci right 9.714531e-01	k: 1952157	n:2010000
KS ci ratio: 1.507438e-01	ci left: 3.109651e-04	ci right 3.621343e-04	k: 675	n:2010000
CPNE3   2010000 perm   2146 sec   (937 perm/sec)   p_kst 3.358209e-04   p_cons 9.712224e-01   p_joint 3.358209e-04

Joint ci ratio: 1.504105e-01	ci left: 3.108549e-04	ci right 3.618826e-04	k: 678	n:2020000
Cons ci ratio: 4.748786e-04	ci left: 9.709779e-01	ci right 9.714396e-01	k: 1961843	n:2020000
KS ci ratio: 1.504105e-01	ci left: 3.108549e-04	ci right 3.618826e-04	k: 678	n:2020000
CPNE3   2020000 perm   2165 sec   (933 perm/sec)   p_kst 3.356436e-04   p_cons 9.712094e-01   p_joint 3.356436e-04

Joint ci ratio: 1.499694e-01	ci left: 3.112200e-04	ci right 3.621444e-04	k: 682	n:2030000
Cons ci ratio: 4.737204e-04	ci left: 9.709769e-01	ci right 9.714375e-01	k: 1971552	n:2030000
KS ci ratio: 1.499694e-01	ci left: 3.112200e-04	ci right 3.621444e-04	k: 682	n:2030000
CPNE3   2030000 perm   2184 sec   (929 perm/sec)   p_kst 3.359606e-04   p_cons 9.712079e-01   p_joint 3.359606e-04

Joint ci ratio: 1.493148e-01	ci left: 3.125255e-04	ci right 3.634204e-04	k: 688	n:2040000
Cons ci ratio: 4.725664e-04	ci left: 9.709765e-01	ci right 9.714359e-01	k: 1981262	n:2040000
KS ci ratio: 1.493148e-01	ci left: 3.125255e-04	ci right 3.634204e-04	k: 688	n:2040000
CPNE3   2040000 perm   2204 sec   (926 perm/sec)   p_kst 3.372549e-04   p_cons 9.712069e-01   p_joint 3.372549e-04

Joint ci ratio: 1.492067e-01	ci left: 3.114705e-04	ci right 3.621536e-04	k: 689	n:2050000
Cons ci ratio: 4.713716e-04	ci left: 9.709819e-01	ci right 9.714402e-01	k: 1990984	n:2050000
KS ci ratio: 1.492067e-01	ci left: 3.114705e-04	ci right 3.621536e-04	k: 689	n:2050000
CPNE3   2050000 perm   2223 sec   (922 perm/sec)   p_kst 3.360976e-04   p_cons 9.712117e-01   p_joint 3.360976e-04

Joint ci ratio: 1.488834e-01	ci left: 3.113605e-04	ci right 3.619062e-04	k: 692	n:2060000
Cons ci ratio: 4.702265e-04	ci left: 9.709824e-01	ci right 9.714396e-01	k: 2000696	n:2060000
KS ci ratio: 1.488834e-01	ci left: 3.113605e-04	ci right 3.619062e-04	k: 692	n:2060000
CPNE3   2060000 perm   2243 sec   (919 perm/sec)   p_kst 3.359223e-04   p_cons 9.712117e-01   p_joint 3.359223e-04

Joint ci ratio: 1.482429e-01	ci left: 3.126472e-04	ci right 3.631640e-04	k: 698	n:2070000
Cons ci ratio: 4.690979e-04	ci left: 9.709819e-01	ci right 9.714380e-01	k: 2010406	n:2070000
KS ci ratio: 1.482429e-01	ci left: 3.126472e-04	ci right 3.631640e-04	k: 698	n:2070000
CPNE3   2070000 perm   2262 sec   (915 perm/sec)   p_kst 3.371981e-04   p_cons 9.712106e-01   p_joint 3.371981e-04

Joint ci ratio: 1.481371e-01	ci left: 3.116070e-04	ci right 3.619166e-04	k: 699	n:2080000
Cons ci ratio: 4.679613e-04	ci left: 9.709834e-01	ci right 9.714384e-01	k: 2020120	n:2080000
KS ci ratio: 1.481371e-01	ci left: 3.116070e-04	ci right 3.619166e-04	k: 699	n:2080000
CPNE3   2080000 perm   2282 sec   (912 perm/sec)   p_kst 3.360577e-04   p_cons 9.712115e-01   p_joint 3.360577e-04

Joint ci ratio: 1.479260e-01	ci left: 3.110376e-04	ci right 3.611773e-04	k: 701	n:2090000
Cons ci ratio: 4.668688e-04	ci left: 9.709805e-01	ci right 9.714344e-01	k: 2029825	n:2090000
KS ci ratio: 1.479260e-01	ci left: 3.110376e-04	ci right 3.611773e-04	k: 701	n:2090000
CPNE3   2090000 perm   2301 sec   (908 perm/sec)   p_kst 3.354067e-04   p_cons 9.712081e-01   p_joint 3.354067e-04

Joint ci ratio: 1.472977e-01	ci left: 3.123081e-04	ci right 3.624200e-04	k: 707	n:2100000
Cons ci ratio: 4.658078e-04	ci left: 9.709748e-01	ci right 9.714277e-01	k: 2039524	n:2100000
KS ci ratio: 1.472977e-01	ci left: 3.123081e-04	ci right 3.624200e-04	k: 707	n:2100000
CPNE3   2100000 perm   2322 sec   (905 perm/sec)   p_kst 3.366667e-04   p_cons 9.712019e-01   p_joint 3.366667e-04

Joint ci ratio: 1.467803e-01	ci left: 3.131104e-04	ci right 3.631592e-04	k: 712	n:2110000
Cons ci ratio: 4.647263e-04	ci left: 9.709725e-01	ci right 9.714243e-01	k: 2049230	n:2110000
KS ci ratio: 1.467803e-01	ci left: 3.131104e-04	ci right 3.631592e-04	k: 712	n:2110000
CPNE3   2110000 perm   2342 sec   (901 perm/sec)   p_kst 3.374408e-04   p_cons 9.711991e-01   p_joint 3.374408e-04

Joint ci ratio: 1.465749e-01	ci left: 3.125423e-04	ci right 3.624242e-04	k: 714	n:2120000
Cons ci ratio: 4.636445e-04	ci left: 9.709711e-01	ci right 9.714219e-01	k: 2058938	n:2120000
KS ci ratio: 1.465749e-01	ci left: 3.125423e-04	ci right 3.624242e-04	k: 714	n:2120000
CPNE3   2120000 perm   2362 sec   (898 perm/sec)   p_kst 3.367925e-04   p_cons 9.711972e-01   p_joint 3.367925e-04

Joint ci ratio: 1.460650e-01	ci left: 3.133364e-04	ci right 3.631559e-04	k: 719	n:2130000
Cons ci ratio: 4.625819e-04	ci left: 9.709684e-01	ci right 9.714181e-01	k: 2068643	n:2130000
KS ci ratio: 1.460650e-01	ci left: 3.133364e-04	ci right 3.631559e-04	k: 719	n:2130000
CPNE3   2130000 perm   2382 sec   (894 perm/sec)   p_kst 3.375587e-04   p_cons 9.711939e-01   p_joint 3.375587e-04

Joint ci ratio: 1.454601e-01	ci left: 3.145737e-04	ci right 3.643648e-04	k: 725	n:2140000
Cons ci ratio: 4.615073e-04	ci left: 9.709680e-01	ci right 9.714167e-01	k: 2078353	n:2140000
KS ci ratio: 1.454601e-01	ci left: 3.145737e-04	ci right 3.643648e-04	k: 725	n:2140000
CPNE3   2140000 perm   2402 sec   (891 perm/sec)   p_kst 3.387850e-04   p_cons 9.711930e-01   p_joint 3.387850e-04

Joint ci ratio: 1.452602e-01	ci left: 3.140070e-04	ci right 3.636342e-04	k: 727	n:2150000
Cons ci ratio: 4.604670e-04	ci left: 9.709644e-01	ci right 9.714120e-01	k: 2088056	n:2150000
KS ci ratio: 1.452602e-01	ci left: 3.140070e-04	ci right 3.636342e-04	k: 727	n:2150000
CPNE3   2150000 perm   2422 sec   (888 perm/sec)   p_kst 3.381395e-04   p_cons 9.711888e-01   p_joint 3.381395e-04

Joint ci ratio: 1.448628e-01	ci left: 3.143379e-04	ci right 3.638697e-04	k: 731	n:2160000
Cons ci ratio: 4.595970e-04	ci left: 9.709408e-01	ci right 9.713876e-01	k: 2097716	n:2160000
KS ci ratio: 1.448628e-01	ci left: 3.143379e-04	ci right 3.638697e-04	k: 731	n:2160000
CPNE3   2160000 perm   2443 sec   (884 perm/sec)   p_kst 3.384259e-04   p_cons 9.711648e-01   p_joint 3.384259e-04

Joint ci ratio: 1.446653e-01	ci left: 3.137776e-04	ci right 3.631479e-04	k: 733	n:2170000
Cons ci ratio: 4.584487e-04	ci left: 9.709521e-01	ci right 9.713978e-01	k: 2107451	n:2170000
KS ci ratio: 1.446653e-01	ci left: 3.137776e-04	ci right 3.631479e-04	k: 733	n:2170000
CPNE3   2170000 perm   2463 sec   (881 perm/sec)   p_kst 3.377880e-04   p_cons 9.711756e-01   p_joint 3.377880e-04

Joint ci ratio: 1.445670e-01	ci left: 3.127804e-04	ci right 3.619574e-04	k: 734	n:2180000
Cons ci ratio: 4.574138e-04	ci left: 9.709504e-01	ci right 9.713951e-01	k: 2117158	n:2180000
KS ci ratio: 1.445670e-01	ci left: 3.127804e-04	ci right 3.619574e-04	k: 734	n:2180000
CPNE3   2180000 perm   2483 sec   (878 perm/sec)   p_kst 3.366972e-04   p_cons 9.711734e-01   p_joint 3.366972e-04

Joint ci ratio: 1.444688e-01	ci left: 3.117922e-04	ci right 3.607777e-04	k: 735	n:2190000
Cons ci ratio: 4.564491e-04	ci left: 9.709410e-01	ci right 9.713847e-01	k: 2126848	n:2190000
KS ci ratio: 1.444688e-01	ci left: 3.117922e-04	ci right 3.607777e-04	k: 735	n:2190000
CPNE3   2190000 perm   2504 sec   (875 perm/sec)   p_kst 3.356164e-04   p_cons 9.711635e-01   p_joint 3.356164e-04

Joint ci ratio: 1.442730e-01	ci left: 3.112513e-04	ci right 3.600798e-04	k: 737	n:2200000
Cons ci ratio: 4.554535e-04	ci left: 9.709362e-01	ci right 9.713789e-01	k: 2136548	n:2200000
KS ci ratio: 1.442730e-01	ci left: 3.112513e-04	ci right 3.600798e-04	k: 737	n:2200000
CPNE3   2200000 perm   2525 sec   (871 perm/sec)   p_kst 3.350000e-04   p_cons 9.711582e-01   p_joint 3.350000e-04

Joint ci ratio: 1.442731e-01	ci left: 3.098429e-04	ci right 3.584505e-04	k: 737	n:2210000
Cons ci ratio: 4.544534e-04	ci left: 9.709328e-01	ci right 9.713746e-01	k: 2146251	n:2210000
KS ci ratio: 1.442731e-01	ci left: 3.098429e-04	ci right 3.584505e-04	k: 737	n:2210000
CPNE3   2210000 perm   2545 sec   (868 perm/sec)   p_kst 3.334842e-04   p_cons 9.711543e-01   p_joint 3.334842e-04

Joint ci ratio: 1.442732e-01	ci left: 3.084472e-04	ci right 3.568358e-04	k: 737	n:2220000
Cons ci ratio: 4.533140e-04	ci left: 9.709475e-01	ci right 9.713882e-01	k: 2155994	n:2220000
KS ci ratio: 1.442732e-01	ci left: 3.084472e-04	ci right 3.568358e-04	k: 737	n:2220000
CPNE3   2220000 perm   2566 sec   (865 perm/sec)   p_kst 3.319820e-04   p_cons 9.711685e-01   p_joint 3.319820e-04

Joint ci ratio: 1.440781e-01	ci left: 3.079285e-04	ci right 3.561649e-04	k: 739	n:2230000
Cons ci ratio: 4.522700e-04	ci left: 9.709513e-01	ci right 9.713910e-01	k: 2165713	n:2230000
KS ci ratio: 1.440781e-01	ci left: 3.079285e-04	ci right 3.561649e-04	k: 739	n:2230000
CPNE3   2230000 perm   2587 sec   (862 perm/sec)   p_kst 3.313901e-04   p_cons 9.711717e-01   p_joint 3.313901e-04

Joint ci ratio: 1.432097e-01	ci left: 3.104273e-04	ci right 3.587370e-04	k: 748	n:2240000
Cons ci ratio: 4.513266e-04	ci left: 9.709434e-01	ci right 9.713822e-01	k: 2175406	n:2240000
KS ci ratio: 1.432097e-01	ci left: 3.104273e-04	ci right 3.587370e-04	k: 748	n:2240000
CPNE3   2240000 perm   2609 sec   (859 perm/sec)   p_kst 3.339286e-04   p_cons 9.711634e-01   p_joint 3.339286e-04

Joint ci ratio: 1.430189e-01	ci left: 3.099047e-04	ci right 3.580633e-04	k: 750	n:2250000
Cons ci ratio: 4.503641e-04	ci left: 9.709387e-01	ci right 9.713765e-01	k: 2185106	n:2250000
KS ci ratio: 1.430189e-01	ci left: 3.099047e-04	ci right 3.580633e-04	k: 750	n:2250000
CPNE3   2250000 perm   2630 sec   (856 perm/sec)   p_kst 3.333333e-04   p_cons 9.711582e-01   p_joint 3.333333e-04

Joint ci ratio: 1.426395e-01	ci left: 3.102401e-04	ci right 3.583121e-04	k: 754	n:2260000
Cons ci ratio: 4.493332e-04	ci left: 9.709434e-01	ci right 9.713802e-01	k: 2194827	n:2260000
KS ci ratio: 1.426395e-01	ci left: 3.102401e-04	ci right 3.583121e-04	k: 754	n:2260000
CPNE3   2260000 perm   2651 sec   (853 perm/sec)   p_kst 3.336283e-04   p_cons 9.711624e-01   p_joint 3.336283e-04

Joint ci ratio: 1.424510e-01	ci left: 3.097230e-04	ci right 3.576461e-04	k: 756	n:2270000
Cons ci ratio: 4.482987e-04	ci left: 9.709493e-01	ci right 9.713851e-01	k: 2204551	n:2270000
KS ci ratio: 1.424510e-01	ci left: 3.097230e-04	ci right 3.576461e-04	k: 756	n:2270000
CPNE3   2270000 perm   2672 sec   (850 perm/sec)   p_kst 3.330396e-04   p_cons 9.711678e-01   p_joint 3.330396e-04

Joint ci ratio: 1.421696e-01	ci left: 3.096335e-04	ci right 3.574400e-04	k: 759	n:2280000
Cons ci ratio: 4.474220e-04	ci left: 9.709363e-01	ci right 9.713713e-01	k: 2214232	n:2280000
KS ci ratio: 1.421696e-01	ci left: 3.096335e-04	ci right 3.574400e-04	k: 759	n:2280000
CPNE3   2280000 perm   2693 sec   (847 perm/sec)   p_kst 3.328947e-04   p_cons 9.711544e-01   p_joint 3.328947e-04

Joint ci ratio: 1.419830e-01	ci left: 3.091237e-04	ci right 3.567836e-04	k: 761	n:2290000
Cons ci ratio: 4.464981e-04	ci left: 9.709300e-01	ci right 9.713640e-01	k: 2223928	n:2290000
KS ci ratio: 1.419830e-01	ci left: 3.091237e-04	ci right 3.567836e-04	k: 761	n:2290000
CPNE3   2290000 perm   2714 sec   (844 perm/sec)   p_kst 3.323144e-04   p_cons 9.711476e-01   p_joint 3.323144e-04

Joint ci ratio: 1.418900e-01	ci left: 3.081990e-04	ci right 3.556826e-04	k: 762	n:2300000
Cons ci ratio: 4.455557e-04	ci left: 9.709268e-01	ci right 9.713599e-01	k: 2233631	n:2300000
KS ci ratio: 1.418900e-01	ci left: 3.081990e-04	ci right 3.556826e-04	k: 762	n:2300000
CPNE3   2300000 perm   2736 sec   (841 perm/sec)   p_kst 3.313043e-04   p_cons 9.711439e-01   p_joint 3.313043e-04

Joint ci ratio: 1.411518e-01	ci left: 3.102055e-04	ci right 3.577285e-04	k: 770	n:2310000
Cons ci ratio: 4.445745e-04	ci left: 9.709292e-01	ci right 9.713614e-01	k: 2243347	n:2310000
KS ci ratio: 1.411518e-01	ci left: 3.102055e-04	ci right 3.577285e-04	k: 770	n:2310000
CPNE3   2310000 perm   2757 sec   (838 perm/sec)   p_kst 3.333333e-04   p_cons 9.711459e-01   p_joint 3.333333e-04

Joint ci ratio: 1.409691e-01	ci left: 3.097000e-04	ci right 3.570791e-04	k: 772	n:2320000
Cons ci ratio: 4.435930e-04	ci left: 9.709325e-01	ci right 9.713637e-01	k: 2253065	n:2320000
KS ci ratio: 1.409691e-01	ci left: 3.097000e-04	ci right 3.570791e-04	k: 772	n:2320000
CPNE3   2320000 perm   2779 sec   (835 perm/sec)   p_kst 3.327586e-04   p_cons 9.711487e-01   p_joint 3.327586e-04

Joint ci ratio: 1.406963e-01	ci left: 3.096130e-04	ci right 3.568794e-04	k: 775	n:2330000
Cons ci ratio: 4.426824e-04	ci left: 9.709276e-01	ci right 9.713579e-01	k: 2262764	n:2330000
KS ci ratio: 1.406963e-01	ci left: 3.096130e-04	ci right 3.568794e-04	k: 775	n:2330000
CPNE3   2330000 perm   2800 sec   (832 perm/sec)   p_kst 3.326180e-04   p_cons 9.711433e-01   p_joint 3.326180e-04

Joint ci ratio: 1.402452e-01	ci left: 3.103515e-04	ci right 3.575661e-04	k: 780	n:2340000
Cons ci ratio: 4.416426e-04	ci left: 9.709399e-01	ci right 9.713692e-01	k: 2272503	n:2340000
KS ci ratio: 1.402452e-01	ci left: 3.103515e-04	ci right 3.575661e-04	k: 780	n:2340000
CPNE3   2340000 perm   2823 sec   (829 perm/sec)   p_kst 3.333333e-04   p_cons 9.711551e-01   p_joint 3.333333e-04

Joint ci ratio: 1.401556e-01	ci left: 3.094415e-04	ci right 3.564850e-04	k: 781	n:2350000
Cons ci ratio: 4.406569e-04	ci left: 9.709461e-01	ci right 9.713745e-01	k: 2282228	n:2350000
KS ci ratio: 1.401556e-01	ci left: 3.094415e-04	ci right 3.564850e-04	k: 781	n:2350000
CPNE3   2350000 perm   2845 sec   (826 perm/sec)   p_kst 3.323404e-04   p_cons 9.711609e-01   p_joint 3.323404e-04

Joint ci ratio: 1.397096e-01	ci left: 3.101748e-04	ci right 3.571672e-04	k: 786	n:2360000
Cons ci ratio: 4.397842e-04	ci left: 9.709386e-01	ci right 9.713661e-01	k: 2291921	n:2360000
KS ci ratio: 1.397096e-01	ci left: 3.101748e-04	ci right 3.571672e-04	k: 786	n:2360000
CPNE3   2360000 perm   2868 sec   (823 perm/sec)   p_kst 3.330508e-04   p_cons 9.711530e-01   p_joint 3.330508e-04

Joint ci ratio: 1.396210e-01	ci left: 3.092732e-04	ci right 3.560969e-04	k: 787	n:2370000
Cons ci ratio: 4.389266e-04	ci left: 9.709300e-01	ci right 9.713566e-01	k: 2301611	n:2370000
KS ci ratio: 1.396210e-01	ci left: 3.092732e-04	ci right 3.560969e-04	k: 787	n:2370000
CPNE3   2370000 perm   2891 sec   (820 perm/sec)   p_kst 3.320675e-04   p_cons 9.711439e-01   p_joint 3.320675e-04

Joint ci ratio: 1.389175e-01	ci left: 3.112180e-04	ci right 3.580790e-04	k: 795	n:2380000
Cons ci ratio: 4.379786e-04	ci left: 9.709336e-01	ci right 9.713594e-01	k: 2311330	n:2380000
KS ci ratio: 1.389175e-01	ci left: 3.112180e-04	ci right 3.580790e-04	k: 795	n:2380000
CPNE3   2380000 perm   2913 sec   (817 perm/sec)   p_kst 3.340336e-04   p_cons 9.711471e-01   p_joint 3.340336e-04

Joint ci ratio: 1.385697e-01	ci left: 3.115314e-04	ci right 3.583125e-04	k: 799	n:2390000
Cons ci ratio: 4.371021e-04	ci left: 9.709288e-01	ci right 9.713537e-01	k: 2321029	n:2390000
KS ci ratio: 1.385697e-01	ci left: 3.115314e-04	ci right 3.583125e-04	k: 799	n:2390000
CPNE3   2390000 perm   2936 sec   (814 perm/sec)   p_kst 3.343096e-04   p_cons 9.711418e-01   p_joint 3.343096e-04

Joint ci ratio: 1.381386e-01	ci left: 3.122446e-04	ci right 3.589749e-04	k: 804	n:2400000
Cons ci ratio: 4.362729e-04	ci left: 9.709186e-01	ci right 9.713427e-01	k: 2330715	n:2400000
KS ci ratio: 1.381386e-01	ci left: 3.122446e-04	ci right 3.589749e-04	k: 804	n:2400000
CPNE3   2400000 perm   2959 sec   (811 perm/sec)   p_kst 3.350000e-04   p_cons 9.711313e-01   p_joint 3.350000e-04

Joint ci ratio: 1.379674e-01	ci left: 3.117501e-04	ci right 3.583439e-04	k: 806	n:2410000
Cons ci ratio: 4.353968e-04	ci left: 9.709152e-01	ci right 9.713384e-01	k: 2340417	n:2410000
KS ci ratio: 1.379674e-01	ci left: 3.117501e-04	ci right 3.583439e-04	k: 806	n:2410000
CPNE3   2410000 perm   2980 sec   (809 perm/sec)   p_kst 3.344398e-04   p_cons 9.711274e-01   p_joint 3.344398e-04

Joint ci ratio: 1.377117e-01	ci left: 3.116588e-04	ci right 3.581456e-04	k: 809	n:2420000
Cons ci ratio: 4.344716e-04	ci left: 9.709188e-01	ci right 9.713412e-01	k: 2350136	n:2420000
KS ci ratio: 1.377117e-01	ci left: 3.116588e-04	ci right 3.581456e-04	k: 809	n:2420000
CPNE3   2420000 perm   3003 sec   (806 perm/sec)   p_kst 3.342975e-04   p_cons 9.711306e-01   p_joint 3.342975e-04

Joint ci ratio: 1.375420e-01	ci left: 3.111710e-04	ci right 3.575231e-04	k: 811	n:2430000
Cons ci ratio: 4.336699e-04	ci left: 9.709072e-01	ci right 9.713287e-01	k: 2359818	n:2430000
KS ci ratio: 1.375420e-01	ci left: 3.111710e-04	ci right 3.575231e-04	k: 811	n:2430000
CPNE3   2430000 perm   3026 sec   (803 perm/sec)   p_kst 3.337449e-04   p_cons 9.711185e-01   p_joint 3.337449e-04

Joint ci ratio: 1.374575e-01	ci left: 3.102914e-04	ci right 3.564818e-04	k: 812	n:2440000
Cons ci ratio: 4.328536e-04	ci left: 9.708981e-01	ci right 9.713188e-01	k: 2369506	n:2440000
KS ci ratio: 1.374575e-01	ci left: 3.102914e-04	ci right 3.564818e-04	k: 812	n:2440000
CPNE3   2440000 perm   3048 sec   (801 perm/sec)   p_kst 3.327869e-04   p_cons 9.711090e-01   p_joint 3.327869e-04

Joint ci ratio: 1.370367e-01	ci left: 3.109957e-04	ci right 3.571376e-04	k: 817	n:2450000
Cons ci ratio: 4.320010e-04	ci left: 9.708944e-01	ci right 9.713143e-01	k: 2379207	n:2450000
KS ci ratio: 1.370367e-01	ci left: 3.109957e-04	ci right 3.571376e-04	k: 817	n:2450000
CPNE3   2450000 perm   3071 sec   (798 perm/sec)   p_kst 3.334694e-04   p_cons 9.711049e-01   p_joint 3.334694e-04

Joint ci ratio: 1.368695e-01	ci left: 3.105166e-04	ci right 3.565266e-04	k: 819	n:2460000
Cons ci ratio: 4.310566e-04	ci left: 9.709034e-01	ci right 9.713224e-01	k: 2388939	n:2460000
KS ci ratio: 1.368695e-01	ci left: 3.105166e-04	ci right 3.565266e-04	k: 819	n:2460000
CPNE3   2460000 perm   3093 sec   (795 perm/sec)   p_kst 3.329268e-04   p_cons 9.711134e-01   p_joint 3.329268e-04

Joint ci ratio: 1.367029e-01	ci left: 3.100415e-04	ci right 3.559206e-04	k: 821	n:2470000
Cons ci ratio: 4.301774e-04	ci left: 9.709045e-01	ci right 9.713227e-01	k: 2398652	n:2470000
KS ci ratio: 1.367029e-01	ci left: 3.100415e-04	ci right 3.559206e-04	k: 821	n:2470000
CPNE3   2470000 perm   3116 sec   (793 perm/sec)   p_kst 3.323887e-04   p_cons 9.711142e-01   p_joint 3.323887e-04

Joint ci ratio: 1.367030e-01	ci left: 3.087913e-04	ci right 3.544855e-04	k: 821	n:2480000
Cons ci ratio: 4.292726e-04	ci left: 9.709098e-01	ci right 9.713270e-01	k: 2408375	n:2480000
KS ci ratio: 1.367030e-01	ci left: 3.087913e-04	ci right 3.544855e-04	k: 821	n:2480000
CPNE3   2480000 perm   3139 sec   (790 perm/sec)   p_kst 3.310484e-04   p_cons 9.711190e-01   p_joint 3.310484e-04

Joint ci ratio: 1.364542e-01	ci left: 3.087148e-04	ci right 3.543078e-04	k: 824	n:2490000
Cons ci ratio: 4.283766e-04	ci left: 9.709145e-01	ci right 9.713309e-01	k: 2418097	n:2490000
KS ci ratio: 1.364542e-01	ci left: 3.087148e-04	ci right 3.543078e-04	k: 824	n:2490000
CPNE3   2490000 perm   3162 sec   (787 perm/sec)   p_kst 3.309237e-04   p_cons 9.711233e-01   p_joint 3.309237e-04

Joint ci ratio: 1.363717e-01	ci left: 3.078663e-04	ci right 3.533042e-04	k: 825	n:2500000
Cons ci ratio: 4.275166e-04	ci left: 9.709153e-01	ci right 9.713308e-01	k: 2427809	n:2500000
KS ci ratio: 1.363717e-01	ci left: 3.078663e-04	ci right 3.533042e-04	k: 825	n:2500000
CPNE3   2500000 perm   3185 sec   (785 perm/sec)   p_kst 3.300000e-04   p_cons 9.711236e-01   p_joint 3.300000e-04

Joint ci ratio: 1.360427e-01	ci left: 3.081791e-04	ci right 3.535445e-04	k: 829	n:2510000
Cons ci ratio: 4.266376e-04	ci left: 9.709192e-01	ci right 9.713339e-01	k: 2437529	n:2510000
KS ci ratio: 1.360427e-01	ci left: 3.081791e-04	ci right 3.535445e-04	k: 829	n:2510000
CPNE3   2510000 perm   3208 sec   (782 perm/sec)   p_kst 3.302789e-04   p_cons 9.711271e-01   p_joint 3.302789e-04

Joint ci ratio: 1.357975e-01	ci left: 3.081061e-04	ci right 3.533725e-04	k: 832	n:2520000
Cons ci ratio: 4.258031e-04	ci left: 9.709179e-01	ci right 9.713318e-01	k: 2447236	n:2520000
KS ci ratio: 1.357975e-01	ci left: 3.081061e-04	ci right 3.533725e-04	k: 832	n:2520000
CPNE3   2520000 perm   3231 sec   (780 perm/sec)   p_kst 3.301587e-04   p_cons 9.711254e-01   p_joint 3.301587e-04

Joint ci ratio: 1.355536e-01	ci left: 3.080338e-04	ci right 3.532018e-04	k: 835	n:2530000
Cons ci ratio: 4.249795e-04	ci left: 9.709158e-01	ci right 9.713289e-01	k: 2456941	n:2530000
KS ci ratio: 1.355536e-01	ci left: 3.080338e-04	ci right 3.532018e-04	k: 835	n:2530000
CPNE3   2530000 perm   3254 sec   (777 perm/sec)   p_kst 3.300395e-04   p_cons 9.711229e-01   p_joint 3.300395e-04

Joint ci ratio: 1.353110e-01	ci left: 3.079622e-04	ci right 3.530323e-04	k: 838	n:2540000
Cons ci ratio: 4.241904e-04	ci left: 9.709098e-01	ci right 9.713222e-01	k: 2466636	n:2540000
KS ci ratio: 1.353110e-01	ci left: 3.079622e-04	ci right 3.530323e-04	k: 838	n:2540000
CPNE3   2540000 perm   3278 sec   (775 perm/sec)   p_kst 3.299213e-04   p_cons 9.711165e-01   p_joint 3.299213e-04

Joint ci ratio: 1.349096e-01	ci left: 3.086490e-04	ci right 3.536749e-04	k: 843	n:2550000
Cons ci ratio: 4.233790e-04	ci left: 9.709074e-01	ci right 9.713190e-01	k: 2476340	n:2550000
KS ci ratio: 1.349096e-01	ci left: 3.086490e-04	ci right 3.536749e-04	k: 843	n:2550000
CPNE3   2550000 perm   3302 sec   (772 perm/sec)   p_kst 3.305882e-04   p_cons 9.711137e-01   p_joint 3.305882e-04

Joint ci ratio: 1.348298e-01	ci left: 3.078208e-04	ci right 3.526972e-04	k: 844	n:2560000
Cons ci ratio: 4.226164e-04	ci left: 9.708992e-01	ci right 9.713099e-01	k: 2486029	n:2560000
KS ci ratio: 1.348298e-01	ci left: 3.078208e-04	ci right 3.526972e-04	k: 844	n:2560000
CPNE3   2560000 perm   3326 sec   (770 perm/sec)   p_kst 3.296875e-04   p_cons 9.711051e-01   p_joint 3.296875e-04

Joint ci ratio: 1.345911e-01	ci left: 3.077510e-04	ci right 3.525314e-04	k: 847	n:2570000
Cons ci ratio: 4.217555e-04	ci left: 9.709046e-01	ci right 9.713146e-01	k: 2495753	n:2570000
KS ci ratio: 1.345911e-01	ci left: 3.077510e-04	ci right 3.525314e-04	k: 847	n:2570000
CPNE3   2570000 perm   3349 sec   (767 perm/sec)   p_kst 3.295720e-04   p_cons 9.711101e-01   p_joint 3.295720e-04

Joint ci ratio: 1.344327e-01	ci left: 3.073073e-04	ci right 3.519663e-04	k: 849	n:2580000
Cons ci ratio: 4.208707e-04	ci left: 9.709139e-01	ci right 9.713230e-01	k: 2505487	n:2580000
KS ci ratio: 1.344327e-01	ci left: 3.073073e-04	ci right 3.519663e-04	k: 849	n:2580000
CPNE3   2580000 perm   3373 sec   (765 perm/sec)   p_kst 3.290698e-04   p_cons 9.711190e-01   p_joint 3.290698e-04

Joint ci ratio: 1.340390e-01	ci left: 3.079864e-04	ci right 3.526026e-04	k: 854	n:2590000
Cons ci ratio: 4.200378e-04	ci left: 9.709170e-01	ci right 9.713252e-01	k: 2515205	n:2590000
KS ci ratio: 1.340390e-01	ci left: 3.079864e-04	ci right 3.526026e-04	k: 854	n:2590000
CPNE3   2590000 perm   3396 sec   (763 perm/sec)   p_kst 3.297297e-04   p_cons 9.711216e-01   p_joint 3.297297e-04

Joint ci ratio: 1.337266e-01	ci left: 3.082888e-04	ci right 3.528364e-04	k: 858	n:2600000
Cons ci ratio: 4.191781e-04	ci left: 9.709242e-01	ci right 9.713317e-01	k: 2524934	n:2600000
KS ci ratio: 1.337266e-01	ci left: 3.082888e-04	ci right 3.528364e-04	k: 858	n:2600000
CPNE3   2600000 perm   3420 sec   (760 perm/sec)   p_kst 3.300000e-04   p_cons 9.711285e-01   p_joint 3.300000e-04

Joint ci ratio: 1.336488e-01	ci left: 3.074780e-04	ci right 3.518805e-04	k: 859	n:2610000
Cons ci ratio: 4.183065e-04	ci left: 9.709337e-01	ci right 9.713403e-01	k: 2534669	n:2610000
KS ci ratio: 1.336488e-01	ci left: 3.074780e-04	ci right 3.518805e-04	k: 859	n:2610000
CPNE3   2610000 perm   3444 sec   (758 perm/sec)   p_kst 3.291188e-04   p_cons 9.711375e-01   p_joint 3.291188e-04

Joint ci ratio: 1.332620e-01	ci left: 3.081491e-04	ci right 3.525095e-04	k: 864	n:2620000
Cons ci ratio: 4.176421e-04	ci left: 9.709160e-01	ci right 9.713219e-01	k: 2544333	n:2620000
KS ci ratio: 1.332620e-01	ci left: 3.081491e-04	ci right 3.525095e-04	k: 864	n:2620000
CPNE3   2620000 perm   3468 sec   (755 perm/sec)   p_kst 3.297710e-04   p_cons 9.711195e-01   p_joint 3.297710e-04

Joint ci ratio: 1.329549e-01	ci left: 3.084477e-04	ci right 3.527407e-04	k: 868	n:2630000
Cons ci ratio: 4.168450e-04	ci left: 9.709167e-01	ci right 9.713218e-01	k: 2554045	n:2630000
KS ci ratio: 1.329549e-01	ci left: 3.084477e-04	ci right 3.527407e-04	k: 868	n:2630000
CPNE3   2630000 perm   3493 sec   (753 perm/sec)   p_kst 3.300380e-04   p_cons 9.711198e-01   p_joint 3.300380e-04

Joint ci ratio: 1.327260e-01	ci left: 3.083779e-04	ci right 3.525787e-04	k: 871	n:2640000
Cons ci ratio: 4.160413e-04	ci left: 9.709189e-01	ci right 9.713233e-01	k: 2563761	n:2640000
KS ci ratio: 1.327260e-01	ci left: 3.083779e-04	ci right 3.525787e-04	k: 871	n:2640000
CPNE3   2640000 perm   3517 sec   (751 perm/sec)   p_kst 3.299242e-04   p_cons 9.711216e-01   p_joint 3.299242e-04

Joint ci ratio: 1.324226e-01	ci left: 3.086736e-04	ci right 3.528077e-04	k: 875	n:2650000
Cons ci ratio: 4.152506e-04	ci left: 9.709199e-01	ci right 9.713236e-01	k: 2573474	n:2650000
KS ci ratio: 1.324226e-01	ci left: 3.086736e-04	ci right 3.528077e-04	k: 875	n:2650000
CPNE3   2650000 perm   3542 sec   (748 perm/sec)   p_kst 3.301887e-04   p_cons 9.711223e-01   p_joint 3.301887e-04

Joint ci ratio: 1.322717e-01	ci left: 3.082401e-04	ci right 3.522581e-04	k: 877	n:2660000
Cons ci ratio: 4.144866e-04	ci left: 9.709180e-01	ci right 9.713209e-01	k: 2583179	n:2660000
KS ci ratio: 1.322717e-01	ci left: 3.082401e-04	ci right 3.522581e-04	k: 877	n:2660000
CPNE3   2660000 perm   3566 sec   (746 perm/sec)   p_kst 3.296992e-04   p_cons 9.711199e-01   p_joint 3.296992e-04

Joint ci ratio: 1.318220e-01	ci left: 3.092587e-04	ci right 3.532601e-04	k: 883	n:2670000
Cons ci ratio: 4.137433e-04	ci left: 9.709138e-01	ci right 9.713159e-01	k: 2592878	n:2670000
KS ci ratio: 1.318220e-01	ci left: 3.092587e-04	ci right 3.532601e-04	k: 883	n:2670000
CPNE3   2670000 perm   3591 sec   (744 perm/sec)   p_kst 3.307116e-04   p_cons 9.711154e-01   p_joint 3.307116e-04

Joint ci ratio: 1.316732e-01	ci left: 3.088264e-04	ci right 3.527129e-04	k: 885	n:2680000
Cons ci ratio: 4.129766e-04	ci left: 9.709133e-01	ci right 9.713147e-01	k: 2602587	n:2680000
KS ci ratio: 1.316732e-01	ci left: 3.088264e-04	ci right 3.527129e-04	k: 885	n:2680000
CPNE3   2680000 perm   3615 sec   (741 perm/sec)   p_kst 3.302239e-04   p_cons 9.711146e-01   p_joint 3.302239e-04

Joint ci ratio: 1.315248e-01	ci left: 3.083973e-04	ci right 3.521696e-04	k: 887	n:2690000
Cons ci ratio: 4.122333e-04	ci left: 9.709103e-01	ci right 9.713110e-01	k: 2612289	n:2690000
KS ci ratio: 1.315248e-01	ci left: 3.083973e-04	ci right 3.521696e-04	k: 887	n:2690000
CPNE3   2690000 perm   3642 sec   (739 perm/sec)   p_kst 3.297398e-04   p_cons 9.711112e-01   p_joint 3.297398e-04

Joint ci ratio: 1.312296e-01	ci left: 3.086879e-04	ci right 3.523954e-04	k: 891	n:2700000
Cons ci ratio: 4.114993e-04	ci left: 9.709065e-01	ci right 9.713065e-01	k: 2621989	n:2700000
KS ci ratio: 1.312296e-01	ci left: 3.086879e-04	ci right 3.523954e-04	k: 891	n:2700000
CPNE3   2700000 perm   3668 sec   (736 perm/sec)   p_kst 3.300000e-04   p_cons 9.711070e-01   p_joint 3.300000e-04

Joint ci ratio: 1.309363e-01	ci left: 3.089765e-04	ci right 3.526195e-04	k: 895	n:2710000
Cons ci ratio: 4.107396e-04	ci left: 9.709069e-01	ci right 9.713061e-01	k: 2631700	n:2710000
KS ci ratio: 1.309363e-01	ci left: 3.089765e-04	ci right 3.526195e-04	k: 895	n:2710000
CPNE3   2710000 perm   3693 sec   (734 perm/sec)   p_kst 3.302583e-04   p_cons 9.711070e-01   p_joint 3.302583e-04

Joint ci ratio: 1.307177e-01	ci left: 3.089074e-04	ci right 3.524621e-04	k: 898	n:2720000
Cons ci ratio: 4.099733e-04	ci left: 9.709087e-01	ci right 9.713072e-01	k: 2641415	n:2720000
KS ci ratio: 1.307177e-01	ci left: 3.089074e-04	ci right 3.524621e-04	k: 898	n:2720000
CPNE3   2720000 perm   3718 sec   (732 perm/sec)   p_kst 3.301471e-04   p_cons 9.711085e-01   p_joint 3.301471e-04

Joint ci ratio: 1.305726e-01	ci left: 3.084845e-04	ci right 3.519276e-04	k: 900	n:2730000
Cons ci ratio: 4.092700e-04	ci left: 9.709024e-01	ci right 9.713002e-01	k: 2651108	n:2730000
KS ci ratio: 1.305726e-01	ci left: 3.084845e-04	ci right 3.519276e-04	k: 900	n:2730000
CPNE3   2730000 perm   3743 sec   (729 perm/sec)   p_kst 3.296703e-04   p_cons 9.711018e-01   p_joint 3.296703e-04

Joint ci ratio: 1.305002e-01	ci left: 3.077117e-04	ci right 3.510200e-04	k: 901	n:2740000
Cons ci ratio: 4.085465e-04	ci left: 9.708995e-01	ci right 9.712966e-01	k: 2660810	n:2740000
KS ci ratio: 1.305002e-01	ci left: 3.077117e-04	ci right 3.510200e-04	k: 901	n:2740000
CPNE3   2740000 perm   3767 sec   (727 perm/sec)   p_kst 3.288321e-04   p_cons 9.710985e-01   p_joint 3.288321e-04

Joint ci ratio: 1.299967e-01	ci left: 3.090553e-04	ci right 3.523719e-04	k: 908	n:2750000
Cons ci ratio: 4.077289e-04	ci left: 9.709101e-01	ci right 9.713064e-01	k: 2670549	n:2750000
KS ci ratio: 1.299967e-01	ci left: 3.090553e-04	ci right 3.523719e-04	k: 908	n:2750000
CPNE3   2750000 perm   3792 sec   (725 perm/sec)   p_kst 3.301818e-04   p_cons 9.711087e-01   p_joint 3.301818e-04

Joint ci ratio: 1.298539e-01	ci left: 3.086366e-04	ci right 3.518434e-04	k: 910	n:2760000
Cons ci ratio: 4.069399e-04	ci left: 9.709173e-01	ci right 9.713129e-01	k: 2680279	n:2760000
KS ci ratio: 1.298539e-01	ci left: 3.086366e-04	ci right 3.518434e-04	k: 910	n:2760000
CPNE3   2760000 perm   3818 sec   (723 perm/sec)   p_kst 3.297101e-04   p_cons 9.711156e-01   p_joint 3.297101e-04

Joint ci ratio: 1.296407e-01	ci left: 3.085702e-04	ci right 3.516914e-04	k: 913	n:2770000
Cons ci ratio: 4.062757e-04	ci left: 9.709078e-01	ci right 9.713027e-01	k: 2689963	n:2770000
KS ci ratio: 1.296407e-01	ci left: 3.085702e-04	ci right 3.516914e-04	k: 913	n:2770000
CPNE3   2770000 perm   3844 sec   (721 perm/sec)   p_kst 3.296029e-04   p_cons 9.711058e-01   p_joint 3.296029e-04

Joint ci ratio: 1.294284e-01	ci left: 3.085044e-04	ci right 3.515404e-04	k: 916	n:2780000
Cons ci ratio: 4.055730e-04	ci left: 9.709042e-01	ci right 9.712984e-01	k: 2699663	n:2780000
KS ci ratio: 1.294284e-01	ci left: 3.085044e-04	ci right 3.515404e-04	k: 916	n:2780000
CPNE3   2780000 perm   3870 sec   (718 perm/sec)   p_kst 3.294964e-04   p_cons 9.711018e-01   p_joint 3.294964e-04

Joint ci ratio: 1.291470e-01	ci left: 3.087860e-04	ci right 3.517604e-04	k: 920	n:2790000
Cons ci ratio: 4.048430e-04	ci left: 9.709049e-01	ci right 9.712984e-01	k: 2709375	n:2790000
KS ci ratio: 1.291470e-01	ci left: 3.087860e-04	ci right 3.517604e-04	k: 920	n:2790000
CPNE3   2790000 perm   3895 sec   (716 perm/sec)   p_kst 3.297491e-04   p_cons 9.711022e-01   p_joint 3.297491e-04

Joint ci ratio: 1.288675e-01	ci left: 3.090657e-04	ci right 3.519788e-04	k: 924	n:2800000
Cons ci ratio: 4.041221e-04	ci left: 9.709049e-01	ci right 9.712977e-01	k: 2719085	n:2800000
KS ci ratio: 1.288675e-01	ci left: 3.090657e-04	ci right 3.519788e-04	k: 924	n:2800000
CPNE3   2800000 perm   3921 sec   (714 perm/sec)   p_kst 3.300000e-04   p_cons 9.711018e-01   p_joint 3.300000e-04

Joint ci ratio: 1.286590e-01	ci left: 3.089990e-04	ci right 3.518282e-04	k: 927	n:2810000
Cons ci ratio: 4.033845e-04	ci left: 9.709077e-01	ci right 9.712998e-01	k: 2728803	n:2810000
KS ci ratio: 1.286590e-01	ci left: 3.089990e-04	ci right 3.518282e-04	k: 927	n:2810000
CPNE3   2810000 perm   3947 sec   (712 perm/sec)   p_kst 3.298932e-04   p_cons 9.711043e-01   p_joint 3.298932e-04

Joint ci ratio: 1.284516e-01	ci left: 3.089329e-04	ci right 3.516786e-04	k: 930	n:2820000
Cons ci ratio: 4.026255e-04	ci left: 9.709141e-01	ci right 9.713055e-01	k: 2738531	n:2820000
KS ci ratio: 1.284516e-01	ci left: 3.089329e-04	ci right 3.516786e-04	k: 930	n:2820000
CPNE3   2820000 perm   3973 sec   (710 perm/sec)   p_kst 3.297872e-04   p_cons 9.711103e-01   p_joint 3.297872e-04

Joint ci ratio: 1.280396e-01	ci left: 3.098934e-04	ci right 3.526240e-04	k: 936	n:2830000
Cons ci ratio: 4.018504e-04	ci left: 9.709233e-01	ci right 9.713139e-01	k: 2748267	n:2830000
KS ci ratio: 1.280396e-01	ci left: 3.098934e-04	ci right 3.526240e-04	k: 936	n:2830000
CPNE3   2830000 perm   3999 sec   (708 perm/sec)   p_kst 3.307420e-04   p_cons 9.711191e-01   p_joint 3.307420e-04

Joint ci ratio: 1.277672e-01	ci left: 3.101656e-04	ci right 3.528359e-04	k: 940	n:2840000
Cons ci ratio: 4.012309e-04	ci left: 9.709112e-01	ci right 9.713012e-01	k: 2757943	n:2840000
KS ci ratio: 1.277672e-01	ci left: 3.101656e-04	ci right 3.528359e-04	k: 940	n:2840000
CPNE3   2840000 perm   4025 sec   (706 perm/sec)   p_kst 3.309859e-04   p_cons 9.711067e-01   p_joint 3.309859e-04

Joint ci ratio: 1.276994e-01	ci left: 3.094170e-04	ci right 3.519599e-04	k: 941	n:2850000
Cons ci ratio: 4.005842e-04	ci left: 9.709034e-01	ci right 9.712928e-01	k: 2767631	n:2850000
KS ci ratio: 1.276994e-01	ci left: 3.094170e-04	ci right 3.519599e-04	k: 941	n:2850000
CPNE3   2850000 perm   4051 sec   (704 perm/sec)   p_kst 3.301754e-04   p_cons 9.710986e-01   p_joint 3.301754e-04

Joint ci ratio: 1.276317e-01	ci left: 3.086736e-04	ci right 3.510901e-04	k: 942	n:2860000
Cons ci ratio: 3.998359e-04	ci left: 9.709105e-01	ci right 9.712991e-01	k: 2777361	n:2860000
KS ci ratio: 1.276317e-01	ci left: 3.086736e-04	ci right 3.510901e-04	k: 942	n:2860000
CPNE3   2860000 perm   4076 sec   (702 perm/sec)   p_kst 3.293706e-04   p_cons 9.711052e-01   p_joint 3.293706e-04

Joint ci ratio: 1.274966e-01	ci left: 3.082727e-04	ci right 3.505859e-04	k: 944	n:2870000
Cons ci ratio: 3.990694e-04	ci left: 9.709206e-01	ci right 9.713084e-01	k: 2787100	n:2870000
KS ci ratio: 1.274966e-01	ci left: 3.082727e-04	ci right 3.505859e-04	k: 944	n:2870000
CPNE3   2870000 perm   4102 sec   (700 perm/sec)   p_kst 3.289199e-04   p_cons 9.711150e-01   p_joint 3.289199e-04

Joint ci ratio: 1.273619e-01	ci left: 3.078746e-04	ci right 3.500852e-04	k: 946	n:2880000
Cons ci ratio: 3.983147e-04	ci left: 9.709296e-01	ci right 9.713167e-01	k: 2796836	n:2880000
KS ci ratio: 1.273619e-01	ci left: 3.078746e-04	ci right 3.500852e-04	k: 946	n:2880000
CPNE3   2880000 perm   4129 sec   (698 perm/sec)   p_kst 3.284722e-04   p_cons 9.711236e-01   p_joint 3.284722e-04

Joint ci ratio: 1.272948e-01	ci left: 3.071443e-04	ci right 3.492308e-04	k: 947	n:2890000
Cons ci ratio: 3.976280e-04	ci left: 9.709295e-01	ci right 9.713160e-01	k: 2806546	n:2890000
KS ci ratio: 1.272948e-01	ci left: 3.071443e-04	ci right 3.492308e-04	k: 947	n:2890000
CPNE3   2890000 perm   4157 sec   (695 perm/sec)   p_kst 3.276817e-04   p_cons 9.711232e-01   p_joint 3.276817e-04

Joint ci ratio: 1.268938e-01	ci left: 3.080883e-04	ci right 3.501613e-04	k: 953	n:2900000
Cons ci ratio: 3.969595e-04	ci left: 9.709273e-01	ci right 9.713131e-01	k: 2816250	n:2900000
KS ci ratio: 1.268938e-01	ci left: 3.080883e-04	ci right 3.501613e-04	k: 953	n:2900000
CPNE3   2900000 perm   4185 sec   (693 perm/sec)   p_kst 3.286207e-04   p_cons 9.711207e-01   p_joint 3.286207e-04

Joint ci ratio: 1.266947e-01	ci left: 3.080279e-04	ci right 3.500216e-04	k: 956	n:2910000
Cons ci ratio: 3.961972e-04	ci left: 9.709389e-01	ci right 9.713240e-01	k: 2825994	n:2910000
KS ci ratio: 1.266947e-01	ci left: 3.080279e-04	ci right 3.500216e-04	k: 956	n:2910000
CPNE3   2910000 perm   4212 sec   (691 perm/sec)   p_kst 3.285223e-04   p_cons 9.711320e-01   p_joint 3.285223e-04

Joint ci ratio: 1.266287e-01	ci left: 3.073046e-04	ci right 3.491762e-04	k: 957	n:2920000
Cons ci ratio: 3.954634e-04	ci left: 9.709471e-01	ci right 9.713315e-01	k: 2835728	n:2920000
KS ci ratio: 1.266287e-01	ci left: 3.073046e-04	ci right 3.491762e-04	k: 957	n:2920000
CPNE3   2920000 perm   4239 sec   (689 perm/sec)   p_kst 3.277397e-04   p_cons 9.711397e-01   p_joint 3.277397e-04

Joint ci ratio: 1.263651e-01	ci left: 3.075777e-04	ci right 3.493929e-04	k: 961	n:2930000
Cons ci ratio: 3.948153e-04	ci left: 9.709435e-01	ci right 9.713272e-01	k: 2845428	n:2930000
KS ci ratio: 1.263651e-01	ci left: 3.075777e-04	ci right 3.493929e-04	k: 961	n:2930000
CPNE3   2930000 perm   4265 sec   (687 perm/sec)   p_kst 3.279863e-04   p_cons 9.711358e-01   p_joint 3.279863e-04

Joint ci ratio: 1.262340e-01	ci left: 3.071903e-04	ci right 3.489062e-04	k: 963	n:2940000
Cons ci ratio: 3.941490e-04	ci left: 9.709430e-01	ci right 9.713261e-01	k: 2855137	n:2940000
KS ci ratio: 1.262340e-01	ci left: 3.071903e-04	ci right 3.489062e-04	k: 963	n:2940000
CPNE3   2940000 perm   4292 sec   (685 perm/sec)   p_kst 3.275510e-04   p_cons 9.711350e-01   p_joint 3.275510e-04

Joint ci ratio: 1.261033e-01	ci left: 3.068056e-04	ci right 3.484228e-04	k: 965	n:2950000
Cons ci ratio: 3.934502e-04	ci left: 9.709476e-01	ci right 9.713301e-01	k: 2864861	n:2950000
KS ci ratio: 1.261033e-01	ci left: 3.068056e-04	ci right 3.484228e-04	k: 965	n:2950000
CPNE3   2950000 perm   4319 sec   (683 perm/sec)   p_kst 3.271186e-04   p_cons 9.711393e-01   p_joint 3.271186e-04

Joint ci ratio: 1.260381e-01	ci left: 3.060962e-04	ci right 3.475942e-04	k: 966	n:2960000
Cons ci ratio: 3.927978e-04	ci left: 9.709461e-01	ci right 9.713279e-01	k: 2874567	n:2960000
KS ci ratio: 1.260381e-01	ci left: 3.060962e-04	ci right 3.475942e-04	k: 966	n:2960000
CPNE3   2960000 perm   4346 sec   (681 perm/sec)   p_kst 3.263514e-04   p_cons 9.711375e-01   p_joint 3.263514e-04

Joint ci ratio: 1.259080e-01	ci left: 3.057178e-04	ci right 3.471185e-04	k: 968	n:2970000
Cons ci ratio: 3.921981e-04	ci left: 9.709376e-01	ci right 9.713188e-01	k: 2884252	n:2970000
KS ci ratio: 1.259080e-01	ci left: 3.057178e-04	ci right 3.471185e-04	k: 968	n:2970000
CPNE3   2970000 perm   4373 sec   (679 perm/sec)   p_kst 3.259259e-04   p_cons 9.711286e-01   p_joint 3.259259e-04

Joint ci ratio: 1.256489e-01	ci left: 3.059920e-04	ci right 3.473381e-04	k: 972	n:2980000
Cons ci ratio: 3.914886e-04	ci left: 9.709452e-01	ci right 9.713257e-01	k: 2893985	n:2980000
KS ci ratio: 1.256489e-01	ci left: 3.059920e-04	ci right 3.473381e-04	k: 972	n:2980000
CPNE3   2980000 perm   4400 sec   (677 perm/sec)   p_kst 3.261745e-04   p_cons 9.711359e-01   p_joint 3.261745e-04

Joint ci ratio: 1.253914e-01	ci left: 3.062644e-04	ci right 3.475563e-04	k: 976	n:2990000
Cons ci ratio: 3.908132e-04	ci left: 9.709484e-01	ci right 9.713283e-01	k: 2903705	n:2990000
KS ci ratio: 1.253914e-01	ci left: 3.062644e-04	ci right 3.475563e-04	k: 976	n:2990000
CPNE3   2990000 perm   4427 sec   (675 perm/sec)   p_kst 3.264214e-04   p_cons 9.711388e-01   p_joint 3.264214e-04

Joint ci ratio: 1.253273e-01	ci left: 3.055664e-04	ci right 3.467415e-04	k: 977	n:3000000
Cons ci ratio: 3.901437e-04	ci left: 9.709513e-01	ci right 9.713305e-01	k: 2913424	n:3000000
KS ci ratio: 1.253273e-01	ci left: 3.055664e-04	ci right 3.467415e-04	k: 977	n:3000000
CPNE3   3000000 perm   4455 sec   (673 perm/sec)   p_kst 3.256667e-04   p_cons 9.711413e-01   p_joint 3.256667e-04

Joint ci ratio: 1.252633e-01	ci left: 3.048730e-04	ci right 3.459322e-04	k: 978	n:3010000
Cons ci ratio: 3.894614e-04	ci left: 9.709565e-01	ci right 9.713350e-01	k: 2923150	n:3010000
KS ci ratio: 1.252633e-01	ci left: 3.048730e-04	ci right 3.459322e-04	k: 978	n:3010000
CPNE3   3010000 perm   4481 sec   (672 perm/sec)   p_kst 3.249169e-04   p_cons 9.711462e-01   p_joint 3.249169e-04

Joint ci ratio: 1.250719e-01	ci left: 3.048257e-04	ci right 3.458112e-04	k: 981	n:3020000
Cons ci ratio: 3.887505e-04	ci left: 9.709662e-01	ci right 9.713441e-01	k: 2932890	n:3020000
KS ci ratio: 1.250719e-01	ci left: 3.048257e-04	ci right 3.458112e-04	k: 981	n:3020000
CPNE3   3020000 perm   4509 sec   (670 perm/sec)   p_kst 3.248344e-04   p_cons 9.711556e-01   p_joint 3.248344e-04

Joint ci ratio: 1.249447e-01	ci left: 3.044591e-04	ci right 3.453506e-04	k: 983	n:3030000
Cons ci ratio: 3.881783e-04	ci left: 9.709564e-01	ci right 9.713337e-01	k: 2942571	n:3030000
KS ci ratio: 1.249447e-01	ci left: 3.044591e-04	ci right 3.453506e-04	k: 983	n:3030000
CPNE3   3030000 perm   4536 sec   (668 perm/sec)   p_kst 3.244224e-04   p_cons 9.711455e-01   p_joint 3.244224e-04

Joint ci ratio: 1.246915e-01	ci left: 3.047323e-04	ci right 3.455714e-04	k: 987	n:3040000
Cons ci ratio: 3.875744e-04	ci left: 9.709517e-01	ci right 9.713284e-01	k: 2952267	n:3040000
KS ci ratio: 1.246915e-01	ci left: 3.047323e-04	ci right 3.455714e-04	k: 987	n:3040000
CPNE3   3040000 perm   4563 sec   (666 perm/sec)   p_kst 3.246711e-04   p_cons 9.711405e-01   p_joint 3.246711e-04

Joint ci ratio: 1.245655e-01	ci left: 3.043685e-04	ci right 3.451146e-04	k: 989	n:3050000
Cons ci ratio: 3.869847e-04	ci left: 9.709453e-01	ci right 9.713214e-01	k: 2961958	n:3050000
KS ci ratio: 1.245655e-01	ci left: 3.043685e-04	ci right 3.451146e-04	k: 989	n:3050000
CPNE3   3050000 perm   4591 sec   (664 perm/sec)   p_kst 3.242623e-04   p_cons 9.711338e-01   p_joint 3.242623e-04

Joint ci ratio: 1.245027e-01	ci left: 3.036905e-04	ci right 3.443237e-04	k: 990	n:3060000
Cons ci ratio: 3.863954e-04	ci left: 9.709392e-01	ci right 9.713148e-01	k: 2971650	n:3060000
KS ci ratio: 1.245027e-01	ci left: 3.036905e-04	ci right 3.443237e-04	k: 990	n:3060000
CPNE3   3060000 perm   4618 sec   (663 perm/sec)   p_kst 3.235294e-04   p_cons 9.711275e-01   p_joint 3.235294e-04

Joint ci ratio: 1.240652e-01	ci left: 3.049105e-04	ci right 3.455531e-04	k: 997	n:3070000
Cons ci ratio: 3.858177e-04	ci left: 9.709319e-01	ci right 9.713069e-01	k: 2981338	n:3070000
KS ci ratio: 1.240652e-01	ci left: 3.049105e-04	ci right 3.455531e-04	k: 997	n:3070000
CPNE3   3070000 perm   4647 sec   (661 perm/sec)   p_kst 3.247557e-04   p_cons 9.711199e-01   p_joint 3.247557e-04

Joint ci ratio: 1.238173e-01	ci left: 3.051790e-04	ci right 3.457701e-04	k: 1001	n:3080000
Cons ci ratio: 3.851534e-04	ci left: 9.709377e-01	ci right 9.713121e-01	k: 2991066	n:3080000
KS ci ratio: 1.238173e-01	ci left: 3.051790e-04	ci right 3.457701e-04	k: 1001	n:3080000
CPNE3   3080000 perm   4675 sec   (659 perm/sec)   p_kst 3.250000e-04   p_cons 9.711253e-01   p_joint 3.250000e-04

Joint ci ratio: 1.235709e-01	ci left: 3.054458e-04	ci right 3.459857e-04	k: 1005	n:3090000
Cons ci ratio: 3.845325e-04	ci left: 9.709376e-01	ci right 9.713113e-01	k: 3000776	n:3090000
KS ci ratio: 1.235709e-01	ci left: 3.054458e-04	ci right 3.459857e-04	k: 1005	n:3090000
CPNE3   3090000 perm   4704 sec   (657 perm/sec)   p_kst 3.252427e-04   p_cons 9.711249e-01   p_joint 3.252427e-04

Joint ci ratio: 1.234483e-01	ci left: 3.050857e-04	ci right 3.455347e-04	k: 1007	n:3100000
Cons ci ratio: 3.838924e-04	ci left: 9.709407e-01	ci right 9.713139e-01	k: 3010496	n:3100000
KS ci ratio: 1.234483e-01	ci left: 3.050857e-04	ci right 3.455347e-04	k: 1007	n:3100000
CPNE3   3100000 perm   4732 sec   (655 perm/sec)   p_kst 3.248387e-04   p_cons 9.711277e-01   p_joint 3.248387e-04

Joint ci ratio: 1.232650e-01	ci left: 3.050396e-04	ci right 3.454180e-04	k: 1010	n:3110000
Cons ci ratio: 3.832248e-04	ci left: 9.709484e-01	ci right 9.713208e-01	k: 3020230	n:3110000
KS ci ratio: 1.232650e-01	ci left: 3.050396e-04	ci right 3.454180e-04	k: 1010	n:3110000
CPNE3   3110000 perm   4760 sec   (653 perm/sec)   p_kst 3.247588e-04   p_cons 9.711350e-01   p_joint 3.247588e-04

Joint ci ratio: 1.232651e-01	ci left: 3.040619e-04	ci right 3.443109e-04	k: 1010	n:3120000
Cons ci ratio: 3.826350e-04	ci left: 9.709450e-01	ci right 9.713169e-01	k: 3029930	n:3120000
KS ci ratio: 1.232651e-01	ci left: 3.040619e-04	ci right 3.443109e-04	k: 1010	n:3120000
CPNE3   3120000 perm   4789 sec   (652 perm/sec)   p_kst 3.237179e-04   p_cons 9.711314e-01   p_joint 3.237179e-04

Joint ci ratio: 1.230219e-01	ci left: 3.043290e-04	ci right 3.445282e-04	k: 1014	n:3130000
Cons ci ratio: 3.820544e-04	ci left: 9.709407e-01	ci right 9.713121e-01	k: 3039627	n:3130000
KS ci ratio: 1.230219e-01	ci left: 3.043290e-04	ci right 3.445282e-04	k: 1014	n:3130000
CPNE3   3130000 perm   4817 sec   (650 perm/sec)   p_kst 3.239617e-04   p_cons 9.711268e-01   p_joint 3.239617e-04

Joint ci ratio: 1.229009e-01	ci left: 3.039772e-04	ci right 3.440875e-04	k: 1016	n:3140000
Cons ci ratio: 3.814873e-04	ci left: 9.709349e-01	ci right 9.713057e-01	k: 3049319	n:3140000
KS ci ratio: 1.229009e-01	ci left: 3.039772e-04	ci right 3.440875e-04	k: 1016	n:3140000
CPNE3   3140000 perm   4846 sec   (648 perm/sec)   p_kst 3.235669e-04   p_cons 9.711207e-01   p_joint 3.235669e-04

Joint ci ratio: 1.226599e-01	ci left: 3.042430e-04	ci right 3.443040e-04	k: 1020	n:3150000
Cons ci ratio: 3.809550e-04	ci left: 9.709243e-01	ci right 9.712945e-01	k: 3058996	n:3150000
KS ci ratio: 1.226599e-01	ci left: 3.042430e-04	ci right 3.443040e-04	k: 1020	n:3150000
CPNE3   3150000 perm   4874 sec   (646 perm/sec)   p_kst 3.238095e-04   p_cons 9.711098e-01   p_joint 3.238095e-04

Joint ci ratio: 1.224801e-01	ci left: 3.042005e-04	ci right 3.441929e-04	k: 1023	n:3160000
Cons ci ratio: 3.802769e-04	ci left: 9.709357e-01	ci right 9.713053e-01	k: 3068742	n:3160000
KS ci ratio: 1.224801e-01	ci left: 3.042005e-04	ci right 3.441929e-04	k: 1023	n:3160000
CPNE3   3160000 perm   4903 sec   (645 perm/sec)   p_kst 3.237342e-04   p_cons 9.711209e-01   p_joint 3.237342e-04

Joint ci ratio: 1.223011e-01	ci left: 3.041582e-04	ci right 3.440824e-04	k: 1026	n:3170000
Cons ci ratio: 3.796471e-04	ci left: 9.709403e-01	ci right 9.713093e-01	k: 3078467	n:3170000
KS ci ratio: 1.223011e-01	ci left: 3.041582e-04	ci right 3.440824e-04	k: 1026	n:3170000
CPNE3   3170000 perm   4932 sec   (643 perm/sec)   p_kst 3.236593e-04   p_cons 9.711252e-01   p_joint 3.236593e-04

Joint ci ratio: 1.221229e-01	ci left: 3.041163e-04	ci right 3.439726e-04	k: 1029	n:3180000
Cons ci ratio: 3.790099e-04	ci left: 9.709465e-01	ci right 9.713149e-01	k: 3088197	n:3180000
KS ci ratio: 1.221229e-01	ci left: 3.041163e-04	ci right 3.439726e-04	k: 1029	n:3180000
CPNE3   3180000 perm   4962 sec   (641 perm/sec)   p_kst 3.235849e-04   p_cons 9.711311e-01   p_joint 3.235849e-04

Joint ci ratio: 1.220045e-01	ci left: 3.037708e-04	ci right 3.435404e-04	k: 1031	n:3190000
Cons ci ratio: 3.784033e-04	ci left: 9.709486e-01	ci right 9.713164e-01	k: 3097914	n:3190000
KS ci ratio: 1.220045e-01	ci left: 3.037708e-04	ci right 3.435404e-04	k: 1031	n:3190000
CPNE3   3190000 perm   4990 sec   (639 perm/sec)   p_kst 3.231975e-04   p_cons 9.711329e-01   p_joint 3.231975e-04

Joint ci ratio: 1.218276e-01	ci left: 3.037304e-04	ci right 3.434329e-04	k: 1034	n:3200000
Cons ci ratio: 3.778144e-04	ci left: 9.709485e-01	ci right 9.713157e-01	k: 3107624	n:3200000
KS ci ratio: 1.218276e-01	ci left: 3.037304e-04	ci right 3.434329e-04	k: 1034	n:3200000
CPNE3   3200000 perm   5020 sec   (637 perm/sec)   p_kst 3.231250e-04   p_cons 9.711325e-01   p_joint 3.231250e-04

Joint ci ratio: 1.215343e-01	ci left: 3.042945e-04	ci right 3.439681e-04	k: 1039	n:3210000
Cons ci ratio: 3.771989e-04	ci left: 9.709527e-01	ci right 9.713193e-01	k: 3117348	n:3210000
KS ci ratio: 1.215343e-01	ci left: 3.042945e-04	ci right 3.439681e-04	k: 1039	n:3210000
CPNE3   3210000 perm   5049 sec   (636 perm/sec)   p_kst 3.236760e-04   p_cons 9.711364e-01   p_joint 3.236760e-04

Joint ci ratio: 1.214760e-01	ci left: 3.036506e-04	ci right 3.432198e-04	k: 1040	n:3220000
Cons ci ratio: 3.765759e-04	ci left: 9.709585e-01	ci right 9.713245e-01	k: 3127077	n:3220000
KS ci ratio: 1.214760e-01	ci left: 3.036506e-04	ci right 3.432198e-04	k: 1040	n:3220000
CPNE3   3220000 perm   5078 sec   (634 perm/sec)   p_kst 3.229814e-04   p_cons 9.711419e-01   p_joint 3.229814e-04

Joint ci ratio: 1.211853e-01	ci left: 3.042115e-04	ci right 3.437522e-04	k: 1045	n:3230000
Cons ci ratio: 3.760619e-04	ci left: 9.709484e-01	ci right 9.713139e-01	k: 3136755	n:3230000
KS ci ratio: 1.211853e-01	ci left: 3.042115e-04	ci right 3.437522e-04	k: 1045	n:3230000
CPNE3   3230000 perm   5107 sec   (632 perm/sec)   p_kst 3.235294e-04   p_cons 9.711316e-01   p_joint 3.235294e-04

Joint ci ratio: 1.208391e-01	ci left: 3.050684e-04	ci right 3.445991e-04	k: 1051	n:3240000
Cons ci ratio: 3.754177e-04	ci left: 9.709582e-01	ci right 9.713231e-01	k: 3146497	n:3240000
KS ci ratio: 1.208391e-01	ci left: 3.050684e-04	ci right 3.445991e-04	k: 1051	n:3240000
CPNE3   3240000 perm   5137 sec   (631 perm/sec)   p_kst 3.243827e-04   p_cons 9.711410e-01   p_joint 3.243827e-04

Joint ci ratio: 1.207245e-01	ci left: 3.047265e-04	ci right 3.441728e-04	k: 1053	n:3250000
Cons ci ratio: 3.748179e-04	ci left: 9.709617e-01	ci right 9.713260e-01	k: 3156219	n:3250000
KS ci ratio: 1.207245e-01	ci left: 3.047265e-04	ci right 3.441728e-04	k: 1053	n:3250000
CPNE3   3250000 perm   5167 sec   (629 perm/sec)   p_kst 3.240000e-04   p_cons 9.711443e-01   p_joint 3.240000e-04

Joint ci ratio: 1.206101e-01	ci left: 3.043867e-04	ci right 3.437490e-04	k: 1055	n:3260000
Cons ci ratio: 3.743418e-04	ci left: 9.709471e-01	ci right 9.713109e-01	k: 3165882	n:3260000
KS ci ratio: 1.206101e-01	ci left: 3.043867e-04	ci right 3.437490e-04	k: 1055	n:3260000
CPNE3   3260000 perm   5198 sec   (627 perm/sec)   p_kst 3.236196e-04   p_cons 9.711294e-01   p_joint 3.236196e-04

Joint ci ratio: 1.204961e-01	ci left: 3.040490e-04	ci right 3.433279e-04	k: 1057	n:3270000
Cons ci ratio: 3.737858e-04	ci left: 9.709448e-01	ci right 9.713081e-01	k: 3175585	n:3270000
KS ci ratio: 1.204961e-01	ci left: 3.040490e-04	ci right 3.433279e-04	k: 1057	n:3270000
CPNE3   3270000 perm   5227 sec   (626 perm/sec)   p_kst 3.232416e-04   p_cons 9.711269e-01   p_joint 3.232416e-04

Joint ci ratio: 1.203824e-01	ci left: 3.037134e-04	ci right 3.429092e-04	k: 1059	n:3280000
Cons ci ratio: 3.732547e-04	ci left: 9.709392e-01	ci right 9.713020e-01	k: 3185277	n:3280000
KS ci ratio: 1.203824e-01	ci left: 3.037134e-04	ci right 3.429092e-04	k: 1059	n:3280000
CPNE3   3280000 perm   5256 sec   (624 perm/sec)   p_kst 3.228659e-04   p_cons 9.711210e-01   p_joint 3.228659e-04

Joint ci ratio: 1.203257e-01	ci left: 3.030851e-04	ci right 3.421801e-04	k: 1060	n:3290000
Cons ci ratio: 3.726571e-04	ci left: 9.709440e-01	ci right 9.713062e-01	k: 3195003	n:3290000
KS ci ratio: 1.203257e-01	ci left: 3.030851e-04	ci right 3.421801e-04	k: 1060	n:3290000
CPNE3   3290000 perm   5287 sec   (622 perm/sec)   p_kst 3.221884e-04   p_cons 9.711255e-01   p_joint 3.221884e-04

Joint ci ratio: 1.200995e-01	ci left: 3.033423e-04	ci right 3.423917e-04	k: 1064	n:3300000
Cons ci ratio: 3.720745e-04	ci left: 9.709470e-01	ci right 9.713086e-01	k: 3204723	n:3300000
KS ci ratio: 1.200995e-01	ci left: 3.033423e-04	ci right 3.423917e-04	k: 1064	n:3300000
CPNE3   3300000 perm   5317 sec   (621 perm/sec)   p_kst 3.224242e-04   p_cons 9.711282e-01   p_joint 3.224242e-04

Joint ci ratio: 1.198746e-01	ci left: 3.035981e-04	ci right 3.426020e-04	k: 1068	n:3310000
Cons ci ratio: 3.714205e-04	ci left: 9.709611e-01	ci right 9.713221e-01	k: 3214480	n:3310000
KS ci ratio: 1.198746e-01	ci left: 3.035981e-04	ci right 3.426020e-04	k: 1068	n:3310000
CPNE3   3310000 perm   5347 sec   (619 perm/sec)   p_kst 3.226586e-04   p_cons 9.711420e-01   p_joint 3.226586e-04

Joint ci ratio: 1.195952e-01	ci left: 3.041445e-04	ci right 3.431212e-04	k: 1073	n:3320000
Cons ci ratio: 3.708914e-04	ci left: 9.709567e-01	ci right 9.713172e-01	k: 3224176	n:3320000
KS ci ratio: 1.195952e-01	ci left: 3.041445e-04	ci right 3.431212e-04	k: 1073	n:3320000
CPNE3   3320000 perm   5377 sec   (617 perm/sec)   p_kst 3.231928e-04   p_cons 9.711373e-01   p_joint 3.231928e-04

Joint ci ratio: 1.192624e-01	ci left: 3.049792e-04	ci right 3.439464e-04	k: 1079	n:3330000
Cons ci ratio: 3.702833e-04	ci left: 9.709647e-01	ci right 9.713246e-01	k: 3233913	n:3330000
KS ci ratio: 1.192624e-01	ci left: 3.049792e-04	ci right 3.439464e-04	k: 1079	n:3330000
CPNE3   3330000 perm   5408 sec   (616 perm/sec)   p_kst 3.240240e-04   p_cons 9.711450e-01   p_joint 3.240240e-04

Joint ci ratio: 1.190422e-01	ci left: 3.052280e-04	ci right 3.441499e-04	k: 1083	n:3340000
Cons ci ratio: 3.697354e-04	ci left: 9.709639e-01	ci right 9.713233e-01	k: 3243621	n:3340000
KS ci ratio: 1.190422e-01	ci left: 3.052280e-04	ci right 3.441499e-04	k: 1083	n:3340000
CPNE3   3340000 perm   5438 sec   (614 perm/sec)   p_kst 3.242515e-04   p_cons 9.711440e-01   p_joint 3.242515e-04

Joint ci ratio: 1.186596e-01	ci left: 3.063443e-04	ci right 3.452742e-04	k: 1090	n:3350000
Cons ci ratio: 3.691230e-04	ci left: 9.709733e-01	ci right 9.713321e-01	k: 3253363	n:3350000
KS ci ratio: 1.186596e-01	ci left: 3.063443e-04	ci right 3.452742e-04	k: 1090	n:3350000
CPNE3   3350000 perm   5468 sec   (613 perm/sec)   p_kst 3.253731e-04   p_cons 9.711531e-01   p_joint 3.253731e-04

Joint ci ratio: 1.183886e-01	ci left: 3.068765e-04	ci right 3.457788e-04	k: 1095	n:3360000
Cons ci ratio: 3.686057e-04	ci left: 9.709687e-01	ci right 9.713269e-01	k: 3263058	n:3360000
KS ci ratio: 1.183886e-01	ci left: 3.068765e-04	ci right 3.457788e-04	k: 1095	n:3360000
CPNE3   3360000 perm   5499 sec   (611 perm/sec)   p_kst 3.258929e-04   p_cons 9.711482e-01   p_joint 3.258929e-04

Joint ci ratio: 1.181731e-01	ci left: 3.071178e-04	ci right 3.459748e-04	k: 1099	n:3370000
Cons ci ratio: 3.680067e-04	ci left: 9.709768e-01	ci right 9.713345e-01	k: 3272796	n:3370000
KS ci ratio: 1.181731e-01	ci left: 3.071178e-04	ci right 3.459748e-04	k: 1099	n:3370000
CPNE3   3370000 perm   5530 sec   (609 perm/sec)   p_kst 3.261128e-04   p_cons 9.711561e-01   p_joint 3.261128e-04

Joint ci ratio: 1.181732e-01	ci left: 3.062091e-04	ci right 3.449512e-04	k: 1099	n:3380000
Cons ci ratio: 3.674067e-04	ci left: 9.709855e-01	ci right 9.713426e-01	k: 3282536	n:3380000
KS ci ratio: 1.181732e-01	ci left: 3.062091e-04	ci right 3.449512e-04	k: 1099	n:3380000
CPNE3   3380000 perm   5561 sec   (608 perm/sec)   p_kst 3.251479e-04   p_cons 9.711645e-01   p_joint 3.251479e-04

Joint ci ratio: 1.179589e-01	ci left: 3.064509e-04	ci right 3.451484e-04	k: 1103	n:3390000
Cons ci ratio: 3.668347e-04	ci left: 9.709904e-01	ci right 9.713469e-01	k: 3292263	n:3390000
KS ci ratio: 1.179589e-01	ci left: 3.064509e-04	ci right 3.451484e-04	k: 1103	n:3390000
CPNE3   3390000 perm   5592 sec   (606 perm/sec)   p_kst 3.253687e-04   p_cons 9.711690e-01   p_joint 3.253687e-04

Joint ci ratio: 1.178522e-01	ci left: 3.061205e-04	ci right 3.447388e-04	k: 1105	n:3400000
Cons ci ratio: 3.663327e-04	ci left: 9.709848e-01	ci right 9.713409e-01	k: 3301955	n:3400000
KS ci ratio: 1.178522e-01	ci left: 3.061205e-04	ci right 3.447388e-04	k: 1105	n:3400000
CPNE3   3400000 perm   5623 sec   (605 perm/sec)   p_kst 3.250000e-04   p_cons 9.711632e-01   p_joint 3.250000e-04

Joint ci ratio: 1.175867e-01	ci left: 3.066459e-04	ci right 3.452373e-04	k: 1110	n:3410000
Cons ci ratio: 3.657619e-04	ci left: 9.709902e-01	ci right 9.713457e-01	k: 3311684	n:3410000
KS ci ratio: 1.175867e-01	ci left: 3.066459e-04	ci right 3.452373e-04	k: 1110	n:3410000
CPNE3   3410000 perm   5654 sec   (603 perm/sec)   p_kst 3.255132e-04   p_cons 9.711683e-01   p_joint 3.255132e-04

Joint ci ratio: 1.174283e-01	ci left: 3.066007e-04	ci right 3.451308e-04	k: 1113	n:3420000
Cons ci ratio: 3.652071e-04	ci left: 9.709935e-01	ci right 9.713484e-01	k: 3321406	n:3420000
KS ci ratio: 1.174283e-01	ci left: 3.066007e-04	ci right 3.451308e-04	k: 1113	n:3420000
CPNE3   3420000 perm   5685 sec   (602 perm/sec)   p_kst 3.254386e-04   p_cons 9.711713e-01   p_joint 3.254386e-04

Joint ci ratio: 1.173756e-01	ci left: 3.059898e-04	ci right 3.444247e-04	k: 1114	n:3430000
Cons ci ratio: 3.646776e-04	ci left: 9.709932e-01	ci right 9.713477e-01	k: 3331116	n:3430000
KS ci ratio: 1.173756e-01	ci left: 3.059898e-04	ci right 3.444247e-04	k: 1114	n:3430000
CPNE3   3430000 perm   5716 sec   (600 perm/sec)   p_kst 3.247813e-04   p_cons 9.711708e-01   p_joint 3.247813e-04

Joint ci ratio: 1.172705e-01	ci left: 3.056646e-04	ci right 3.440219e-04	k: 1116	n:3440000
Cons ci ratio: 3.641787e-04	ci left: 9.709886e-01	ci right 9.713426e-01	k: 3340811	n:3440000
KS ci ratio: 1.172705e-01	ci left: 3.056646e-04	ci right 3.440219e-04	k: 1116	n:3440000
CPNE3   3440000 perm   5746 sec   (599 perm/sec)   p_kst 3.244186e-04   p_cons 9.711660e-01   p_joint 3.244186e-04

Joint ci ratio: 1.170611e-01	ci left: 3.059041e-04	ci right 3.442181e-04	k: 1120	n:3450000
Cons ci ratio: 3.635859e-04	ci left: 9.709989e-01	ci right 9.713522e-01	k: 3350557	n:3450000
KS ci ratio: 1.170611e-01	ci left: 3.059041e-04	ci right 3.442181e-04	k: 1120	n:3450000
CPNE3   3450000 perm   5778 sec   (597 perm/sec)   p_kst 3.246377e-04   p_cons 9.711759e-01   p_joint 3.246377e-04

Joint ci ratio: 1.169568e-01	ci left: 3.055811e-04	ci right 3.438182e-04	k: 1122	n:3460000
Cons ci ratio: 3.630503e-04	ci left: 9.710006e-01	ci right 9.713535e-01	k: 3360274	n:3460000
KS ci ratio: 1.169568e-01	ci left: 3.055811e-04	ci right 3.438182e-04	k: 1122	n:3460000
CPNE3   3460000 perm   5809 sec   (596 perm/sec)   p_kst 3.242775e-04   p_cons 9.711775e-01   p_joint 3.242775e-04

Joint ci ratio: 1.168009e-01	ci left: 3.055397e-04	ci right 3.437172e-04	k: 1125	n:3470000
Cons ci ratio: 3.625637e-04	ci left: 9.709952e-01	ci right 9.713476e-01	k: 3369966	n:3470000
KS ci ratio: 1.168009e-01	ci left: 3.055397e-04	ci right 3.437172e-04	k: 1125	n:3470000
CPNE3   3470000 perm   5841 sec   (594 perm/sec)   p_kst 3.242075e-04   p_cons 9.711718e-01   p_joint 3.242075e-04

Joint ci ratio: 1.167491e-01	ci left: 3.049407e-04	ci right 3.430253e-04	k: 1126	n:3480000
Cons ci ratio: 3.620660e-04	ci left: 9.709918e-01	ci right 9.713437e-01	k: 3379665	n:3480000
KS ci ratio: 1.167491e-01	ci left: 3.049407e-04	ci right 3.430253e-04	k: 1126	n:3480000
CPNE3   3480000 perm   5872 sec   (593 perm/sec)   p_kst 3.235632e-04   p_cons 9.711681e-01   p_joint 3.235632e-04

Joint ci ratio: 1.163882e-01	ci left: 3.060142e-04	ci right 3.441066e-04	k: 1133	n:3490000
Cons ci ratio: 3.615556e-04	ci left: 9.709907e-01	ci right 9.713421e-01	k: 3389372	n:3490000
KS ci ratio: 1.163882e-01	ci left: 3.060142e-04	ci right 3.441066e-04	k: 1133	n:3490000
CPNE3   3490000 perm   5904 sec   (591 perm/sec)   p_kst 3.246418e-04   p_cons 9.711668e-01   p_joint 3.246418e-04

Joint ci ratio: 1.159290e-01	ci left: 3.076366e-04	ci right 3.457695e-04	k: 1142	n:3500000
Cons ci ratio: 3.610841e-04	ci left: 9.709838e-01	ci right 9.713348e-01	k: 3399059	n:3500000
KS ci ratio: 1.159290e-01	ci left: 3.076366e-04	ci right 3.457695e-04	k: 1142	n:3500000
CPNE3   3500000 perm   5936 sec   (590 perm/sec)   p_kst 3.262857e-04   p_cons 9.711597e-01   p_joint 3.262857e-04

Joint ci ratio: 1.156762e-01	ci left: 3.081434e-04	ci right 3.462501e-04	k: 1147	n:3510000
Cons ci ratio: 3.605595e-04	ci left: 9.709856e-01	ci right 9.713361e-01	k: 3408776	n:3510000
KS ci ratio: 1.156762e-01	ci left: 3.081434e-04	ci right 3.462501e-04	k: 1147	n:3510000
CPNE3   3510000 perm   5967 sec   (588 perm/sec)   p_kst 3.267806e-04   p_cons 9.711613e-01   p_joint 3.267806e-04

Joint ci ratio: 1.154251e-01	ci left: 3.086474e-04	ci right 3.467280e-04	k: 1152	n:3520000
Cons ci ratio: 3.600042e-04	ci left: 9.709926e-01	ci right 9.713425e-01	k: 3418511	n:3520000
KS ci ratio: 1.154251e-01	ci left: 3.086474e-04	ci right 3.467280e-04	k: 1152	n:3520000
CPNE3   3520000 perm   5999 sec   (587 perm/sec)   p_kst 3.272727e-04   p_cons 9.711679e-01   p_joint 3.272727e-04

Joint ci ratio: 1.153251e-01	ci left: 3.083232e-04	ci right 3.463286e-04	k: 1154	n:3530000
Cons ci ratio: 3.595207e-04	ci left: 9.709886e-01	ci right 9.713381e-01	k: 3428208	n:3530000
KS ci ratio: 1.153251e-01	ci left: 3.083232e-04	ci right 3.463286e-04	k: 1154	n:3530000
CPNE3   3530000 perm   6032 sec   (585 perm/sec)   p_kst 3.269122e-04   p_cons 9.711637e-01   p_joint 3.269122e-04

Joint ci ratio: 1.151757e-01	ci left: 3.082753e-04	ci right 3.462222e-04	k: 1157	n:3540000
Cons ci ratio: 3.589666e-04	ci left: 9.709961e-01	ci right 9.713450e-01	k: 3437945	n:3540000
KS ci ratio: 1.151757e-01	ci left: 3.082753e-04	ci right 3.462222e-04	k: 1157	n:3540000
CPNE3   3540000 perm   6064 sec   (584 perm/sec)   p_kst 3.268362e-04   p_cons 9.711709e-01   p_joint 3.268362e-04

Joint ci ratio: 1.151260e-01	ci left: 3.076805e-04	ci right 3.455367e-04	k: 1158	n:3550000
Cons ci ratio: 3.584168e-04	ci left: 9.710032e-01	ci right 9.713515e-01	k: 3447681	n:3550000
KS ci ratio: 1.151260e-01	ci left: 3.076805e-04	ci right 3.455367e-04	k: 1158	n:3550000
CPNE3   3550000 perm   6096 sec   (582 perm/sec)   p_kst 3.261972e-04   p_cons 9.711777e-01   p_joint 3.261972e-04

Joint ci ratio: 1.150764e-01	ci left: 3.070890e-04	ci right 3.448551e-04	k: 1159	n:3560000
Cons ci ratio: 3.578642e-04	ci left: 9.710111e-01	ci right 9.713589e-01	k: 3457420	n:3560000
KS ci ratio: 1.150764e-01	ci left: 3.070890e-04	ci right 3.448551e-04	k: 1159	n:3560000
CPNE3   3560000 perm   6128 sec   (581 perm/sec)   p_kst 3.255618e-04   p_cons 9.711854e-01   p_joint 3.255618e-04

Joint ci ratio: 1.149279e-01	ci left: 3.070450e-04	ci right 3.447536e-04	k: 1162	n:3570000
Cons ci ratio: 3.573284e-04	ci left: 9.710167e-01	ci right 9.713640e-01	k: 3467151	n:3570000
KS ci ratio: 1.149279e-01	ci left: 3.070450e-04	ci right 3.447536e-04	k: 1162	n:3570000
CPNE3   3570000 perm   6161 sec   (579 perm/sec)   p_kst 3.254902e-04   p_cons 9.711908e-01   p_joint 3.254902e-04

Joint ci ratio: 1.147307e-01	ci left: 3.072725e-04	ci right 3.449400e-04	k: 1166	n:3580000
Cons ci ratio: 3.568163e-04	ci left: 9.710190e-01	ci right 9.713658e-01	k: 3476870	n:3580000
KS ci ratio: 1.147307e-01	ci left: 3.072725e-04	ci right 3.449400e-04	k: 1166	n:3580000
CPNE3   3580000 perm   6194 sec   (578 perm/sec)   p_kst 3.256983e-04   p_cons 9.711927e-01   p_joint 3.256983e-04

Joint ci ratio: 1.145346e-01	ci left: 3.074989e-04	ci right 3.451253e-04	k: 1170	n:3590000
Cons ci ratio: 3.562834e-04	ci left: 9.710248e-01	ci right 9.713711e-01	k: 3486602	n:3590000
KS ci ratio: 1.145346e-01	ci left: 3.074989e-04	ci right 3.451253e-04	k: 1170	n:3590000
CPNE3   3590000 perm   6226 sec   (577 perm/sec)   p_kst 3.259053e-04   p_cons 9.711983e-01   p_joint 3.259053e-04

Joint ci ratio: 1.143882e-01	ci left: 3.074542e-04	ci right 3.450238e-04	k: 1173	n:3600000
Cons ci ratio: 3.557935e-04	ci left: 9.710242e-01	ci right 9.713700e-01	k: 3496311	n:3600000
KS ci ratio: 1.143882e-01	ci left: 3.074542e-04	ci right 3.450238e-04	k: 1173	n:3600000
CPNE3   3600000 perm   6259 sec   (575 perm/sec)   p_kst 3.258333e-04   p_cons 9.711975e-01   p_joint 3.258333e-04

Joint ci ratio: 1.143395e-01	ci left: 3.068716e-04	ci right 3.443530e-04	k: 1174	n:3610000
Cons ci ratio: 3.553355e-04	ci left: 9.710189e-01	ci right 9.713643e-01	k: 3506003	n:3610000
KS ci ratio: 1.143395e-01	ci left: 3.068716e-04	ci right 3.443530e-04	k: 1174	n:3610000
CPNE3   3610000 perm   6291 sec   (574 perm/sec)   p_kst 3.252078e-04   p_cons 9.711920e-01   p_joint 3.252078e-04

Joint ci ratio: 1.139040e-01	ci left: 3.084391e-04	ci right 3.459589e-04	k: 1183	n:3620000
Cons ci ratio: 3.548862e-04	ci left: 9.710125e-01	ci right 9.713574e-01	k: 3515691	n:3620000
KS ci ratio: 1.139040e-01	ci left: 3.084391e-04	ci right 3.459589e-04	k: 1183	n:3620000
CPNE3   3620000 perm   6324 sec   (572 perm/sec)   p_kst 3.267956e-04   p_cons 9.711854e-01   p_joint 3.267956e-04

Joint ci ratio: 1.139041e-01	ci left: 3.075894e-04	ci right 3.450058e-04	k: 1183	n:3630000
Cons ci ratio: 3.543201e-04	ci left: 9.710250e-01	ci right 9.713693e-01	k: 3525447	n:3630000
KS ci ratio: 1.139041e-01	ci left: 3.075894e-04	ci right 3.450058e-04	k: 1183	n:3630000
CPNE3   3630000 perm   6357 sec   (571 perm/sec)   p_kst 3.258953e-04   p_cons 9.711975e-01   p_joint 3.258953e-04

Joint ci ratio: 1.137122e-01	ci left: 3.078120e-04	ci right 3.451882e-04	k: 1187	n:3640000
Cons ci ratio: 3.538417e-04	ci left: 9.710238e-01	ci right 9.713677e-01	k: 3535154	n:3640000
KS ci ratio: 1.137122e-01	ci left: 3.078120e-04	ci right 3.451882e-04	k: 1187	n:3640000
CPNE3   3640000 perm   6390 sec   (570 perm/sec)   p_kst 3.260989e-04   p_cons 9.711962e-01   p_joint 3.260989e-04

Joint ci ratio: 1.136166e-01	ci left: 3.075011e-04	ci right 3.448060e-04	k: 1189	n:3650000
Cons ci ratio: 3.533496e-04	ci left: 9.710252e-01	ci right 9.713686e-01	k: 3544870	n:3650000
KS ci ratio: 1.136166e-01	ci left: 3.075011e-04	ci right 3.448060e-04	k: 1189	n:3650000
CPNE3   3650000 perm   6423 sec   (568 perm/sec)   p_kst 3.257534e-04   p_cons 9.711973e-01   p_joint 3.257534e-04

Joint ci ratio: 1.133312e-01	ci left: 3.082537e-04	ci right 3.455497e-04	k: 1195	n:3660000
Cons ci ratio: 3.528769e-04	ci left: 9.710238e-01	ci right 9.713667e-01	k: 3554576	n:3660000
KS ci ratio: 1.133312e-01	ci left: 3.082537e-04	ci right 3.455497e-04	k: 1195	n:3660000
CPNE3   3660000 perm   6457 sec   (567 perm/sec)   p_kst 3.265027e-04   p_cons 9.711956e-01   p_joint 3.265027e-04

Joint ci ratio: 1.132366e-01	ci left: 3.079433e-04	ci right 3.451686e-04	k: 1197	n:3670000
Cons ci ratio: 3.524695e-04	ci left: 9.710123e-01	ci right 9.713548e-01	k: 3564245	n:3670000
KS ci ratio: 1.132366e-01	ci left: 3.079433e-04	ci right 3.451686e-04	k: 1197	n:3670000
CPNE3   3670000 perm   6489 sec   (566 perm/sec)   p_kst 3.261580e-04   p_cons 9.711839e-01   p_joint 3.261580e-04

Joint ci ratio: 1.131422e-01	ci left: 3.076346e-04	ci right 3.447895e-04	k: 1199	n:3680000
Cons ci ratio: 3.520088e-04	ci left: 9.710095e-01	ci right 9.713517e-01	k: 3573946	n:3680000
KS ci ratio: 1.131422e-01	ci left: 3.076346e-04	ci right 3.447895e-04	k: 1199	n:3680000
CPNE3   3680000 perm   6523 sec   (564 perm/sec)   p_kst 3.258152e-04   p_cons 9.711810e-01   p_joint 3.258152e-04

Joint ci ratio: 1.130480e-01	ci left: 3.073276e-04	ci right 3.444124e-04	k: 1201	n:3690000
Cons ci ratio: 3.515516e-04	ci left: 9.710066e-01	ci right 9.713482e-01	k: 3583646	n:3690000
KS ci ratio: 1.130480e-01	ci left: 3.073276e-04	ci right 3.444124e-04	k: 1201	n:3690000
CPNE3   3690000 perm   6556 sec   (563 perm/sec)   p_kst 3.254743e-04   p_cons 9.711778e-01   p_joint 3.254743e-04

Joint ci ratio: 1.128604e-01	ci left: 3.075475e-04	ci right 3.445932e-04	k: 1205	n:3700000
Cons ci ratio: 3.509894e-04	ci left: 9.710207e-01	ci right 9.713618e-01	k: 3593409	n:3700000
KS ci ratio: 1.128604e-01	ci left: 3.075475e-04	ci right 3.445932e-04	k: 1205	n:3700000
CPNE3   3700000 perm   6589 sec   (562 perm/sec)   p_kst 3.256757e-04   p_cons 9.711916e-01   p_joint 3.256757e-04

Joint ci ratio: 1.126737e-01	ci left: 3.077663e-04	ci right 3.447729e-04	k: 1209	n:3710000
Cons ci ratio: 3.504855e-04	ci left: 9.710258e-01	ci right 9.713665e-01	k: 3603139	n:3710000
KS ci ratio: 1.126737e-01	ci left: 3.077663e-04	ci right 3.447729e-04	k: 1209	n:3710000
CPNE3   3710000 perm   6623 sec   (560 perm/sec)   p_kst 3.258760e-04   p_cons 9.711965e-01   p_joint 3.258760e-04

Joint ci ratio: 1.124879e-01	ci left: 3.079840e-04	ci right 3.449516e-04	k: 1213	n:3720000
Cons ci ratio: 3.500157e-04	ci left: 9.710258e-01	ci right 9.713660e-01	k: 3612850	n:3720000
KS ci ratio: 1.124879e-01	ci left: 3.079840e-04	ci right 3.449516e-04	k: 1213	n:3720000
CPNE3   3720000 perm   6656 sec   (559 perm/sec)   p_kst 3.260753e-04   p_cons 9.711962e-01   p_joint 3.260753e-04

Joint ci ratio: 1.122569e-01	ci left: 3.084611e-04	ci right 3.454050e-04	k: 1218	n:3730000
Cons ci ratio: 3.495595e-04	ci left: 9.710239e-01	ci right 9.713636e-01	k: 3622554	n:3730000
KS ci ratio: 1.122569e-01	ci left: 3.084611e-04	ci right 3.454050e-04	k: 1218	n:3730000
CPNE3   3730000 perm   6690 sec   (558 perm/sec)   p_kst 3.265416e-04   p_cons 9.711941e-01   p_joint 3.265416e-04

Joint ci ratio: 1.121650e-01	ci left: 3.081561e-04	ci right 3.450312e-04	k: 1220	n:3740000
Cons ci ratio: 3.491085e-04	ci left: 9.710214e-01	ci right 9.713607e-01	k: 3632256	n:3740000
KS ci ratio: 1.121650e-01	ci left: 3.081561e-04	ci right 3.450312e-04	k: 1220	n:3740000
CPNE3   3740000 perm   6724 sec   (556 perm/sec)   p_kst 3.262032e-04   p_cons 9.711914e-01   p_joint 3.262032e-04

Joint ci ratio: 1.120274e-01	ci left: 3.081119e-04	ci right 3.449335e-04	k: 1223	n:3750000
Cons ci ratio: 3.486608e-04	ci left: 9.710187e-01	ci right 9.713576e-01	k: 3641957	n:3750000
KS ci ratio: 1.120274e-01	ci left: 3.081119e-04	ci right 3.449335e-04	k: 1223	n:3750000
CPNE3   3750000 perm   6757 sec   (555 perm/sec)   p_kst 3.261333e-04   p_cons 9.711885e-01   p_joint 3.261333e-04

Joint ci ratio: 1.119360e-01	ci left: 3.078094e-04	ci right 3.445630e-04	k: 1225	n:3760000
Cons ci ratio: 3.481983e-04	ci left: 9.710187e-01	ci right 9.713571e-01	k: 3651668	n:3760000
KS ci ratio: 1.119360e-01	ci left: 3.078094e-04	ci right 3.445630e-04	k: 1225	n:3760000
CPNE3   3760000 perm   6791 sec   (554 perm/sec)   p_kst 3.257979e-04   p_cons 9.711883e-01   p_joint 3.257979e-04

Joint ci ratio: 1.117085e-01	ci left: 3.082821e-04	ci right 3.450123e-04	k: 1230	n:3770000
Cons ci ratio: 3.477574e-04	ci left: 9.710155e-01	ci right 9.713535e-01	k: 3661367	n:3770000
KS ci ratio: 1.117085e-01	ci left: 3.082821e-04	ci right 3.450123e-04	k: 1230	n:3770000
CPNE3   3770000 perm   6825 sec   (552 perm/sec)   p_kst 3.262599e-04   p_cons 9.711849e-01   p_joint 3.262599e-04

Joint ci ratio: 1.115274e-01	ci left: 3.084952e-04	ci right 3.451873e-04	k: 1234	n:3780000
Cons ci ratio: 3.472378e-04	ci left: 9.710253e-01	ci right 9.713628e-01	k: 3671115	n:3780000
KS ci ratio: 1.115274e-01	ci left: 3.084952e-04	ci right 3.451873e-04	k: 1234	n:3780000
CPNE3   3780000 perm   6860 sec   (551 perm/sec)   p_kst 3.264550e-04   p_cons 9.711944e-01   p_joint 3.264550e-04

Joint ci ratio: 1.113922e-01	ci left: 3.084508e-04	ci right 3.450902e-04	k: 1237	n:3790000
Cons ci ratio: 3.468267e-04	ci left: 9.710179e-01	ci right 9.713550e-01	k: 3680798	n:3790000
KS ci ratio: 1.113922e-01	ci left: 3.084508e-04	ci right 3.450902e-04	k: 1237	n:3790000
CPNE3   3790000 perm   6894 sec   (550 perm/sec)   p_kst 3.263852e-04   p_cons 9.711868e-01   p_joint 3.263852e-04

Joint ci ratio: 1.110339e-01	ci left: 3.096858e-04	ci right 3.463458e-04	k: 1245	n:3800000
Cons ci ratio: 3.463910e-04	ci left: 9.710147e-01	ci right 9.713514e-01	k: 3690497	n:3800000
KS ci ratio: 1.110339e-01	ci left: 3.096858e-04	ci right 3.463458e-04	k: 1245	n:3800000
CPNE3   3800000 perm   6929 sec   (548 perm/sec)   p_kst 3.276316e-04   p_cons 9.711834e-01   p_joint 3.276316e-04

Joint ci ratio: 1.110340e-01	ci left: 3.088729e-04	ci right 3.454368e-04	k: 1245	n:3810000
Cons ci ratio: 3.459407e-04	ci left: 9.710142e-01	ci right 9.713504e-01	k: 3700206	n:3810000
KS ci ratio: 1.110340e-01	ci left: 3.088729e-04	ci right 3.454368e-04	k: 1245	n:3810000
CPNE3   3810000 perm   6963 sec   (547 perm/sec)   p_kst 3.267717e-04   p_cons 9.711827e-01   p_joint 3.267717e-04

Joint ci ratio: 1.109450e-01	ci left: 3.085734e-04	ci right 3.450706e-04	k: 1247	n:3820000
Cons ci ratio: 3.454679e-04	ci left: 9.710176e-01	ci right 9.713534e-01	k: 3709930	n:3820000
KS ci ratio: 1.109450e-01	ci left: 3.085734e-04	ci right 3.450706e-04	k: 1247	n:3820000
CPNE3   3820000 perm   6998 sec   (546 perm/sec)   p_kst 3.264398e-04   p_cons 9.711859e-01   p_joint 3.264398e-04

Joint ci ratio: 1.109006e-01	ci left: 3.080216e-04	ci right 3.444380e-04	k: 1248	n:3830000
Cons ci ratio: 3.450647e-04	ci left: 9.710100e-01	ci right 9.713454e-01	k: 3719612	n:3830000
KS ci ratio: 1.109006e-01	ci left: 3.080216e-04	ci right 3.444380e-04	k: 1248	n:3830000
CPNE3   3830000 perm   7032 sec   (545 perm/sec)   p_kst 3.258486e-04   p_cons 9.711781e-01   p_joint 3.258486e-04

Joint ci ratio: 1.107677e-01	ci left: 3.079790e-04	ci right 3.443439e-04	k: 1251	n:3840000
Cons ci ratio: 3.446356e-04	ci left: 9.710069e-01	ci right 9.713419e-01	k: 3729311	n:3840000
KS ci ratio: 1.107677e-01	ci left: 3.079790e-04	ci right 3.443439e-04	k: 1251	n:3840000
CPNE3   3840000 perm   7067 sec   (543 perm/sec)   p_kst 3.257813e-04   p_cons 9.711747e-01   p_joint 3.257813e-04

Joint ci ratio: 1.106352e-01	ci left: 3.079367e-04	ci right 3.442503e-04	k: 1254	n:3850000
Cons ci ratio: 3.441713e-04	ci left: 9.710098e-01	ci right 9.713443e-01	k: 3739033	n:3850000
KS ci ratio: 1.106352e-01	ci left: 3.079367e-04	ci right 3.442503e-04	k: 1254	n:3850000
CPNE3   3850000 perm   7101 sec   (542 perm/sec)   p_kst 3.257143e-04   p_cons 9.711774e-01   p_joint 3.257143e-04

Joint ci ratio: 1.105472e-01	ci left: 3.076428e-04	ci right 3.438909e-04	k: 1256	n:3860000
Cons ci ratio: 3.437233e-04	ci left: 9.710103e-01	ci right 9.713444e-01	k: 3748746	n:3860000
KS ci ratio: 1.105472e-01	ci left: 3.076428e-04	ci right 3.438909e-04	k: 1256	n:3860000
CPNE3   3860000 perm   7136 sec   (541 perm/sec)   p_kst 3.253886e-04   p_cons 9.711777e-01   p_joint 3.253886e-04

Joint ci ratio: 1.104155e-01	ci left: 3.076016e-04	ci right 3.437989e-04	k: 1259	n:3870000
Cons ci ratio: 3.432960e-04	ci left: 9.710078e-01	ci right 9.713414e-01	k: 3758447	n:3870000
KS ci ratio: 1.104155e-01	ci left: 3.076016e-04	ci right 3.437989e-04	k: 1259	n:3870000
CPNE3   3870000 perm   7170 sec   (540 perm/sec)   p_kst 3.253230e-04   p_cons 9.711749e-01   p_joint 3.253230e-04

Joint ci ratio: 1.100666e-01	ci left: 3.088138e-04	ci right 3.450315e-04	k: 1267	n:3880000
Cons ci ratio: 3.428813e-04	ci left: 9.710034e-01	ci right 9.713366e-01	k: 3768141	n:3880000
KS ci ratio: 1.100666e-01	ci left: 3.088138e-04	ci right 3.450315e-04	k: 1267	n:3880000
CPNE3   3880000 perm   7205 sec   (539 perm/sec)   p_kst 3.265464e-04   p_cons 9.711704e-01   p_joint 3.265464e-04

Joint ci ratio: 1.098934e-01	ci left: 3.090199e-04	ci right 3.452011e-04	k: 1271	n:3890000
Cons ci ratio: 3.424728e-04	ci left: 9.709983e-01	ci right 9.713311e-01	k: 3777832	n:3890000
KS ci ratio: 1.098934e-01	ci left: 3.090199e-04	ci right 3.452011e-04	k: 1271	n:3890000
CPNE3   3890000 perm   7240 sec   (537 perm/sec)   p_kst 3.267352e-04   p_cons 9.711650e-01   p_joint 3.267352e-04

Joint ci ratio: 1.097640e-01	ci left: 3.089757e-04	ci right 3.451063e-04	k: 1274	n:3900000
Cons ci ratio: 3.420423e-04	ci left: 9.709970e-01	ci right 9.713295e-01	k: 3787538	n:3900000
KS ci ratio: 1.097640e-01	ci left: 3.089757e-04	ci right 3.451063e-04	k: 1274	n:3900000
CPNE3   3900000 perm   7275 sec   (536 perm/sec)   p_kst 3.266667e-04   p_cons 9.711636e-01   p_joint 3.266667e-04

Joint ci ratio: 1.095922e-01	ci left: 3.091804e-04	ci right 3.452747e-04	k: 1278	n:3910000
Cons ci ratio: 3.416072e-04	ci left: 9.709968e-01	ci right 9.713288e-01	k: 3797248	n:3910000
KS ci ratio: 1.095922e-01	ci left: 3.091804e-04	ci right 3.452747e-04	k: 1278	n:3910000
CPNE3   3910000 perm   7311 sec   (535 perm/sec)   p_kst 3.268542e-04   p_cons 9.711632e-01   p_joint 3.268542e-04

Joint ci ratio: 1.095494e-01	ci left: 3.086398e-04	ci right 3.446560e-04	k: 1279	n:3920000
Cons ci ratio: 3.411955e-04	ci left: 9.709930e-01	ci right 9.713246e-01	k: 3806944	n:3920000
KS ci ratio: 1.095494e-01	ci left: 3.086398e-04	ci right 3.446560e-04	k: 1279	n:3920000
CPNE3   3920000 perm   7346 sec   (534 perm/sec)   p_kst 3.262755e-04   p_cons 9.711592e-01   p_joint 3.262755e-04

Joint ci ratio: 1.095067e-01	ci left: 3.081019e-04	ci right 3.440405e-04	k: 1280	n:3930000
Cons ci ratio: 3.407713e-04	ci left: 9.709916e-01	ci right 9.713228e-01	k: 3816649	n:3930000
KS ci ratio: 1.095067e-01	ci left: 3.081019e-04	ci right 3.440405e-04	k: 1280	n:3930000
CPNE3   3930000 perm   7381 sec   (532 perm/sec)   p_kst 3.256997e-04   p_cons 9.711575e-01   p_joint 3.256997e-04

Joint ci ratio: 1.092087e-01	ci left: 3.090480e-04	ci right 3.449925e-04	k: 1287	n:3940000
Cons ci ratio: 3.403287e-04	ci left: 9.709934e-01	ci right 9.713242e-01	k: 3826367	n:3940000
KS ci ratio: 1.092087e-01	ci left: 3.090480e-04	ci right 3.449925e-04	k: 1287	n:3940000
CPNE3   3940000 perm   7417 sec   (531 perm/sec)   p_kst 3.266497e-04   p_cons 9.711591e-01   p_joint 3.266497e-04

Joint ci ratio: 1.091240e-01	ci left: 3.087581e-04	ci right 3.446392e-04	k: 1289	n:3950000
Cons ci ratio: 3.399001e-04	ci left: 9.709932e-01	ci right 9.713236e-01	k: 3836077	n:3950000
KS ci ratio: 1.091240e-01	ci left: 3.087581e-04	ci right 3.446392e-04	k: 1289	n:3950000
CPNE3   3950000 perm   7452 sec   (530 perm/sec)   p_kst 3.263291e-04   p_cons 9.711587e-01   p_joint 3.263291e-04

Joint ci ratio: 1.088291e-01	ci left: 3.096979e-04	ci right 3.455848e-04	k: 1296	n:3960000
Cons ci ratio: 3.394945e-04	ci left: 9.709895e-01	ci right 9.713194e-01	k: 3845773	n:3960000
KS ci ratio: 1.088291e-01	ci left: 3.096979e-04	ci right 3.455848e-04	k: 1296	n:3960000
CPNE3   3960000 perm   7488 sec   (529 perm/sec)   p_kst 3.272727e-04   p_cons 9.711548e-01   p_joint 3.272727e-04

Joint ci ratio: 1.087453e-01	ci left: 3.094079e-04	ci right 3.452318e-04	k: 1298	n:3970000
Cons ci ratio: 3.390339e-04	ci left: 9.709951e-01	ci right 9.713246e-01	k: 3855506	n:3970000
KS ci ratio: 1.087453e-01	ci left: 3.094079e-04	ci right 3.452318e-04	k: 1298	n:3970000
CPNE3   3970000 perm   7523 sec   (528 perm/sec)   p_kst 3.269521e-04   p_cons 9.711602e-01   p_joint 3.269521e-04

Joint ci ratio: 1.084950e-01	ci left: 3.100971e-04	ci right 3.459128e-04	k: 1304	n:3980000
Cons ci ratio: 3.386026e-04	ci left: 9.709962e-01	ci right 9.713253e-01	k: 3865221	n:3980000
KS ci ratio: 1.084950e-01	ci left: 3.100971e-04	ci right 3.459128e-04	k: 1304	n:3980000
CPNE3   3980000 perm   7558 sec   (527 perm/sec)   p_kst 3.276382e-04   p_cons 9.711611e-01   p_joint 3.276382e-04

Joint ci ratio: 1.084534e-01	ci left: 3.095637e-04	ci right 3.453033e-04	k: 1305	n:3990000
Cons ci ratio: 3.381819e-04	ci left: 9.709957e-01	ci right 9.713244e-01	k: 3874930	n:3990000
KS ci ratio: 1.084534e-01	ci left: 3.095637e-04	ci right 3.453033e-04	k: 1305	n:3990000
CPNE3   3990000 perm   7593 sec   (525 perm/sec)   p_kst 3.270677e-04   p_cons 9.711604e-01   p_joint 3.270677e-04

Joint ci ratio: 1.083705e-01	ci left: 3.092763e-04	ci right 3.449536e-04	k: 1307	n:4000000
Cons ci ratio: 3.378066e-04	ci left: 9.709880e-01	ci right 9.713163e-01	k: 3884610	n:4000000
KS ci ratio: 1.083705e-01	ci left: 3.092763e-04	ci right 3.449536e-04	k: 1307	n:4000000
CPNE3   4000000 perm   7629 sec   (524 perm/sec)   p_kst 3.267500e-04   p_cons 9.711525e-01   p_joint 3.267500e-04

Joint ci ratio: 1.083291e-01	ci left: 3.087476e-04	ci right 3.443495e-04	k: 1308	n:4010000
Cons ci ratio: 3.373784e-04	ci left: 9.709893e-01	ci right 9.713172e-01	k: 3894326	n:4010000
KS ci ratio: 1.083291e-01	ci left: 3.087476e-04	ci right 3.443495e-04	k: 1308	n:4010000
CPNE3   4010000 perm   7665 sec   (523 perm/sec)   p_kst 3.261845e-04   p_cons 9.711536e-01   p_joint 3.261845e-04

Joint ci ratio: 1.082465e-01	ci left: 3.084636e-04	ci right 3.440039e-04	k: 1310	n:4020000
Cons ci ratio: 3.369399e-04	ci left: 9.709926e-01	ci right 9.713201e-01	k: 3904050	n:4020000
KS ci ratio: 1.082465e-01	ci left: 3.084636e-04	ci right 3.440039e-04	k: 1310	n:4020000
CPNE3   4020000 perm   7701 sec   (522 perm/sec)   p_kst 3.258706e-04   p_cons 9.711567e-01   p_joint 3.258706e-04

Joint ci ratio: 1.080817e-01	ci left: 3.086639e-04	ci right 3.441697e-04	k: 1314	n:4030000
Cons ci ratio: 3.364941e-04	ci left: 9.709974e-01	ci right 9.713245e-01	k: 3913780	n:4030000
KS ci ratio: 1.080817e-01	ci left: 3.086639e-04	ci right 3.441697e-04	k: 1314	n:4030000
CPNE3   4030000 perm   7737 sec   (521 perm/sec)   p_kst 3.260546e-04   p_cons 9.711613e-01   p_joint 3.260546e-04

Joint ci ratio: 1.078768e-01	ci left: 3.091041e-04	ci right 3.445888e-04	k: 1319	n:4040000
Cons ci ratio: 3.361288e-04	ci left: 9.709890e-01	ci right 9.713157e-01	k: 3923457	n:4040000
KS ci ratio: 1.078768e-01	ci left: 3.091041e-04	ci right 3.445888e-04	k: 1319	n:4040000
CPNE3   4040000 perm   7773 sec   (520 perm/sec)   p_kst 3.264851e-04   p_cons 9.711527e-01   p_joint 3.264851e-04

Joint ci ratio: 1.077544e-01	ci left: 3.090616e-04	ci right 3.444987e-04	k: 1322	n:4050000
Cons ci ratio: 3.357069e-04	ci left: 9.709904e-01	ci right 9.713166e-01	k: 3933173	n:4050000
KS ci ratio: 1.077544e-01	ci left: 3.090616e-04	ci right 3.444987e-04	k: 1322	n:4050000
CPNE3   4050000 perm   7810 sec   (519 perm/sec)   p_kst 3.264198e-04   p_cons 9.711538e-01   p_joint 3.264198e-04

Joint ci ratio: 1.077138e-01	ci left: 3.085401e-04	ci right 3.439031e-04	k: 1323	n:4060000
Cons ci ratio: 3.352911e-04	ci left: 9.709909e-01	ci right 9.713168e-01	k: 3942886	n:4060000
KS ci ratio: 1.077138e-01	ci left: 3.085401e-04	ci right 3.439031e-04	k: 1323	n:4060000
CPNE3   4060000 perm   7847 sec   (517 perm/sec)   p_kst 3.258621e-04   p_cons 9.711542e-01   p_joint 3.258621e-04

Joint ci ratio: 1.076325e-01	ci left: 3.082601e-04	ci right 3.435628e-04	k: 1325	n:4070000
Cons ci ratio: 3.348812e-04	ci left: 9.709907e-01	ci right 9.713162e-01	k: 3952596	n:4070000
KS ci ratio: 1.076325e-01	ci left: 3.082601e-04	ci right 3.435628e-04	k: 1325	n:4070000
CPNE3   4070000 perm   7887 sec   (516 perm/sec)   p_kst 3.255528e-04   p_cons 9.711538e-01   p_joint 3.255528e-04

Joint ci ratio: 1.076326e-01	ci left: 3.075046e-04	ci right 3.427207e-04	k: 1325	n:4080000
Cons ci ratio: 3.345020e-04	ci left: 9.709857e-01	ci right 9.713107e-01	k: 3962286	n:4080000
KS ci ratio: 1.076326e-01	ci left: 3.075046e-04	ci right 3.427207e-04	k: 1325	n:4080000
CPNE3   4080000 perm   7924 sec   (515 perm/sec)   p_kst 3.247549e-04   p_cons 9.711485e-01   p_joint 3.247549e-04

Joint ci ratio: 1.074706e-01	ci left: 3.077044e-04	ci right 3.428871e-04	k: 1329	n:4090000
Cons ci ratio: 3.340542e-04	ci left: 9.709924e-01	ci right 9.713170e-01	k: 3972024	n:4090000
KS ci ratio: 1.074706e-01	ci left: 3.077044e-04	ci right 3.428871e-04	k: 1329	n:4090000
CPNE3   4090000 perm   7960 sec   (514 perm/sec)   p_kst 3.249389e-04   p_cons 9.711550e-01   p_joint 3.249389e-04

Joint ci ratio: 1.072289e-01	ci left: 3.083781e-04	ci right 3.435534e-04	k: 1335	n:4100000
Cons ci ratio: 3.336387e-04	ci left: 9.709939e-01	ci right 9.713181e-01	k: 3981741	n:4100000
KS ci ratio: 1.072289e-01	ci left: 3.083781e-04	ci right 3.435534e-04	k: 1335	n:4100000
CPNE3   4100000 perm   7998 sec   (513 perm/sec)   p_kst 3.256098e-04   p_cons 9.711563e-01   p_joint 3.256098e-04

Joint ci ratio: 1.071488e-01	ci left: 3.081013e-04	ci right 3.432172e-04	k: 1337	n:4110000
Cons ci ratio: 3.332406e-04	ci left: 9.709927e-01	ci right 9.713166e-01	k: 3991447	n:4110000
KS ci ratio: 1.071488e-01	ci left: 3.081013e-04	ci right 3.432172e-04	k: 1337	n:4110000
CPNE3   4110000 perm   8035 sec   (511 perm/sec)   p_kst 3.253041e-04   p_cons 9.711550e-01   p_joint 3.253041e-04

Joint ci ratio: 1.069890e-01	ci left: 3.082984e-04	ci right 3.433810e-04	k: 1341	n:4120000
Cons ci ratio: 3.329030e-04	ci left: 9.709816e-01	ci right 9.713051e-01	k: 4001112	n:4120000
KS ci ratio: 1.069890e-01	ci left: 3.082984e-04	ci right 3.433810e-04	k: 1341	n:4120000
CPNE3   4120000 perm   8073 sec   (510 perm/sec)   p_kst 3.254854e-04   p_cons 9.711437e-01   p_joint 3.254854e-04

Joint ci ratio: 1.068299e-01	ci left: 3.084945e-04	ci right 3.435440e-04	k: 1345	n:4130000
Cons ci ratio: 3.325707e-04	ci left: 9.709698e-01	ci right 9.712930e-01	k: 4010774	n:4130000
KS ci ratio: 1.068299e-01	ci left: 3.084945e-04	ci right 3.435440e-04	k: 1345	n:4130000
CPNE3   4130000 perm   8110 sec   (509 perm/sec)   p_kst 3.256659e-04   p_cons 9.711317e-01   p_joint 3.256659e-04

Joint ci ratio: 1.067110e-01	ci left: 3.084547e-04	ci right 3.434581e-04	k: 1348	n:4140000
Cons ci ratio: 3.321364e-04	ci left: 9.709755e-01	ci right 9.712983e-01	k: 4020508	n:4140000
KS ci ratio: 1.067110e-01	ci left: 3.084547e-04	ci right 3.434581e-04	k: 1348	n:4140000
CPNE3   4140000 perm   8147 sec   (508 perm/sec)   p_kst 3.256039e-04   p_cons 9.711372e-01   p_joint 3.256039e-04

Joint ci ratio: 1.064745e-01	ci left: 3.091186e-04	ci right 3.441148e-04	k: 1354	n:4150000
Cons ci ratio: 3.317550e-04	ci left: 9.709724e-01	ci right 9.712949e-01	k: 4030206	n:4150000
KS ci ratio: 1.064745e-01	ci left: 3.091186e-04	ci right 3.441148e-04	k: 1354	n:4150000
CPNE3   4150000 perm   8183 sec   (507 perm/sec)   p_kst 3.262651e-04   p_cons 9.711340e-01   p_joint 3.262651e-04

Joint ci ratio: 1.063568e-01	ci left: 3.090775e-04	ci right 3.440280e-04	k: 1357	n:4160000
Cons ci ratio: 3.313594e-04	ci left: 9.709721e-01	ci right 9.712941e-01	k: 4039915	n:4160000
KS ci ratio: 1.063568e-01	ci left: 3.090775e-04	ci right 3.440280e-04	k: 1357	n:4160000
CPNE3   4160000 perm   8220 sec   (506 perm/sec)   p_kst 3.262019e-04   p_cons 9.711334e-01   p_joint 3.262019e-04

Joint ci ratio: 1.062395e-01	ci left: 3.090366e-04	ci right 3.439415e-04	k: 1360	n:4170000
Cons ci ratio: 3.309736e-04	ci left: 9.709703e-01	ci right 9.712919e-01	k: 4049618	n:4170000
KS ci ratio: 1.062395e-01	ci left: 3.090366e-04	ci right 3.439415e-04	k: 1360	n:4170000
CPNE3   4170000 perm   8258 sec   (505 perm/sec)   p_kst 3.261391e-04   p_cons 9.711314e-01   p_joint 3.261391e-04

Joint ci ratio: 1.061616e-01	ci left: 3.087631e-04	ci right 3.436099e-04	k: 1362	n:4180000
Cons ci ratio: 3.305497e-04	ci left: 9.709752e-01	ci right 9.712964e-01	k: 4059349	n:4180000
KS ci ratio: 1.061616e-01	ci left: 3.087631e-04	ci right 3.436099e-04	k: 1362	n:4180000
CPNE3   4180000 perm   8295 sec   (504 perm/sec)   p_kst 3.258373e-04   p_cons 9.711361e-01   p_joint 3.258373e-04

Joint ci ratio: 1.060449e-01	ci left: 3.087231e-04	ci right 3.435248e-04	k: 1365	n:4190000
Cons ci ratio: 3.301612e-04	ci left: 9.709743e-01	ci right 9.712952e-01	k: 4069056	n:4190000
KS ci ratio: 1.060449e-01	ci left: 3.087231e-04	ci right 3.435248e-04	k: 1365	n:4190000
CPNE3   4190000 perm   8334 sec   (503 perm/sec)   p_kst 3.257757e-04   p_cons 9.711351e-01   p_joint 3.257757e-04

Joint ci ratio: 1.058900e-01	ci left: 3.089152e-04	ci right 3.436845e-04	k: 1369	n:4200000
Cons ci ratio: 3.297389e-04	ci left: 9.709794e-01	ci right 9.712999e-01	k: 4078788	n:4200000
KS ci ratio: 1.058900e-01	ci left: 3.089152e-04	ci right 3.436845e-04	k: 1369	n:4200000
CPNE3   4200000 perm   8373 sec   (502 perm/sec)   p_kst 3.259524e-04   p_cons 9.711400e-01   p_joint 3.259524e-04

Joint ci ratio: 1.056588e-01	ci left: 3.095689e-04	ci right 3.443310e-04	k: 1375	n:4210000
Cons ci ratio: 3.293337e-04	ci left: 9.709819e-01	ci right 9.713020e-01	k: 4088509	n:4210000
KS ci ratio: 1.056588e-01	ci left: 3.095689e-04	ci right 3.443310e-04	k: 1375	n:4210000
CPNE3   4210000 perm   8412 sec   (500 perm/sec)   p_kst 3.266033e-04   p_cons 9.711423e-01   p_joint 3.266033e-04

Joint ci ratio: 1.055056e-01	ci left: 3.097582e-04	ci right 3.444879e-04	k: 1379	n:4220000
Cons ci ratio: 3.289452e-04	ci left: 9.709818e-01	ci right 9.713015e-01	k: 4098219	n:4220000
KS ci ratio: 1.055056e-01	ci left: 3.097582e-04	ci right 3.444879e-04	k: 1379	n:4220000
CPNE3   4220000 perm   8450 sec   (499 perm/sec)   p_kst 3.267773e-04   p_cons 9.711419e-01   p_joint 3.267773e-04

Joint ci ratio: 1.053149e-01	ci left: 3.101768e-04	ci right 3.448867e-04	k: 1384	n:4230000
Cons ci ratio: 3.285706e-04	ci left: 9.709795e-01	ci right 9.712988e-01	k: 4107920	n:4230000
KS ci ratio: 1.053149e-01	ci left: 3.101768e-04	ci right 3.448867e-04	k: 1384	n:4230000
CPNE3   4230000 perm   8488 sec   (498 perm/sec)   p_kst 3.271868e-04   p_cons 9.711395e-01   p_joint 3.271868e-04

Joint ci ratio: 1.052770e-01	ci left: 3.096749e-04	ci right 3.443154e-04	k: 1385	n:4240000
Cons ci ratio: 3.281614e-04	ci left: 9.709834e-01	ci right 9.713023e-01	k: 4117647	n:4240000
KS ci ratio: 1.052770e-01	ci left: 3.096749e-04	ci right 3.443154e-04	k: 1385	n:4240000
CPNE3   4240000 perm   8526 sec   (497 perm/sec)   p_kst 3.266509e-04   p_cons 9.711432e-01   p_joint 3.266509e-04

Joint ci ratio: 1.052011e-01	ci left: 3.094044e-04	ci right 3.439882e-04	k: 1387	n:4250000
Cons ci ratio: 3.277922e-04	ci left: 9.709806e-01	ci right 9.712992e-01	k: 4127346	n:4250000
KS ci ratio: 1.052011e-01	ci left: 3.094044e-04	ci right 3.439882e-04	k: 1387	n:4250000
CPNE3   4250000 perm   8565 sec   (496 perm/sec)   p_kst 3.263529e-04   p_cons 9.711402e-01   p_joint 3.263529e-04

Joint ci ratio: 1.051254e-01	ci left: 3.091353e-04	ci right 3.436625e-04	k: 1389	n:4260000
Cons ci ratio: 3.274091e-04	ci left: 9.709805e-01	ci right 9.712987e-01	k: 4137056	n:4260000
KS ci ratio: 1.051254e-01	ci left: 3.091353e-04	ci right 3.436625e-04	k: 1389	n:4260000
CPNE3   4260000 perm   8603 sec   (495 perm/sec)   p_kst 3.260563e-04   p_cons 9.711399e-01   p_joint 3.260563e-04

Joint ci ratio: 1.050499e-01	ci left: 3.088674e-04	ci right 3.433384e-04	k: 1391	n:4270000
Cons ci ratio: 3.270575e-04	ci left: 9.709752e-01	ci right 9.712930e-01	k: 4146744	n:4270000
KS ci ratio: 1.050499e-01	ci left: 3.088674e-04	ci right 3.433384e-04	k: 1391	n:4270000
CPNE3   4270000 perm   8640 sec   (494 perm/sec)   p_kst 3.257611e-04   p_cons 9.711344e-01   p_joint 3.257611e-04

Joint ci ratio: 1.048993e-01	ci left: 3.090558e-04	ci right 3.434953e-04	k: 1395	n:4280000
Cons ci ratio: 3.266770e-04	ci left: 9.709751e-01	ci right 9.712925e-01	k: 4156454	n:4280000
KS ci ratio: 1.048993e-01	ci left: 3.090558e-04	ci right 3.434953e-04	k: 1395	n:4280000
CPNE3   4280000 perm   8680 sec   (493 perm/sec)   p_kst 3.259346e-04   p_cons 9.711341e-01   p_joint 3.259346e-04

Joint ci ratio: 1.046745e-01	ci left: 3.096973e-04	ci right 3.441298e-04	k: 1401	n:4290000
Cons ci ratio: 3.263264e-04	ci left: 9.709700e-01	ci right 9.712872e-01	k: 4166143	n:4290000
KS ci ratio: 1.046745e-01	ci left: 3.096973e-04	ci right 3.441298e-04	k: 1401	n:4290000
CPNE3   4290000 perm   8719 sec   (492 perm/sec)   p_kst 3.265734e-04   p_cons 9.711289e-01   p_joint 3.265734e-04

Joint ci ratio: 1.046373e-01	ci left: 3.092035e-04	ci right 3.435682e-04	k: 1402	n:4300000
Cons ci ratio: 3.259173e-04	ci left: 9.709753e-01	ci right 9.712920e-01	k: 4175876	n:4300000
KS ci ratio: 1.046373e-01	ci left: 3.092035e-04	ci right 3.435682e-04	k: 1402	n:4300000
CPNE3   4300000 perm   8759 sec   (491 perm/sec)   p_kst 3.260465e-04   p_cons 9.711340e-01   p_joint 3.260465e-04

Joint ci ratio: 1.045256e-01	ci left: 3.091640e-04	ci right 3.434853e-04	k: 1405	n:4310000
Cons ci ratio: 3.255516e-04	ci left: 9.709733e-01	ci right 9.712897e-01	k: 4185578	n:4310000
KS ci ratio: 1.045256e-01	ci left: 3.091640e-04	ci right 3.434853e-04	k: 1405	n:4310000
CPNE3   4310000 perm   8797 sec   (490 perm/sec)   p_kst 3.259861e-04   p_cons 9.711318e-01   p_joint 3.259861e-04

Joint ci ratio: 1.044513e-01	ci left: 3.088992e-04	ci right 3.431653e-04	k: 1407	n:4320000
Cons ci ratio: 3.251723e-04	ci left: 9.709739e-01	ci right 9.712899e-01	k: 4195291	n:4320000
KS ci ratio: 1.044513e-01	ci left: 3.088992e-04	ci right 3.431653e-04	k: 1407	n:4320000
CPNE3   4320000 perm   8835 sec   (489 perm/sec)   p_kst 3.256944e-04   p_cons 9.711322e-01   p_joint 3.256944e-04

Joint ci ratio: 1.043033e-01	ci left: 3.090855e-04	ci right 3.433206e-04	k: 1411	n:4330000
Cons ci ratio: 3.247422e-04	ci left: 9.709835e-01	ci right 9.712991e-01	k: 4205043	n:4330000
KS ci ratio: 1.043033e-01	ci left: 3.090855e-04	ci right 3.433206e-04	k: 1411	n:4330000
CPNE3   4330000 perm   8874 sec   (488 perm/sec)   p_kst 3.258661e-04   p_cons 9.711416e-01   p_joint 3.258661e-04

Joint ci ratio: 1.042295e-01	ci left: 3.088221e-04	ci right 3.430024e-04	k: 1413	n:4340000
Cons ci ratio: 3.243897e-04	ci left: 9.709798e-01	ci right 9.712951e-01	k: 4214738	n:4340000
KS ci ratio: 1.042295e-01	ci left: 3.088221e-04	ci right 3.430024e-04	k: 1413	n:4340000
CPNE3   4340000 perm   8913 sec   (487 perm/sec)   p_kst 3.255760e-04   p_cons 9.711378e-01   p_joint 3.255760e-04

Joint ci ratio: 1.041559e-01	ci left: 3.085600e-04	ci right 3.426856e-04	k: 1415	n:4350000
Cons ci ratio: 3.240092e-04	ci left: 9.709813e-01	ci right 9.712962e-01	k: 4224455	n:4350000
KS ci ratio: 1.041559e-01	ci left: 3.085600e-04	ci right 3.426856e-04	k: 1415	n:4350000
CPNE3   4350000 perm   8952 sec   (486 perm/sec)   p_kst 3.252874e-04   p_cons 9.711391e-01   p_joint 3.252874e-04

Joint ci ratio: 1.041191e-01	ci left: 3.080756e-04	ci right 3.421350e-04	k: 1416	n:4360000
Cons ci ratio: 3.236459e-04	ci left: 9.709800e-01	ci right 9.712946e-01	k: 4234160	n:4360000
KS ci ratio: 1.041191e-01	ci left: 3.080756e-04	ci right 3.421350e-04	k: 1416	n:4360000
CPNE3   4360000 perm   8991 sec   (485 perm/sec)   p_kst 3.247706e-04   p_cons 9.711376e-01   p_joint 3.247706e-04

Joint ci ratio: 1.038994e-01	ci left: 3.087079e-04	ci right 3.427608e-04	k: 1422	n:4370000
Cons ci ratio: 3.233062e-04	ci left: 9.709749e-01	ci right 9.712891e-01	k: 4243848	n:4370000
KS ci ratio: 1.038994e-01	ci left: 3.087079e-04	ci right 3.427608e-04	k: 1422	n:4370000
CPNE3   4370000 perm   9030 sec   (484 perm/sec)   p_kst 3.254005e-04   p_cons 9.711323e-01   p_joint 3.254005e-04

Joint ci ratio: 1.035723e-01	ci left: 3.100046e-04	ci right 3.440863e-04	k: 1431	n:4380000
Cons ci ratio: 3.229755e-04	ci left: 9.709683e-01	ci right 9.712822e-01	k: 4253530	n:4380000
KS ci ratio: 1.035723e-01	ci left: 3.100046e-04	ci right 3.440863e-04	k: 1431	n:4380000
CPNE3   4380000 perm   9070 sec   (483 perm/sec)   p_kst 3.267123e-04   p_cons 9.711256e-01   p_joint 3.267123e-04

Joint ci ratio: 1.034279e-01	ci left: 3.101860e-04	ci right 3.442372e-04	k: 1435	n:4390000
Cons ci ratio: 3.226182e-04	ci left: 9.709666e-01	ci right 9.712801e-01	k: 4263233	n:4390000
KS ci ratio: 1.034279e-01	ci left: 3.101860e-04	ci right 3.442372e-04	k: 1435	n:4390000
CPNE3   4390000 perm   9110 sec   (482 perm/sec)   p_kst 3.268793e-04   p_cons 9.711237e-01   p_joint 3.268793e-04

Joint ci ratio: 1.033560e-01	ci left: 3.099239e-04	ci right 3.439212e-04	k: 1437	n:4400000
Cons ci ratio: 3.222922e-04	ci left: 9.709597e-01	ci right 9.712729e-01	k: 4272913	n:4400000
KS ci ratio: 1.033560e-01	ci left: 3.099239e-04	ci right 3.439212e-04	k: 1437	n:4400000
CPNE3   4400000 perm   9149 sec   (481 perm/sec)   p_kst 3.265909e-04   p_cons 9.711166e-01   p_joint 3.265909e-04

Joint ci ratio: 1.032842e-01	ci left: 3.096629e-04	ci right 3.436065e-04	k: 1439	n:4410000
Cons ci ratio: 3.219359e-04	ci left: 9.709582e-01	ci right 9.712711e-01	k: 4282617	n:4410000
KS ci ratio: 1.032842e-01	ci left: 3.096629e-04	ci right 3.436065e-04	k: 1439	n:4410000
CPNE3   4410000 perm   9189 sec   (480 perm/sec)   p_kst 3.263039e-04   p_cons 9.711150e-01   p_joint 3.263039e-04

Joint ci ratio: 1.032842e-01	ci left: 3.089623e-04	ci right 3.428292e-04	k: 1439	n:4420000
Cons ci ratio: 3.215756e-04	ci left: 9.709577e-01	ci right 9.712702e-01	k: 4292325	n:4420000
KS ci ratio: 1.032842e-01	ci left: 3.089623e-04	ci right 3.428292e-04	k: 1439	n:4420000
CPNE3   4420000 perm   9228 sec   (479 perm/sec)   p_kst 3.255656e-04   p_cons 9.711143e-01   p_joint 3.255656e-04

Joint ci ratio: 1.031768e-01	ci left: 3.089246e-04	ci right 3.427500e-04	k: 1442	n:4430000
Cons ci ratio: 3.211945e-04	ci left: 9.709610e-01	ci right 9.712731e-01	k: 4302050	n:4430000
KS ci ratio: 1.031768e-01	ci left: 3.089246e-04	ci right 3.427500e-04	k: 1442	n:4430000
CPNE3   4430000 perm   9267 sec   (478 perm/sec)   p_kst 3.255079e-04   p_cons 9.711174e-01   p_joint 3.255079e-04

Joint ci ratio: 1.030697e-01	ci left: 3.088870e-04	ci right 3.426711e-04	k: 1445	n:4440000
Cons ci ratio: 3.208187e-04	ci left: 9.709636e-01	ci right 9.712754e-01	k: 4311772	n:4440000
KS ci ratio: 1.030697e-01	ci left: 3.088870e-04	ci right 3.426711e-04	k: 1445	n:4440000
CPNE3   4440000 perm   9306 sec   (477 perm/sec)   p_kst 3.254505e-04   p_cons 9.711198e-01   p_joint 3.254505e-04

Joint ci ratio: 1.029630e-01	ci left: 3.088497e-04	ci right 3.425926e-04	k: 1448	n:4450000
Cons ci ratio: 3.205032e-04	ci left: 9.709559e-01	ci right 9.712673e-01	k: 4321448	n:4450000
KS ci ratio: 1.029630e-01	ci left: 3.088497e-04	ci right 3.425926e-04	k: 1448	n:4450000
CPNE3   4450000 perm   9346 sec   (476 perm/sec)   p_kst 3.253933e-04   p_cons 9.711119e-01   p_joint 3.253933e-04

Joint ci ratio: 1.029275e-01	ci left: 3.083756e-04	ci right 3.420544e-04	k: 1449	n:4460000
Cons ci ratio: 3.201604e-04	ci left: 9.709531e-01	ci right 9.712642e-01	k: 4331146	n:4460000
KS ci ratio: 1.029275e-01	ci left: 3.083756e-04	ci right 3.420544e-04	k: 1449	n:4460000
CPNE3   4460000 perm   9386 sec   (475 perm/sec)   p_kst 3.248879e-04   p_cons 9.711090e-01   p_joint 3.248879e-04

Joint ci ratio: 1.028920e-01	ci left: 3.079037e-04	ci right 3.415187e-04	k: 1450	n:4470000
Cons ci ratio: 3.197920e-04	ci left: 9.709550e-01	ci right 9.712658e-01	k: 4340865	n:4470000
KS ci ratio: 1.028920e-01	ci left: 3.079037e-04	ci right 3.415187e-04	k: 1450	n:4470000
CPNE3   4470000 perm   9426 sec   (474 perm/sec)   p_kst 3.243848e-04   p_cons 9.711107e-01   p_joint 3.243848e-04

Joint ci ratio: 1.026799e-01	ci left: 3.085213e-04	ci right 3.421300e-04	k: 1456	n:4480000
Cons ci ratio: 3.194134e-04	ci left: 9.709590e-01	ci right 9.712694e-01	k: 4350593	n:4480000
KS ci ratio: 1.026799e-01	ci left: 3.085213e-04	ci right 3.421300e-04	k: 1456	n:4480000
CPNE3   4480000 perm   9465 sec   (473 perm/sec)   p_kst 3.250000e-04   p_cons 9.711145e-01   p_joint 3.250000e-04

Joint ci ratio: 1.025744e-01	ci left: 3.084852e-04	ci right 3.420534e-04	k: 1459	n:4490000
Cons ci ratio: 3.190780e-04	ci left: 9.709556e-01	ci right 9.712656e-01	k: 4360288	n:4490000
KS ci ratio: 1.025744e-01	ci left: 3.084852e-04	ci right 3.420534e-04	k: 1459	n:4490000
CPNE3   4490000 perm   9504 sec   (472 perm/sec)   p_kst 3.249443e-04   p_cons 9.711109e-01   p_joint 3.249443e-04

Joint ci ratio: 1.025042e-01	ci left: 3.082327e-04	ci right 3.417491e-04	k: 1461	n:4500000
Cons ci ratio: 3.186893e-04	ci left: 9.709617e-01	ci right 9.712714e-01	k: 4370026	n:4500000
KS ci ratio: 1.025042e-01	ci left: 3.082327e-04	ci right 3.417491e-04	k: 1461	n:4500000
CPNE3   4500000 perm   9545 sec   (471 perm/sec)   p_kst 3.246667e-04   p_cons 9.711169e-01   p_joint 3.246667e-04

Joint ci ratio: 1.023643e-01	ci left: 3.084134e-04	ci right 3.419010e-04	k: 1465	n:4510000
Cons ci ratio: 3.183637e-04	ci left: 9.709570e-01	ci right 9.712664e-01	k: 4379715	n:4510000
KS ci ratio: 1.023643e-01	ci left: 3.084134e-04	ci right 3.419010e-04	k: 1465	n:4510000
CPNE3   4510000 perm   9585 sec   (471 perm/sec)   p_kst 3.248337e-04   p_cons 9.711120e-01   p_joint 3.248337e-04

Joint ci ratio: 1.022249e-01	ci left: 3.085934e-04	ci right 3.420521e-04	k: 1469	n:4520000
Cons ci ratio: 3.180203e-04	ci left: 9.709556e-01	ci right 9.712646e-01	k: 4389419	n:4520000
KS ci ratio: 1.022249e-01	ci left: 3.085934e-04	ci right 3.420521e-04	k: 1469	n:4520000
CPNE3   4520000 perm   9625 sec   (470 perm/sec)   p_kst 3.250000e-04   p_cons 9.711104e-01   p_joint 3.250000e-04

Joint ci ratio: 1.021902e-01	ci left: 3.081273e-04	ci right 3.415234e-04	k: 1470	n:4530000
Cons ci ratio: 3.176667e-04	ci left: 9.709562e-01	ci right 9.712649e-01	k: 4399132	n:4530000
KS ci ratio: 1.021902e-01	ci left: 3.081273e-04	ci right 3.415234e-04	k: 1470	n:4530000
CPNE3   4530000 perm   9666 sec   (469 perm/sec)   p_kst 3.245033e-04   p_cons 9.711108e-01   p_joint 3.245033e-04

Joint ci ratio: 1.020861e-01	ci left: 3.080925e-04	ci right 3.414488e-04	k: 1473	n:4540000
Cons ci ratio: 3.173118e-04	ci left: 9.709572e-01	ci right 9.712656e-01	k: 4408847	n:4540000
KS ci ratio: 1.020861e-01	ci left: 3.080925e-04	ci right 3.414488e-04	k: 1473	n:4540000
CPNE3   4540000 perm   9707 sec   (468 perm/sec)   p_kst 3.244493e-04   p_cons 9.711117e-01   p_joint 3.244493e-04

Joint ci ratio: 1.019134e-01	ci left: 3.084863e-04	ci right 3.418253e-04	k: 1478	n:4550000
Cons ci ratio: 3.169469e-04	ci left: 9.709602e-01	ci right 9.712682e-01	k: 4418571	n:4550000
KS ci ratio: 1.019134e-01	ci left: 3.084863e-04	ci right 3.418253e-04	k: 1478	n:4550000
CPNE3   4550000 perm   9748 sec   (467 perm/sec)   p_kst 3.248352e-04   p_cons 9.711145e-01   p_joint 3.248352e-04

Joint ci ratio: 1.017759e-01	ci left: 3.086646e-04	ci right 3.419752e-04	k: 1482	n:4560000
Cons ci ratio: 3.166117e-04	ci left: 9.709581e-01	ci right 9.712658e-01	k: 4428272	n:4560000
KS ci ratio: 1.017759e-01	ci left: 3.086646e-04	ci right 3.419752e-04	k: 1482	n:4560000
CPNE3   4560000 perm   9790 sec   (466 perm/sec)   p_kst 3.250000e-04   p_cons 9.711123e-01   p_joint 3.250000e-04

Joint ci ratio: 1.016731e-01	ci left: 3.086290e-04	ci right 3.419001e-04	k: 1485	n:4570000
Cons ci ratio: 3.162480e-04	ci left: 9.709614e-01	ci right 9.712687e-01	k: 4437997	n:4570000
KS ci ratio: 1.016731e-01	ci left: 3.086290e-04	ci right 3.419001e-04	k: 1485	n:4570000
CPNE3   4570000 perm   9830 sec   (465 perm/sec)   p_kst 3.249453e-04   p_cons 9.711153e-01   p_joint 3.249453e-04

Joint ci ratio: 1.016047e-01	ci left: 3.083807e-04	ci right 3.416014e-04	k: 1487	n:4580000
Cons ci ratio: 3.159200e-04	ci left: 9.709584e-01	ci right 9.712654e-01	k: 4447694	n:4580000
KS ci ratio: 1.016047e-01	ci left: 3.083807e-04	ci right 3.416014e-04	k: 1487	n:4580000
CPNE3   4580000 perm   9871 sec   (464 perm/sec)   p_kst 3.246725e-04   p_cons 9.711122e-01   p_joint 3.246725e-04

Joint ci ratio: 1.013327e-01	ci left: 3.094075e-04	ci right 3.426443e-04	k: 1495	n:4590000
Cons ci ratio: 3.155868e-04	ci left: 9.709566e-01	ci right 9.712633e-01	k: 4457396	n:4590000
KS ci ratio: 1.013327e-01	ci left: 3.094075e-04	ci right 3.426443e-04	k: 1495	n:4590000
CPNE3   4590000 perm   9913 sec   (463 perm/sec)   p_kst 3.257081e-04   p_cons 9.711102e-01   p_joint 3.257081e-04

Joint ci ratio: 1.011975e-01	ci left: 3.095824e-04	ci right 3.427910e-04	k: 1499	n:4600000
Cons ci ratio: 3.153097e-04	ci left: 9.709450e-01	ci right 9.712514e-01	k: 4467053	n:4600000
KS ci ratio: 1.011975e-01	ci left: 3.095824e-04	ci right 3.427910e-04	k: 1499	n:4600000
CPNE3   4600000 perm   9954 sec   (462 perm/sec)   p_kst 3.258696e-04   p_cons 9.710985e-01   p_joint 3.258696e-04

Joint ci ratio: 1.011301e-01	ci left: 3.093338e-04	ci right 3.424922e-04	k: 1501	n:4610000
Cons ci ratio: 3.149480e-04	ci left: 9.709486e-01	ci right 9.712547e-01	k: 4476780	n:4610000
KS ci ratio: 1.011301e-01	ci left: 3.093338e-04	ci right 3.424922e-04	k: 1501	n:4610000
CPNE3   4610000 perm   9996 sec   (461 perm/sec)   p_kst 3.255965e-04   p_cons 9.711020e-01   p_joint 3.255965e-04

Joint ci ratio: 1.009621e-01	ci left: 3.097191e-04	ci right 3.428605e-04	k: 1506	n:4620000
Cons ci ratio: 3.145997e-04	ci left: 9.709501e-01	ci right 9.712558e-01	k: 4486497	n:4620000
KS ci ratio: 1.009621e-01	ci left: 3.097191e-04	ci right 3.428605e-04	k: 1506	n:4620000
CPNE3   4620000 perm   10038 sec   (460 perm/sec)   p_kst 3.259740e-04   p_cons 9.711032e-01   p_joint 3.259740e-04

Joint ci ratio: 1.009287e-01	ci left: 3.092607e-04	ci right 3.423414e-04	k: 1507	n:4630000
Cons ci ratio: 3.142768e-04	ci left: 9.709472e-01	ci right 9.712526e-01	k: 4496194	n:4630000
KS ci ratio: 1.009287e-01	ci left: 3.092607e-04	ci right 3.423414e-04	k: 1507	n:4630000
CPNE3   4630000 perm   10079 sec   (459 perm/sec)   p_kst 3.254860e-04   p_cons 9.711002e-01   p_joint 3.254860e-04

Joint ci ratio: 1.008618e-01	ci left: 3.090143e-04	ci right 3.420455e-04	k: 1509	n:4640000
Cons ci ratio: 3.139283e-04	ci left: 9.709491e-01	ci right 9.712542e-01	k: 4505913	n:4640000
KS ci ratio: 1.008618e-01	ci left: 3.090143e-04	ci right 3.420455e-04	k: 1509	n:4640000
CPNE3   4640000 perm   10121 sec   (458 perm/sec)   p_kst 3.252155e-04   p_cons 9.711019e-01   p_joint 3.252155e-04

Joint ci ratio: 1.007618e-01	ci left: 3.089787e-04	ci right 3.419713e-04	k: 1512	n:4650000
Cons ci ratio: 3.135593e-04	ci left: 9.709549e-01	ci right 9.712596e-01	k: 4515650	n:4650000
KS ci ratio: 1.007618e-01	ci left: 3.089787e-04	ci right 3.419713e-04	k: 1512	n:4650000
CPNE3   4650000 perm   10163 sec   (458 perm/sec)   p_kst 3.251613e-04   p_cons 9.711075e-01   p_joint 3.251613e-04

Joint ci ratio: 1.005626e-01	ci left: 3.095708e-04	ci right 3.425574e-04	k: 1518	n:4660000
Cons ci ratio: 3.132216e-04	ci left: 9.709552e-01	ci right 9.712596e-01	k: 4525362	n:4660000
KS ci ratio: 1.005626e-01	ci left: 3.095708e-04	ci right 3.425574e-04	k: 1518	n:4660000
CPNE3   4660000 perm   10205 sec   (457 perm/sec)   p_kst 3.257511e-04   p_cons 9.711077e-01   p_joint 3.257511e-04

Joint ci ratio: 1.004304e-01	ci left: 3.097429e-04	ci right 3.427019e-04	k: 1522	n:4670000
Cons ci ratio: 3.128873e-04	ci left: 9.709552e-01	ci right 9.712592e-01	k: 4535072	n:4670000
KS ci ratio: 1.004304e-01	ci left: 3.097429e-04	ci right 3.427019e-04	k: 1522	n:4670000
CPNE3   4670000 perm   10246 sec   (456 perm/sec)   p_kst 3.259101e-04   p_cons 9.711075e-01   p_joint 3.259101e-04

Joint ci ratio: 1.003316e-01	ci left: 3.097060e-04	ci right 3.426268e-04	k: 1525	n:4680000
Cons ci ratio: 3.125530e-04	ci left: 9.709553e-01	ci right 9.712591e-01	k: 4544783	n:4680000
KS ci ratio: 1.003316e-01	ci left: 3.097060e-04	ci right 3.426268e-04	k: 1525	n:4680000
CPNE3   4680000 perm   10288 sec   (455 perm/sec)   p_kst 3.258547e-04   p_cons 9.711075e-01   p_joint 3.258547e-04

Joint ci ratio: 1.002004e-01	ci left: 3.098771e-04	ci right 3.427705e-04	k: 1529	n:4690000
Cons ci ratio: 3.122327e-04	ci left: 9.709531e-01	ci right 9.712565e-01	k: 4554483	n:4690000
KS ci ratio: 1.002004e-01	ci left: 3.098771e-04	ci right 3.427705e-04	k: 1529	n:4690000
CPNE3   4690000 perm   10331 sec   (454 perm/sec)   p_kst 3.260128e-04   p_cons 9.711051e-01   p_joint 3.260128e-04

Joint ci ratio: 1.000697e-01	ci left: 3.100476e-04	ci right 3.429136e-04	k: 1533	n:4700000
Cons ci ratio: 3.119513e-04	ci left: 9.709441e-01	ci right 9.712472e-01	k: 4564151	n:4700000
KS ci ratio: 1.000697e-01	ci left: 3.100476e-04	ci right 3.429136e-04	k: 1533	n:4700000
CPNE3   4700000 perm   10373 sec   (453 perm/sec)   p_kst 3.261702e-04   p_cons 9.710960e-01   p_joint 3.261702e-04

Joint ci ratio: 9.980970e-02	ci left: 3.110454e-04	ci right 3.439265e-04	k: 1541	n:4710000
Cons ci ratio: 3.116258e-04	ci left: 9.709432e-01	ci right 9.712460e-01	k: 4573857	n:4710000
KS ci ratio: 9.980970e-02	ci left: 3.110454e-04	ci right 3.439265e-04	k: 1541	n:4710000
CPNE3   4710000 perm   10418 sec   (452 perm/sec)   p_kst 3.271762e-04   p_cons 9.710949e-01   p_joint 3.271762e-04

Outputting figure to mutsig2_images.part000000000042/CPNE3.3_1674_4710000_0.00032718_0.97109_0.00032718.png
                gene_name: CPNE3
               theta_stop: 0.100 
                    nperm: 4710000 
                     p_ks: 0.00033 
        ci_ks_bounds_left: 0.00031 
       ci_ks_bounds_right: 0.00034 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.00033 
     ci_joint_bounds_left: 0.00031 
    ci_joint_bounds_right: 0.00034 

Current progress: 14 percent done.
CP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.180661e-01	ci left: 2.787955e-02	ci right 3.479702e-02	k: 312	n:10000
Cons ci ratio: 9.262256e-02	ci left: 1.448193e-01	ci right 1.589842e-01	k: 1518	n:10000
KS ci ratio: 3.716778e-01	ci left: 8.958341e-03	ci right 1.313383e-02	k: 109	n:10000
CP   10000 perm   2 sec   (5497 perm/sec)   p_kst 1.090000e-02   p_cons 1.518000e-01   p_joint 3.120000e-02

Joint ci ratio: 3.677103e-01	ci left: 4.613191e-03	ci right 6.734416e-03	k: 112	n:20000
Cons ci ratio: 6.777275e-02	ci left: 1.384219e-01	ci right 1.481820e-01	k: 2865	n:20000
KS ci ratio: 2.536541e-01	ci left: 1.030287e-02	ci right 1.334154e-02	k: 235	n:20000
CP   20000 perm   4 sec   (4881 perm/sec)   p_kst 1.175000e-02   p_cons 1.432500e-01   p_joint 5.600000e-03

Joint ci ratio: 1.874555e-01	ci left: 1.301884e-02	ci right 1.574306e-02	k: 430	n:30000
Cons ci ratio: 5.561620e-02	ci left: 1.381013e-01	ci right 1.460348e-01	k: 4261	n:30000
KS ci ratio: 2.083036e-01	ci left: 1.045075e-02	ci right 1.291184e-02	k: 349	n:30000
CP   30000 perm   6 sec   (4647 perm/sec)   p_kst 1.163333e-02   p_cons 1.420333e-01   p_joint 1.433333e-02

Joint ci ratio: 1.827220e-01	ci left: 1.033500e-02	ci right 1.243684e-02	k: 454	n:40000
Cons ci ratio: 4.824271e-02	ci left: 1.382465e-01	ci right 1.451056e-01	k: 5666	n:40000
KS ci ratio: 1.772839e-01	ci left: 1.100379e-02	ci right 1.316791e-02	k: 482	n:40000
CP   40000 perm   9 sec   (4479 perm/sec)   p_kst 1.205000e-02   p_cons 1.416500e-01   p_joint 1.135000e-02

Joint ci ratio: 1.436225e-01	ci left: 1.362478e-02	ci right 1.575211e-02	k: 733	n:50000
Cons ci ratio: 4.319852e-02	ci left: 1.383370e-01	ci right 1.444647e-01	k: 7069	n:50000
KS ci ratio: 1.558154e-01	ci left: 1.152531e-02	ci right 1.349189e-02	k: 624	n:50000
CP   50000 perm   11 sec   (4373 perm/sec)   p_kst 1.248000e-02   p_cons 1.413800e-01   p_joint 1.466000e-02

Joint ci ratio: 1.380149e-01	ci left: 1.235035e-02	ci right 1.419718e-02	k: 795	n:60000
Cons ci ratio: 3.955971e-02	ci left: 1.378442e-01	ci right 1.434239e-01	k: 8437	n:60000
KS ci ratio: 1.428192e-01	ci left: 1.151376e-02	ci right 1.330053e-02	k: 743	n:60000
CP   60000 perm   14 sec   (4266 perm/sec)   p_kst 1.238333e-02   p_cons 1.406167e-01   p_joint 1.325000e-02

Joint ci ratio: 1.193716e-01	ci left: 1.426505e-02	ci right 1.608975e-02	k: 1061	n:70000
Cons ci ratio: 3.671277e-02	ci left: 1.374799e-01	ci right 1.426357e-01	k: 9803	n:70000
KS ci ratio: 1.313090e-01	ci left: 1.174535e-02	ci right 1.340970e-02	k: 879	n:70000
CP   70000 perm   17 sec   (4163 perm/sec)   p_kst 1.255714e-02   p_cons 1.400429e-01   p_joint 1.515714e-02

Joint ci ratio: 1.229346e-01	ci left: 1.177794e-02	ci right 1.333271e-02	k: 1003	n:80000
Cons ci ratio: 3.426449e-02	ci left: 1.381856e-01	ci right 1.430155e-01	k: 11247	n:80000
KS ci ratio: 1.236853e-01	ci left: 1.163251e-02	ci right 1.317815e-02	k: 991	n:80000
CP   80000 perm   20 sec   (4075 perm/sec)   p_kst 1.238750e-02   p_cons 1.405875e-01   p_joint 1.253750e-02

Joint ci ratio: 1.245355e-01	ci left: 1.021035e-02	ci right 1.157701e-02	k: 979	n:90000
Cons ci ratio: 3.228559e-02	ci left: 1.384675e-01	ci right 1.430224e-01	k: 12666	n:90000
KS ci ratio: 1.173055e-01	ci left: 1.153615e-02	ci right 1.298443e-02	k: 1102	n:90000
CP   90000 perm   23 sec   (3993 perm/sec)   p_kst 1.224444e-02   p_cons 1.407333e-01   p_joint 1.087778e-02

Joint ci ratio: 1.170034e-01	ci left: 1.045014e-02	ci right 1.175845e-02	k: 1109	n:100000
Cons ci ratio: 3.056369e-02	ci left: 1.390968e-01	ci right 1.434240e-01	k: 14125	n:100000
KS ci ratio: 1.110821e-01	ci left: 1.161630e-02	ci right 1.299220e-02	k: 1229	n:100000
CP   100000 perm   26 sec   (3917 perm/sec)   p_kst 1.229000e-02   p_cons 1.412500e-01   p_joint 1.109000e-02

Joint ci ratio: 1.036481e-01	ci left: 1.217060e-02	ci right 1.350981e-02	k: 1411	n:110000
Cons ci ratio: 2.914637e-02	ci left: 1.391561e-01	ci right 1.432810e-01	k: 15533	n:110000
KS ci ratio: 1.059126e-01	ci left: 1.164813e-02	ci right 1.295959e-02	k: 1352	n:110000
CP   110000 perm   29 sec   (3847 perm/sec)   p_kst 1.229091e-02   p_cons 1.412091e-01   p_joint 1.282727e-02

Joint ci ratio: 9.320912e-02	ci left: 1.384752e-02	ci right 1.520942e-02	k: 1742	n:120000
Cons ci ratio: 2.789038e-02	ci left: 1.393751e-01	ci right 1.433256e-01	k: 16961	n:120000
KS ci ratio: 1.015431e-01	ci left: 1.164340e-02	ci right 1.289701e-02	k: 1471	n:120000
CP   120000 perm   32 sec   (3781 perm/sec)   p_kst 1.225833e-02   p_cons 1.413417e-01   p_joint 1.451667e-02

Joint ci ratio: 9.141887e-02	ci left: 1.330819e-02	ci right 1.459055e-02	k: 1812	n:130000
Cons ci ratio: 2.681619e-02	ci left: 1.392730e-01	ci right 1.430661e-01	k: 18351	n:130000
KS ci ratio: 9.770429e-02	ci left: 1.163282e-02	ci right 1.283523e-02	k: 1589	n:130000
CP   130000 perm   35 sec   (3721 perm/sec)   p_kst 1.222308e-02   p_cons 1.411615e-01   p_joint 1.393846e-02

Outputting figure to mutsig2_images.part000000000042/CP.2_3274_130000_0.012223_0.14116_0.013938.png
                gene_name: CP
               theta_stop: 0.098 
                    nperm: 130000 
                     p_ks: 0.012 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.014 
     ci_joint_bounds_left: 0.013 
    ci_joint_bounds_right: 0.015 

Current progress: 29 percent done.
CPAMD8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.198959e-02	ci left: 4.557846e-01	ci right 4.754354e-01	k: 4656	n:10000
Cons ci ratio: 7.348846e-02	ci left: 2.132945e-01	ci right 2.296681e-01	k: 2214	n:10000
KS ci ratio: 8.208438e-02	ci left: 1.780224e-01	ci right 1.933612e-01	k: 1856	n:10000
CPAMD8   10000 perm   2 sec   (4264 perm/sec)   p_kst 1.856000e-01   p_cons 2.214000e-01   p_joint 4.656000e-01

Outputting figure to mutsig2_images.part000000000042/CPAMD8.2_5967_10000_0.1856_0.2214_0.4656.png
                gene_name: CPAMD8
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 43 percent done.
CPB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.838059e-03	ci left: 9.885089e-01	ci right 9.923974e-01	k: 9906	n:10000
KS ci ratio: 2.936549e-02	ci left: 6.310052e-01	ci right 6.499129e-01	k: 6405	n:10000
CPB2   10000 perm   2 sec   (6515 perm/sec)   p_kst 6.405000e-01   p_cons 9.906000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000042/CPB2.2_1316_10000_0.6405_0.9906_1.png
                gene_name: CPB2
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 57 percent done.
CPN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.217011e-02	ci left: 5.878110e-01	ci right 6.071321e-01	k: 5975	n:10000
KS ci ratio: 1.628821e-02	ci left: 8.457031e-01	ci right 8.596908e-01	k: 8528	n:10000
CPN1   10000 perm   1 sec   (6757 perm/sec)   p_kst 8.528000e-01   p_cons 5.975000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000042/CPN1.2_1413_10000_0.8528_0.5975_1.png
                gene_name: CPN1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
CPSF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.776735e-02	ci left: 8.220852e-01	ci right 8.369224e-01	k: 8296	n:10000
Cons ci ratio: 3.462305e-02	ci left: 5.519083e-01	ci right 5.714558e-01	k: 5617	n:10000
KS ci ratio: 3.507522e-02	ci left: 5.454954e-01	ci right 5.650724e-01	k: 5553	n:10000
CPSF1   10000 perm   2 sec   (4892 perm/sec)   p_kst 5.553000e-01   p_cons 5.617000e-01   p_joint 8.296000e-01

Outputting figure to mutsig2_images.part000000000042/CPSF1.2_4480_10000_0.5553_0.5617_0.8296.png
                gene_name: CPSF1
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.82 
    ci_joint_bounds_right: 0.84 

Current progress: 86 percent done.
CPSF7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.044849e-02	ci left: 7.779303e-01	ci right 7.941028e-01	k: 7861	n:10000
KS ci ratio: 2.015033e-02	ci left: 7.828967e-01	ci right 7.989335e-01	k: 7910	n:10000
CPSF7   10000 perm   2 sec   (6276 perm/sec)   p_kst 7.910000e-01   p_cons 7.861000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000042/CPSF7.2_1581_10000_0.791_0.7861_1.png
                gene_name: CPSF7
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000042
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 42 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4397926: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000043> was used as the working directory.
Started at Wed Oct 24 16:10:50 2012
Results reported at Wed Oct 24 16:12:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000043.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000043.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 43  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000043.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    102.79 sec.
    Max Memory :      1094 MB
    Max Swap   :      4007 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
43
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 43
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 43: processing genes 3769 - 3858
Calculating significance of each gene.
Using projection method.
3769	CPZ	2.538506e-01
3770	CR1	1.862705e-01
3771	CR1L	6.212263e-02
3772	CR2	1
3773	CRABP1	1
3774	CRABP2	1
3775	CRADD	1
3776	CRAMP1L	1
3777	CRAT	6.951060e-02
3778	CRB1	2.601425e-03
3779	CRB2	3.672461e-01
3780	CRB3	1
3781	CRBN	1
3782	CRCP	1
3783	CRCT1	1
3784	CREB1	1
3785	CREB3	1
3786	CREB3L1	1
3787	CREB3L2	1
3788	CREB3L3	1
3789	CREB3L4	7.681570e-02
3790	CREB5	1
3791	CREBBP	1.395336e-02
3792	CREBL2	1
3793	CREBZF	1.882099e-01
3794	CREG1	1
3795	CREG2	1
3796	CRELD1	1
3797	CRELD2	1
3798	CREM	1
3799	CRH	1
3800	CRHBP	1
3801	CRHR1	1
3802	CRHR2	1
3803	CRIM1	3.589306e-01
3804	CRIP1	1
3805	CRIP2	1
3806	CRIP3	1
3807	CRIPAK	1
3808	CRIPT	1
3809	CRISP1	1
3810	CRISP2	1
3811	CRISP3	1
3812	CRISPLD1	1
3813	CRISPLD2	1
3814	CRK	1
3815	CRKL	1
3816	CRLF1	1
3817	CRLF2	1
3818	CRLF3	1.770591e-01
3819	CRLS1	1
3820	CRMP1	2.602624e-01
3821	CRNKL1	3.704664e-01
3822	CRNN	1.751502e-01
3823	CROCC	1.350963e-01
3824	CROT	1
3825	CRP	1
3826	CRTAC1	1
3827	CRTAM	1
3828	CRTAP	1
3829	CRTC1	2.541013e-01
3830	CRTC2	4.783443e-02
3831	CRTC3	5.773881e-02
3832	CRX	7.358409e-02
3833	CRY1	1
3834	CRY2	1
3835	CRYAA	1
3836	CRYAB	1
3837	CRYBA1	1
3838	CRYBA2	1
3839	CRYBA4	1
3840	CRYBB1	1
3841	CRYBB2	1
3842	CRYBB3	1
3843	CRYBG3	1.124554e-01
3844	CRYGA	1
3845	CRYGB	1
3846	CRYGC	1
3847	CRYGD	1
3848	CRYGN	1
3849	CRYGS	1
3850	CRYL1	1
3851	CRYM	1
3852	CRYZ	1
3853	CRYZL1	1.435716e-01
3854	CS	1
3855	CSAD	1
3856	CSAG1	1
3857	CSDA	1
3858	CSDC2	1
Done

Running MutSig 2:
Scatter job 43: processing genes 3769 - 3858
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CRB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.144526e-02	ci left: 4.622748e-01	ci right 4.819415e-01	k: 4721	n:10000
Cons ci ratio: 3.050389e-02	ci left: 6.132157e-01	ci right 6.323128e-01	k: 6228	n:10000
KS ci ratio: 7.062704e-02	ci left: 2.271129e-01	ci right 2.438415e-01	k: 2354	n:10000
CRB1   10000 perm   2 sec   (4749 perm/sec)   p_kst 2.354000e-01   p_cons 6.228000e-01   p_joint 4.721000e-01

Outputting figure to mutsig2_images.part000000000043/CRB1.4_4269_10000_0.2354_0.6228_0.4721.png
                gene_name: CRB1
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 20 percent done.
CREBBP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.941957e-02	ci left: 3.765422e-01	ci right 3.957242e-01	k: 3861	n:10000
Cons ci ratio: 3.589935e-02	ci left: 5.339763e-01	ci right 5.535982e-01	k: 5438	n:10000
KS ci ratio: 8.186790e-02	ci left: 1.788095e-01	ci right 1.941736e-01	k: 1864	n:10000
CREBBP   10000 perm   2 sec   (4383 perm/sec)   p_kst 1.864000e-01   p_cons 5.438000e-01   p_joint 3.861000e-01

Outputting figure to mutsig2_images.part000000000043/CREBBP.4_7453_10000_0.1864_0.5438_0.3861.png
                gene_name: CREBBP
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 40 percent done.
CROCC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.080238e-02	ci left: 4.700652e-01	ci right 4.897466e-01	k: 4799	n:10000
Cons ci ratio: 8.375026e-02	ci left: 1.721207e-01	ci right 1.872663e-01	k: 1796	n:10000
KS ci ratio: 3.099927e-02	ci left: 6.055814e-01	ci right 6.247515e-01	k: 6152	n:10000
CROCC   10000 perm   2 sec   (4546 perm/sec)   p_kst 6.152000e-01   p_cons 1.796000e-01   p_joint 4.799000e-01

Outputting figure to mutsig2_images.part000000000043/CROCC.2_6202_10000_0.6152_0.1796_0.4799.png
                gene_name: CROCC
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 60 percent done.
CRTC2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.943382e-03	ci left: 9.461696e-01	ci right 9.547655e-01	k: 9506	n:10000
Cons ci ratio: 8.363681e-02	ci left: 1.725141e-01	ci right 1.876728e-01	k: 1800	n:10000
KS ci ratio: 9.305635e-02	ci left: 1.436425e-01	ci right 1.577616e-01	k: 1506	n:10000
CRTC2   10000 perm   2 sec   (6139 perm/sec)   p_kst 1.506000e-01   p_cons 1.800000e-01   p_joint 9.506000e-01

Outputting figure to mutsig2_images.part000000000043/CRTC2.2_2138_10000_0.1506_0.18_0.9506.png
                gene_name: CRTC2
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.95 

Current progress: 80 percent done.
CRYBG3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.591398e-01	ci left: 5.263174e-02	ci right 6.182831e-02	k: 571	n:10000
Cons ci ratio: 4.899491e-02	ci left: 3.806225e-01	ci right 3.998415e-01	k: 3902	n:10000
KS ci ratio: 1.888568e-01	ci left: 3.738868e-02	ci right 4.528136e-02	k: 412	n:10000
CRYBG3   10000 perm   2 sec   (5744 perm/sec)   p_kst 4.120000e-02   p_cons 3.902000e-01   p_joint 5.710000e-02

Joint ci ratio: 4.837076e-02	ci left: 2.411839e-01	ci right 2.531897e-01	k: 4943	n:20000
Cons ci ratio: 3.465895e-02	ci left: 3.832815e-01	ci right 3.968505e-01	k: 7801	n:20000
KS ci ratio: 1.309216e-01	ci left: 4.008492e-02	ci right 4.574894e-02	k: 857	n:20000
CRYBG3   20000 perm   4 sec   (5230 perm/sec)   p_kst 4.285000e-02   p_cons 3.900500e-01   p_joint 2.471500e-01

Joint ci ratio: 4.802863e-02	ci left: 1.773179e-01	ci right 1.860771e-01	k: 5450	n:30000
Cons ci ratio: 2.966995e-02	ci left: 3.623398e-01	ci right 3.732858e-01	k: 11034	n:30000
KS ci ratio: 1.072028e-01	ci left: 4.037492e-02	ci right 4.498084e-02	k: 1279	n:30000
CRYBG3   30000 perm   6 sec   (5031 perm/sec)   p_kst 4.263333e-02   p_cons 3.678000e-01   p_joint 1.816667e-01

Joint ci ratio: 4.703570e-02	ci left: 1.444590e-01	ci right 1.514422e-01	k: 5917	n:40000
Cons ci ratio: 2.572718e-02	ci left: 3.624983e-01	ci right 3.719710e-01	k: 14689	n:40000
KS ci ratio: 9.288808e-02	ci left: 4.064166e-02	ci right 4.462508e-02	k: 1704	n:40000
CRYBG3   40000 perm   8 sec   (4898 perm/sec)   p_kst 4.260000e-02   p_cons 3.672250e-01   p_joint 1.479250e-01

Outputting figure to mutsig2_images.part000000000043/CRYBG3.2_3145_40000_0.0426_0.36723_0.14793.png
                gene_name: CRYBG3
               theta_stop: 0.093 
                    nperm: 40000 
                     p_ks: 0.043 
        ci_ks_bounds_left: 0.041 
       ci_ks_bounds_right: 0.045 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.15 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000043
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 43 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4397929: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000044> was used as the working directory.
Started at Wed Oct 24 16:10:50 2012
Results reported at Wed Oct 24 16:13:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000044.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000044.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 44  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000044.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    147.59 sec.
    Max Memory :      1603 MB
    Max Swap   :      4066 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
44
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 44
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 44: processing genes 3859 - 3947
Calculating significance of each gene.
Using projection method.
3859	CSDE1	1.558701e-01
3860	CSE1L	3.990460e-01
3861	CSF1	1
3862	CSF1R	2.682028e-01
3863	CSF2	1
3864	CSF2RA	1
3865	CSF2RB	1.108682e-01
3866	CSF3	1
3867	CSF3R	1
3868	CSGALNACT1	8.378370e-02
3869	CSGALNACT2	1
3870	CSH1	1
3871	CSH2	3.258553e-02
3872	CSHL1	1
3873	CSK	1
3874	CSMD1	3.768205e-01
3875	CSMD2	1
3876	CSMD3	7.415720e-01
3877	CSN1S1	1
3878	CSN2	1
3879	CSN3	1
3880	CSNK1A1	1
3881	CSNK1A1L	6.275215e-02
3882	CSNK1D	1
3883	CSNK1E	1
3884	CSNK1G1	8.792101e-02
3885	CSNK1G2	1
3886	CSNK1G3	1
3887	CSNK2A1	1
3888	CSNK2A2	1
3889	CSNK2B	1
3890	CSPG4	2.887422e-01
3891	CSPG5	1
3892	CSPP1	1
3893	CSRNP1	1
3894	CSRNP2	1
3895	CSRNP3	2.898991e-01
3896	CSRP1	1
3897	CSRP2	1
3898	CSRP2BP	1
3899	CSRP3	1
3900	CST1	1
3901	CST11	1
3902	CST2	3.699626e-02
3903	CST3	1
3904	CST4	1
3905	CST5	1
3906	CST6	1
3907	CST7	1
3908	CST8	1
3909	CST9	1
3910	CST9L	1
3911	CSTA	1
3912	CSTB	2.594233e-02
3913	CSTF1	1
3914	CSTF2	1
3915	CSTF2T	1
3916	CSTF3	1
3917	CSTL1	1
3918	CT45A5	1
3919	CT62	1
3920	CTAG2	1
3921	CTAGE1	3.734274e-03
3922	CTAGE5	2.908483e-02
3923	CTAGE6P	1
3924	CTBP1	1
3925	CTBP2	1
3926	CTBS	1
3927	CTCF	1
3928	CTCFL	1.656922e-01
3929	CTDP1	1
3930	CTDSP1	1
3931	CTDSP2	1
3932	CTDSPL	1
3933	CTDSPL2	1.312500e-01
3934	CTGF	1
3935	CTH	1
3936	CTHRC1	1
3937	CTLA4	1
3938	CTNNA1	3.804744e-02
3939	CTNNA2	4.498455e-02
3940	CTNNA3	6.128026e-03
3941	CTNNAL1	2.173031e-01
3942	CTNNB1	2.901658e-01
3943	CTNNBIP1	9.527158e-03
3944	CTNNBL1	1.135515e-01
3945	CTNND1	1
3946	CTNND2	1
3947	CTNS	1
Done

Running MutSig 2:
Scatter job 44: processing genes 3859 - 3947
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CTAGE1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.942206e-02	ci left: 4.872524e-01	ci right 5.069493e-01	k: 4971	n:10000
Cons ci ratio: 1.044753e-01	ci left: 1.169164e-01	ci right 1.299039e-01	k: 1233	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
CTAGE1   10000 perm   2 sec   (4685 perm/sec)   p_kst 1   p_cons 1.233000e-01   p_joint 4.971000e-01

Joint ci ratio: 2.469823e-02	ci left: 5.504834e-01	ci right 5.642999e-01	k: 11148	n:20000
Cons ci ratio: 7.547245e-02	ci left: 1.143465e-01	ci right 1.233646e-01	k: 2376	n:20000
KS ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
CTAGE1   20000 perm   6 sec   (3300 perm/sec)   p_kst 1   p_cons 1.188000e-01   p_joint 5.574000e-01

Outputting figure to mutsig2_images.part000000000044/CTAGE1.3_2242_20000_1_0.1188_0.5574.png
                gene_name: CTAGE1
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.56 

Current progress: 17 percent done.
CTNNA3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.033790e-02	ci left: 2.877571e-01	ci right 3.057615e-01	k: 2967	n:10000
Cons ci ratio: 9.234243e-03	ci left: 9.429466e-01	ci right 9.517905e-01	k: 9475	n:10000
KS ci ratio: 1.041866e-01	ci left: 1.175028e-01	ci right 1.305171e-01	k: 1239	n:10000
CTNNA3   10000 perm   3 sec   (3650 perm/sec)   p_kst 1.239000e-01   p_cons 9.475000e-01   p_joint 2.967000e-01

Joint ci ratio: 5.376942e-02	ci left: 2.042736e-01	ci right 2.156109e-01	k: 4198	n:20000
Cons ci ratio: 6.491022e-03	ci left: 9.448836e-01	ci right 9.510854e-01	k: 18961	n:20000
KS ci ratio: 7.389360e-02	ci left: 1.187734e-01	ci right 1.279364e-01	k: 2466	n:20000
CTNNA3   20000 perm   6 sec   (3085 perm/sec)   p_kst 1.233000e-01   p_cons 9.480500e-01   p_joint 2.099000e-01

Outputting figure to mutsig2_images.part000000000044/CTNNA3.3_2756_20000_0.1233_0.94805_0.2099.png
                gene_name: CTNNA3
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 33 percent done.
CSMD2
Processing conservation and coverage...
93% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.596680e-02	ci left: 6.858703e-01	ci right 7.040160e-01	k: 6950	n:10000
KS ci ratio: 4.485854e-02	ci left: 4.231596e-01	ci right 4.426795e-01	k: 4329	n:10000
CSMD2   10000 perm   3 sec   (3617 perm/sec)   p_kst 4.329000e-01   p_cons 6.950000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000044/CSMD2.2_10740_10000_0.4329_0.695_1.png
                gene_name: CSMD2
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.70 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
CTAGE5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.164979e-02	ci left: 2.789393e-01	ci right 2.967844e-01	k: 2878	n:10000
Cons ci ratio: 3.145295e-03	ci left: 9.919467e-01	ci right 9.951556e-01	k: 9937	n:10000
KS ci ratio: 6.707253e-02	ci left: 2.459853e-01	ci right 2.631579e-01	k: 2545	n:10000
CTAGE5   10000 perm   2 sec   (5814 perm/sec)   p_kst 2.545000e-01   p_cons 9.937000e-01   p_joint 2.878000e-01

Outputting figure to mutsig2_images.part000000000044/CTAGE5.2_2542_10000_0.2545_0.9937_0.2878.png
                gene_name: CTAGE5
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.30 

Current progress: 67 percent done.
CTNNA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.175161e-02	ci left: 9.120382e-01	ci right 9.229172e-01	k: 9176	n:10000
KS ci ratio: 2.693860e-02	ci left: 6.699500e-01	ci right 6.883455e-01	k: 6792	n:10000
CTNNA1   10000 perm   2 sec   (5775 perm/sec)   p_kst 6.792000e-01   p_cons 9.176000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000044/CTNNA1.2_2789_10000_0.6792_0.9176_1.png
                gene_name: CTNNA1
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
CTNNA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.795959e-02	ci left: 5.061517e-01	ci right 5.258389e-01	k: 5160	n:10000
KS ci ratio: 4.275680e-02	ci left: 4.468010e-01	ci right 4.664243e-01	k: 4566	n:10000
CTNNA2   10000 perm   2 sec   (6055 perm/sec)   p_kst 4.566000e-01   p_cons 5.160000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000044/CTNNA2.2_2578_10000_0.4566_0.516_1.png
                gene_name: CTNNA2
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000044
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 44 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4397933: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000045> was used as the working directory.
Started at Wed Oct 24 16:11:04 2012
Results reported at Wed Oct 24 16:12:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000045.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000045.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 45  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000045.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    143.68 sec.
    Max Memory :      1161 MB
    Max Swap   :      3875 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
45
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 45
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 45: processing genes 3948 - 4037
Calculating significance of each gene.
Using projection method.
3948	CTPS	1
3949	CTPS2	1
3950	CTR9	4.839030e-01
3951	CTRC	1
3952	CTRL	1
3953	CTSA	1
3954	CTSB	1
3955	CTSC	1
3956	CTSD	1
3957	CTSE	1
3958	CTSF	1
3959	CTSG	1
3960	CTSH	7.800636e-02
3961	CTSK	1.203753e-01
3962	CTSL1	1
3963	CTSL2	9.595463e-02
3964	CTSO	2.569259e-02
3965	CTSS	1.688250e-01
3966	CTSW	1
3967	CTSZ	3.348189e-02
3968	CTTN	7.859505e-02
3969	CTTNBP2	2.933734e-01
3970	CTTNBP2NL	1
3971	CTU2	1
3972	CTXN1	1
3973	CTXN3	1
3974	CUBN	2.783058e-01
3975	CUEDC1	1
3976	CUEDC2	1
3977	CUL1	2.136170e-01
3978	CUL2	1
3979	CUL3	1
3980	CUL4A	1.834320e-01
3981	CUL4B	2.121938e-01
3982	CUL5	1.045195e-01
3983	CUL7	1
3984	CUL9	6.069248e-01
3985	CUTA	1
3986	CUTC	1
3987	CUX1	1
3988	CUX2	1
3989	CUZD1	2.320261e-01
3990	CWC15	1
3991	CWC22	1
3992	CWC25	1
3993	CWC27	1
3994	CWF19L1	8.346159e-02
3995	CWF19L2	1
3996	CWH43	5.651347e-02
3997	CX3CL1	1.419780e-02
3998	CX3CR1	7.763949e-02
3999	CXADR	1
4000/17942 4000	CXCL1	1
4001	CXCL10	1
4002	CXCL11	1
4003	CXCL12	1
4004	CXCL13	1
4005	CXCL14	1
4006	CXCL16	1
4007	CXCL17	1
4008	CXCL2	1
4009	CXCL3	1
4010	CXCL5	1
4011	CXCL6	1
4012	CXCL9	1
4013	CXCR1	1
4014	CXCR2	1
4015	CXCR3	1
4016	CXCR4	1
4017	CXCR5	5.650156e-02
4018	CXCR6	1
4019	CXCR7	1
4020	CXXC1	1
4021	CXXC4	1
4022	CXXC5	1
4023	CXorf1	1
4024	CXorf21	5.267934e-02
4025	CXorf22	1.472079e-01
4026	CXorf23	8.942017e-02
4027	CXorf26	2.016746e-02
4028	CXorf27	1
4029	CXorf36	1
4030	CXorf38	1
4031	CXorf40A	1
4032	CXorf40B	1
4033	CXorf41	1
4034	CXorf48	1
4035	CXorf56	1
4036	CXorf57	1
4037	CXorf58	7.929413e-02
Done

Running MutSig 2:
Scatter job 45: processing genes 3948 - 4037
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CUBN
Processing conservation and coverage...
89% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.264337e-02	ci left: 3.472048e-01	ci right 3.660788e-01	k: 3566	n:10000
Cons ci ratio: 5.377486e-02	ci left: 3.375666e-01	ci right 3.563226e-01	k: 3469	n:10000
KS ci ratio: 5.454299e-02	ci left: 3.312097e-01	ci right 3.498832e-01	k: 3405	n:10000
CUBN   10000 perm   3 sec   (3611 perm/sec)   p_kst 3.405000e-01   p_cons 3.469000e-01   p_joint 3.566000e-01

Outputting figure to mutsig2_images.part000000000045/CUBN.3_11140_10000_0.3405_0.3469_0.3566.png
                gene_name: CUBN
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 50 percent done.
CX3CL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.108764e-01	ci left: 1.049071e-01	ci right 1.173205e-01	k: 1110	n:10000
Cons ci ratio: 1.127108e-01	ci left: 1.017865e-01	ci right 1.140430e-01	k: 1078	n:10000
KS ci ratio: 5.109680e-02	ci left: 3.609240e-01	ci right 3.799515e-01	k: 3704	n:10000
CX3CL1   10000 perm   2 sec   (5341 perm/sec)   p_kst 3.704000e-01   p_cons 1.078000e-01   p_joint 1.110000e-01

Joint ci ratio: 7.467253e-02	ci left: 1.165597e-01	ci right 1.256508e-01	k: 2421	n:20000
Cons ci ratio: 7.898397e-02	ci left: 1.053025e-01	ci right 1.140113e-01	k: 2192	n:20000
KS ci ratio: 3.601869e-02	ci left: 3.651958e-01	ci right 3.786415e-01	k: 7438	n:20000
CX3CL1   20000 perm   4 sec   (5158 perm/sec)   p_kst 3.719000e-01   p_cons 1.096000e-01   p_joint 1.210500e-01

Outputting figure to mutsig2_images.part000000000045/CX3CL1.2_1206_20000_0.3719_0.1096_0.12105.png
                gene_name: CX3CL1
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000045
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 45 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4397938: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000046> was used as the working directory.
Started at Wed Oct 24 16:11:04 2012
Results reported at Wed Oct 24 16:12:55 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000046.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000046.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 46  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000046.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    114.85 sec.
    Max Memory :       942 MB
    Max Swap   :      3738 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
46
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 46
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 46: processing genes 4038 - 4127
Calculating significance of each gene.
Using projection method.
4038	CXorf59	1
4039	CXorf61	1
4040	CXorf65	1
4041	CXorf66	1
4042	CYB561	1
4043	CYB561D1	1
4044	CYB561D2	1
4045	CYB5A	1
4046	CYB5B	1
4047	CYB5D1	1
4048	CYB5D2	1
4049	CYB5R1	1
4050	CYB5R2	6.426529e-02
4051	CYB5R3	1
4052	CYB5R4	1
4053	CYB5RL	5.976045e-02
4054	CYBA	1
4055	CYBASC3	1
4056	CYBB	1
4057	CYBRD1	1
4058	CYC1	1
4059	CYCS	1
4060	CYFIP1	1.815733e-01
4061	CYFIP2	1
4062	CYGB	1
4063	CYHR1	1
4064	CYLC1	9.759542e-02
4065	CYLC2	1
4066	CYLD	1
4067	CYP11A1	1
4068	CYP11B1	1
4069	CYP11B2	8.583308e-02
4070	CYP17A1	1
4071	CYP19A1	1
4072	CYP1A1	1
4073	CYP1A2	2.601600e-01
4074	CYP1B1	1
4075	CYP20A1	2.281441e-02
4076	CYP21A2	1
4077	CYP24A1	1
4078	CYP26A1	1
4079	CYP26B1	1
4080	CYP26C1	1
4081	CYP27A1	1
4082	CYP27B1	1
4083	CYP27C1	1
4084	CYP2A13	1
4085	CYP2A6	1
4086	CYP2A7	1
4087	CYP2B6	1
4088	CYP2C18	1
4089	CYP2C19	1
4090	CYP2C8	1
4091	CYP2C9	3.259544e-02
4092	CYP2D6	1
4093	CYP2E1	1
4094	CYP2F1	1
4095	CYP2J2	1
4096	CYP2R1	1
4097	CYP2S1	1
4098	CYP2U1	1
4099	CYP2W1	1
4100	CYP39A1	1
4101	CYP3A4	1
4102	CYP3A43	1.015153e-01
4103	CYP3A5	1
4104	CYP3A7	1
4105	CYP46A1	1
4106	CYP4A11	1
4107	CYP4A22	1
4108	CYP4B1	1
4109	CYP4F11	1
4110	CYP4F12	1
4111	CYP4F2	1
4112	CYP4F22	1
4113	CYP4F3	1
4114	CYP4F8	1
4115	CYP4V2	1
4116	CYP4X1	1
4117	CYP4Z1	1
4118	CYP51A1	1
4119	CYP7A1	1
4120	CYP7B1	1
4121	CYP8B1	1
4122	CYR61	1
4123	CYSLTR1	5.674601e-02
4124	CYSLTR2	1
4125	CYTH1	1
4126	CYTH2	1
4127	CYTH3	1
Done

Running MutSig 2:
Scatter job 46: processing genes 4038 - 4127
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CYP20A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.820712e-03	ci left: 9.672044e-01	ci right 9.739177e-01	k: 9707	n:10000
Cons ci ratio: 1.161915e-02	ci left: 9.137886e-01	ci right 9.245657e-01	k: 9193	n:10000
KS ci ratio: 1.686766e-02	ci left: 8.365345e-01	ci right 8.508647e-01	k: 8438	n:10000
CYP20A1   10000 perm   2 sec   (6120 perm/sec)   p_kst 8.438000e-01   p_cons 9.193000e-01   p_joint 9.707000e-01

Outputting figure to mutsig2_images.part000000000046/CYP20A1.2_1441_10000_0.8438_0.9193_0.9707.png
                gene_name: CYP20A1
               theta_stop: 0.017 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.97 

Current progress: 50 percent done.
CYP2C9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.102425e-02	ci left: 2.831000e-01	ci right 3.010213e-01	k: 2920	n:10000
Cons ci ratio: 7.505740e-02	ci left: 2.061931e-01	ci right 2.223737e-01	k: 2142	n:10000
KS ci ratio: 2.483886e-02	ci left: 7.045272e-01	ci right 7.223483e-01	k: 7135	n:10000
CYP2C9   10000 perm   2 sec   (6665 perm/sec)   p_kst 7.135000e-01   p_cons 2.142000e-01   p_joint 2.920000e-01

Outputting figure to mutsig2_images.part000000000046/CYP2C9.2_1509_10000_0.7135_0.2142_0.292.png
                gene_name: CYP2C9
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.30 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000046
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 46 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4397941: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000047> was used as the working directory.
Started at Wed Oct 24 16:11:08 2012
Results reported at Wed Oct 24 16:14:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000047.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000047.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 47  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000047.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    200.14 sec.
    Max Memory :      1627 MB
    Max Swap   :      4043 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
47
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 47
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 47: processing genes 4128 - 4216
Calculating significance of each gene.
Using projection method.
4128	CYTH4	1
4129	CYTIP	1
4130	CYTL1	1
4131	CYTSA	1.595956e-01
4132	CYTSB	1
4133	CYYR1	1
4134	D2HGDH	1
4135	D4S234E	1
4136	DAAM1	1.981953e-02
4137	DAAM2	1
4138	DAB1	1
4139	DAB2	1
4140	DAB2IP	1
4141	DACH1	1
4142	DACH2	1
4143	DACT1	7.132792e-02
4144	DAD1	1
4145	DAG1	1
4146	DAGLA	1
4147	DAGLB	1
4148	DAK	1
4149	DALRD3	7.744409e-04
4150	DAND5	1
4151	DAO	1.201735e-01
4152	DAOA	1
4153	DAP	1
4154	DAP3	1
4155	DAPK1	2.374688e-01
4156	DAPK2	1
4157	DAPK3	1
4158	DAPL1	1
4159	DAPP1	1
4160	DARC	1.571298e-01
4161	DARS	1
4162	DARS2	1
4163	DAXX	1
4164	DAZAP1	1
4165	DAZAP2	1
4166	DAZL	1
4167	DBC1	1.146322e-01
4168	DBF4	1
4169	DBF4B	1
4170	DBH	1
4171	DBI	1
4172	DBN1	1
4173	DBNDD1	1
4174	DBNDD2	1
4175	DBNL	1
4176	DBP	1
4177	DBR1	1
4178	DBT	1
4179	DBX1	1
4180	DBX2	1
4181	DCAF10	1
4182	DCAF11	2.774106e-01
4183	DCAF12	1
4184	DCAF12L1	1
4185	DCAF12L2	1.545804e-02
4186	DCAF13	1
4187	DCAF15	1
4188	DCAF16	8.558901e-03
4189	DCAF17	1
4190	DCAF4	1
4191	DCAF4L1	5.449718e-02
4192	DCAF4L2	1
4193	DCAF5	1
4194	DCAF6	5.727054e-02
4195	DCAF7	1
4196	DCAF8	1.078184e-01
4197	DCAF8L1	1
4198	DCAKD	1.183845e-01
4199	DCBLD1	1
4200	DCBLD2	1
4201	DCC	5.101912e-02
4202	DCD	1
4203	DCDC1	1
4204	DCDC2	1
4205	DCDC2B	1
4206	DCHS1	1.178355e-01
4207	DCHS2	2.545351e-01
4208	DCI	1
4209	DCK	1
4210	DCLK1	1
4211	DCLK2	8.502571e-02
4212	DCLK3	1
4213	DCLRE1A	4.271791e-01
4214	DCLRE1B	1
4215	DCLRE1C	3.507456e-02
4216	DCN	1
Done

Running MutSig 2:
Scatter job 47: processing genes 4128 - 4216
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DALRD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.872880e-02	ci left: 1.560058e-01	ci right 1.705909e-01	k: 1632	n:10000
Cons ci ratio: 3.314211e-02	ci left: 5.733634e-01	ci right 5.927881e-01	k: 5831	n:10000
KS ci ratio: 2.013935e-01	ci left: 3.281488e-02	ci right 4.025825e-02	k: 364	n:10000
DALRD3   10000 perm   2 sec   (5590 perm/sec)   p_kst 3.640000e-02   p_cons 5.831000e-01   p_joint 1.632000e-01

Joint ci ratio: 7.451510e-02	ci left: 1.170024e-01	ci right 1.261079e-01	k: 2430	n:20000
Cons ci ratio: 2.328727e-02	ci left: 5.793371e-01	ci right 5.930378e-01	k: 11724	n:20000
KS ci ratio: 1.373166e-01	ci left: 3.645585e-02	ci right 4.187918e-02	k: 782	n:20000
DALRD3   20000 perm   6 sec   (3510 perm/sec)   p_kst 3.910000e-02   p_cons 5.862000e-01   p_joint 1.215000e-01

Joint ci ratio: 7.881951e-02	ci left: 7.315672e-02	ci right 7.919233e-02	k: 2284	n:30000
Cons ci ratio: 1.849764e-02	ci left: 5.939291e-01	ci right 6.050516e-01	k: 17985	n:30000
KS ci ratio: 1.134068e-01	ci left: 3.612399e-02	ci right 4.049934e-02	k: 1148	n:30000
DALRD3   30000 perm   8 sec   (3812 perm/sec)   p_kst 3.826667e-02   p_cons 5.995000e-01   p_joint 7.613333e-02

Joint ci ratio: 5.753704e-02	ci left: 1.009755e-01	ci right 1.069822e-01	k: 4158	n:40000
Cons ci ratio: 1.605629e-02	ci left: 5.935764e-01	ci right 6.032093e-01	k: 23936	n:40000
KS ci ratio: 9.841413e-02	ci left: 3.626945e-02	ci right 4.004798e-02	k: 1525	n:40000
DALRD3   40000 perm   10 sec   (3959 perm/sec)   p_kst 3.812500e-02   p_cons 5.984000e-01   p_joint 1.039500e-01

Outputting figure to mutsig2_images.part000000000047/DALRD3.4_1680_40000_0.038125_0.5984_0.10395.png
                gene_name: DALRD3
               theta_stop: 0.098 
                    nperm: 40000 
                     p_ks: 0.038 
        ci_ks_bounds_left: 0.036 
       ci_ks_bounds_right: 0.040 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 12 percent done.
DAAM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.710281e-02	ci left: 3.994411e-01	ci right 4.188118e-01	k: 4091	n:10000
Cons ci ratio: 1.094953e-01	ci left: 1.073461e-01	ci right 1.198799e-01	k: 1135	n:10000
KS ci ratio: 4.916000e-02	ci left: 3.790301e-01	ci right 3.982348e-01	k: 3886	n:10000
DAAM1   10000 perm   2 sec   (5467 perm/sec)   p_kst 3.886000e-01   p_cons 1.135000e-01   p_joint 4.091000e-01

Joint ci ratio: 3.510368e-02	ci left: 3.772518e-01	ci right 3.907819e-01	k: 7680	n:20000
Cons ci ratio: 7.779378e-02	ci left: 1.082507e-01	ci right 1.170623e-01	k: 2252	n:20000
KS ci ratio: 3.515195e-02	ci left: 3.766041e-01	ci right 3.901299e-01	k: 7667	n:20000
DAAM1   20000 perm   4 sec   (4942 perm/sec)   p_kst 3.833500e-01   p_cons 1.126000e-01   p_joint 3.840000e-01

Outputting figure to mutsig2_images.part000000000047/DAAM1.3_3337_20000_0.38335_0.1126_0.384.png
                gene_name: DAAM1
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.39 

Current progress: 25 percent done.
DCHS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.131817e-01	ci left: 1.010066e-01	ci right 1.132234e-01	k: 1070	n:10000
Cons ci ratio: 7.160178e-02	ci left: 2.222750e-01	ci right 2.388823e-01	k: 2305	n:10000
KS ci ratio: 1.277887e-01	ci left: 8.047904e-02	ci right 9.156351e-02	k: 859	n:10000
DCHS1   10000 perm   3 sec   (3782 perm/sec)   p_kst 8.590000e-02   p_cons 2.305000e-01   p_joint 1.070000e-01

Joint ci ratio: 7.791074e-02	ci left: 1.079558e-01	ci right 1.167573e-01	k: 2246	n:20000
Cons ci ratio: 4.839026e-02	ci left: 2.410352e-01	ci right 2.530385e-01	k: 4940	n:20000
KS ci ratio: 9.183013e-02	ci left: 7.965288e-02	ci right 8.736872e-02	k: 1669	n:20000
DCHS1   20000 perm   6 sec   (3486 perm/sec)   p_kst 8.345000e-02   p_cons 2.470000e-01   p_joint 1.123000e-01

Outputting figure to mutsig2_images.part000000000047/DCHS1.3_9977_20000_0.08345_0.247_0.1123.png
                gene_name: DCHS1
               theta_stop: 0.092 
                    nperm: 20000 
                     p_ks: 0.083 
        ci_ks_bounds_left: 0.080 
       ci_ks_bounds_right: 0.087 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

Current progress: 38 percent done.
DCHS2
Processing conservation and coverage...
90% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.190635e-02	ci left: 2.772555e-01	ci right 2.950692e-01	k: 2861	n:10000
Cons ci ratio: 2.612611e-02	ci left: 6.832497e-01	ci right 7.014381e-01	k: 6924	n:10000
KS ci ratio: 1.008704e-01	ci left: 1.245431e-01	ci right 1.378726e-01	k: 1311	n:10000
DCHS2   10000 perm   3 sec   (3730 perm/sec)   p_kst 1.311000e-01   p_cons 6.924000e-01   p_joint 2.861000e-01

Joint ci ratio: 4.219998e-02	ci left: 2.949951e-01	ci right 3.077627e-01	k: 6027	n:20000
Cons ci ratio: 1.890503e-02	ci left: 6.759974e-01	ci right 6.889495e-01	k: 13650	n:20000
KS ci ratio: 6.987848e-02	ci left: 1.311789e-01	ci right 1.407272e-01	k: 2718	n:20000
DCHS2   20000 perm   6 sec   (3431 perm/sec)   p_kst 1.359000e-01   p_cons 6.825000e-01   p_joint 3.013500e-01

Outputting figure to mutsig2_images.part000000000047/DCHS2.3_11085_20000_0.1359_0.6825_0.30135.png
                gene_name: DCHS2
               theta_stop: 0.070 
                    nperm: 20000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.31 

Current progress: 50 percent done.
DCAF12L2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.005121e-02	ci left: 6.202494e-01	ci right 6.392749e-01	k: 6298	n:10000
Cons ci ratio: 4.011404e-02	ci left: 4.785574e-01	ci right 4.982494e-01	k: 4884	n:10000
KS ci ratio: 4.529973e-02	ci left: 4.183742e-01	ci right 4.378677e-01	k: 4281	n:10000
DCAF12L2   10000 perm   2 sec   (6421 perm/sec)   p_kst 4.281000e-01   p_cons 4.884000e-01   p_joint 6.298000e-01

Outputting figure to mutsig2_images.part000000000047/DCAF12L2.2_1396_10000_0.4281_0.4884_0.6298.png
                gene_name: DCAF12L2
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 62 percent done.
DCAF6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.218871e-02	ci left: 9.061740e-01	ci right 9.173848e-01	k: 9119	n:10000
Cons ci ratio: 4.953441e-02	ci left: 3.754476e-01	ci right 3.946195e-01	k: 3850	n:10000
KS ci ratio: 3.389164e-01	ci left: 1.096414e-02	ci right 1.552595e-02	k: 131	n:10000
DCAF6   10000 perm   2 sec   (6033 perm/sec)   p_kst 1.310000e-02   p_cons 3.850000e-01   p_joint 9.119000e-01

Joint ci ratio: 8.261216e-03	ci left: 9.145710e-01	ci right 9.222069e-01	k: 18369	n:20000
Cons ci ratio: 3.462620e-02	ci left: 3.837300e-01	ci right 3.973018e-01	k: 7810	n:20000
KS ci ratio: 2.419888e-01	ci left: 1.138222e-02	ci right 1.456171e-02	k: 258	n:20000
DCAF6   20000 perm   4 sec   (5380 perm/sec)   p_kst 1.290000e-02   p_cons 3.905000e-01   p_joint 9.184500e-01

Joint ci ratio: 6.748546e-03	ci left: 9.152110e-01	ci right 9.214411e-01	k: 27551	n:30000
Cons ci ratio: 2.831273e-02	ci left: 3.843087e-01	ci right 3.953793e-01	k: 11695	n:30000
KS ci ratio: 1.974559e-01	ci left: 1.168546e-02	ci right 1.427680e-02	k: 388	n:30000
DCAF6   30000 perm   6 sec   (5120 perm/sec)   p_kst 1.293333e-02   p_cons 3.898333e-01   p_joint 9.183667e-01

Joint ci ratio: 5.765598e-03	ci left: 9.176789e-01	ci right 9.230098e-01	k: 36815	n:40000
Cons ci ratio: 2.466141e-02	ci left: 3.823225e-01	ci right 3.918939e-01	k: 15484	n:40000
KS ci ratio: 1.689786e-01	ci left: 1.215240e-02	ci right 1.441908e-02	k: 530	n:40000
DCAF6   40000 perm   9 sec   (4607 perm/sec)   p_kst 1.325000e-02   p_cons 3.871000e-01   p_joint 9.203750e-01

Joint ci ratio: 5.150288e-03	ci left: 9.181552e-01	ci right 9.229159e-01	k: 46028	n:50000
Cons ci ratio: 2.201164e-02	ci left: 3.838252e-01	ci right 3.923878e-01	k: 19405	n:50000
KS ci ratio: 1.526320e-01	ci left: 1.202548e-02	ci right 1.403165e-02	k: 650	n:50000
DCAF6   50000 perm   11 sec   (4559 perm/sec)   p_kst 1.300000e-02   p_cons 3.881000e-01   p_joint 9.205600e-01

Joint ci ratio: 4.702339e-03	ci left: 9.183405e-01	ci right 9.226854e-01	k: 55232	n:60000
Cons ci ratio: 2.009744e-02	ci left: 3.841147e-01	ci right 3.919295e-01	k: 23281	n:60000
KS ci ratio: 1.403565e-01	ci left: 1.193192e-02	ci right 1.374899e-02	k: 769	n:60000
DCAF6   60000 perm   13 sec   (4500 perm/sec)   p_kst 1.281667e-02   p_cons 3.880167e-01   p_joint 9.205333e-01

Joint ci ratio: 4.358291e-03	ci left: 9.183413e-01	ci right 9.223666e-01	k: 64426	n:70000
Cons ci ratio: 1.866008e-02	ci left: 3.830472e-01	ci right 3.902765e-01	k: 27066	n:70000
KS ci ratio: 1.302636e-01	ci left: 1.193889e-02	ci right 1.361615e-02	k: 893	n:70000
DCAF6   70000 perm   16 sec   (4435 perm/sec)   p_kst 1.275714e-02   p_cons 3.866571e-01   p_joint 9.203714e-01

Joint ci ratio: 4.084668e-03	ci left: 9.181870e-01	ci right 9.219575e-01	k: 73607	n:80000
Cons ci ratio: 1.745385e-02	ci left: 3.833108e-01	ci right 3.900724e-01	k: 30935	n:80000
KS ci ratio: 1.232458e-01	ci left: 1.171734e-02	ci right 1.326831e-02	k: 998	n:80000
DCAF6   80000 perm   18 sec   (4372 perm/sec)   p_kst 1.247500e-02   p_cons 3.866875e-01   p_joint 9.200875e-01

Joint ci ratio: 3.840519e-03	ci left: 9.187023e-01	ci right 9.222483e-01	k: 82844	n:90000
Cons ci ratio: 1.646721e-02	ci left: 3.831726e-01	ci right 3.895458e-01	k: 34772	n:90000
KS ci ratio: 1.154647e-01	ci left: 1.191385e-02	ci right 1.338448e-02	k: 1137	n:90000
DCAF6   90000 perm   21 sec   (4277 perm/sec)   p_kst 1.263333e-02   p_cons 3.863556e-01   p_joint 9.204889e-01

Joint ci ratio: 3.650356e-03	ci left: 9.185133e-01	ci right 9.218822e-01	k: 92021	n:100000
Cons ci ratio: 1.561810e-02	ci left: 3.834603e-01	ci right 3.895063e-01	k: 38648	n:100000
KS ci ratio: 1.089064e-01	ci left: 1.209298e-02	ci right 1.349549e-02	k: 1278	n:100000
DCAF6   100000 perm   24 sec   (4219 perm/sec)   p_kst 1.278000e-02   p_cons 3.864800e-01   p_joint 9.202100e-01

Joint ci ratio: 3.476391e-03	ci left: 9.187665e-01	ci right 9.219750e-01	k: 101242	n:110000
Cons ci ratio: 1.491382e-02	ci left: 3.828855e-01	ci right 3.886478e-01	k: 42434	n:110000
KS ci ratio: 1.043617e-01	ci left: 1.200232e-02	ci right 1.333265e-02	k: 1392	n:110000
DCAF6   110000 perm   26 sec   (4159 perm/sec)   p_kst 1.265455e-02   p_cons 3.857636e-01   p_joint 9.203818e-01

Joint ci ratio: 3.320770e-03	ci left: 9.191736e-01	ci right 9.222393e-01	k: 110486	n:120000
Cons ci ratio: 1.428611e-02	ci left: 3.827698e-01	ci right 3.882857e-01	k: 46263	n:120000
KS ci ratio: 1.006469e-01	ci left: 1.185465e-02	ci right 1.311908e-02	k: 1497	n:120000
DCAF6   120000 perm   29 sec   (4103 perm/sec)   p_kst 1.247500e-02   p_cons 3.855250e-01   p_joint 9.207167e-01

Joint ci ratio: 3.378601e-03	ci left: 9.103849e-01	ci right 9.134736e-01	k: 118552	n:130000
Cons ci ratio: 1.370592e-02	ci left: 3.835598e-01	ci right 3.888607e-01	k: 50207	n:130000
KS ci ratio: 9.711851e-02	ci left: 1.177546e-02	ci right 1.298490e-02	k: 1608	n:130000
DCAF6   130000 perm   32 sec   (4040 perm/sec)   p_kst 1.236923e-02   p_cons 3.862077e-01   p_joint 9.119385e-01

Outputting figure to mutsig2_images.part000000000047/DCAF6.2_2723_130000_0.012369_0.38621_0.91194.png
                gene_name: DCAF6
               theta_stop: 0.097 
                    nperm: 130000 
                     p_ks: 0.012 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.91 

Current progress: 75 percent done.
DCC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.562761e-02	ci left: 8.560029e-01	ci right 8.695850e-01	k: 8629	n:10000
KS ci ratio: 1.458799e-02	ci left: 8.718340e-01	ci right 8.847448e-01	k: 8784	n:10000
DCC   10000 perm   2 sec   (5139 perm/sec)   p_kst 8.784000e-01   p_cons 8.629000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000047/DCC.2_4460_10000_0.8784_0.8629_1.png
                gene_name: DCC
               theta_stop: 0.016 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.87 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 88 percent done.
DCLRE1C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.282578e-02	ci left: 4.460026e-01	ci right 4.656231e-01	k: 4558	n:10000
KS ci ratio: 6.434124e-02	ci left: 2.619103e-01	ci right 2.794235e-01	k: 2706	n:10000
DCLRE1C   10000 perm   2 sec   (5993 perm/sec)   p_kst 2.706000e-01   p_cons 4.558000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000047/DCLRE1C.2_2135_10000_0.2706_0.4558_1.png
                gene_name: DCLRE1C
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000047
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 47 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1535>
Subject: Job 4397944: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1535>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000048> was used as the working directory.
Started at Wed Oct 24 16:11:08 2012
Results reported at Wed Oct 24 16:14:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000048.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000048.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 48  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000048.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    242.31 sec.
    Max Memory :      1618 MB
    Max Swap   :      4063 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
48
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 48
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 48: processing genes 4217 - 4306
Calculating significance of each gene.
Using projection method.
4217	DCP1A	5.597216e-02
4218	DCP1B	1
4219	DCP2	1
4220	DCPS	1
4221	DCST1	1
4222	DCST2	1
4223	DCT	1
4224	DCTD	1
4225	DCTN1	5.138851e-01
4226	DCTN2	1
4227	DCTN3	1
4228	DCTN4	1
4229	DCTN5	1
4230	DCTN6	1
4231	DCTPP1	1
4232	DCUN1D1	1
4233	DCUN1D2	1
4234	DCUN1D3	1
4235	DCUN1D4	1
4236	DCUN1D5	1
4237	DCX	6.365478e-02
4238	DCXR	1
4239	DDA1	1
4240	DDAH1	1
4241	DDAH2	1
4242	DDB1	2.353328e-01
4243	DDB2	1
4244	DDC	1
4245	DDHD1	4.748299e-02
4246	DDHD2	1
4247	DDI1	1
4248	DDI2	1
4249	DDIT3	1
4250	DDIT4	1.224041e-01
4251	DDIT4L	1
4252	DDN	1
4253	DDO	1
4254	DDOST	1
4255	DDR1	1
4256	DDR2	1
4257	DDRGK1	7.998204e-02
4258	DDTL	1
4259	DDX1	1
4260	DDX10	1
4261	DDX11	2.664791e-01
4262	DDX17	1
4263	DDX18	1
4264	DDX19A	1
4265	DDX19B	1
4266	DDX20	1
4267	DDX21	1
4268	DDX23	2.263934e-01
4269	DDX24	2.790309e-01
4270	DDX25	1
4271	DDX26B	1
4272	DDX27	1
4273	DDX28	1
4274	DDX31	1
4275	DDX39	1
4276	DDX3X	3.136738e-02
4277	DDX4	1
4278	DDX41	1
4279	DDX42	1.397810e-02
4280	DDX43	1
4281	DDX46	4.630767e-01
4282	DDX47	1
4283	DDX49	1
4284	DDX5	2.759950e-01
4285	DDX50	3.333805e-01
4286	DDX51	1
4287	DDX52	1.022534e-01
4288	DDX53	1
4289	DDX54	1
4290	DDX55	1
4291	DDX56	1
4292	DDX58	1
4293	DDX59	1
4294	DDX6	1
4295	DDX60	1
4296	DDX60L	1
4297	DEAF1	1
4298	DEC1	1
4299	DECR1	1
4300	DECR2	1
4301	DEDD	3.071627e-02
4302	DEDD2	4.374739e-02
4303	DEF6	2.387377e-01
4304	DEF8	2.235924e-01
4305	DEFA3	1
4306	DEFA4	1
Done

Running MutSig 2:
Scatter job 48: processing genes 4217 - 4306
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DDX24
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.779280e-02	ci left: 3.059006e-01	ci right 3.242072e-01	k: 3150	n:10000
Cons ci ratio: 7.989902e-02	ci left: 1.861912e-01	ci right 2.017874e-01	k: 1939	n:10000
KS ci ratio: 7.679345e-02	ci left: 1.987011e-01	ci right 2.146701e-01	k: 2066	n:10000
DDX24   10000 perm   2 sec   (5025 perm/sec)   p_kst 2.066000e-01   p_cons 1.939000e-01   p_joint 3.150000e-01

Outputting figure to mutsig2_images.part000000000048/DDX24.3_2612_10000_0.2066_0.1939_0.315.png
                gene_name: DDX24
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.32 

Current progress: 20 percent done.
DCP1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.866511e-02	ci left: 8.074513e-01	ci right 8.227647e-01	k: 8152	n:10000
Cons ci ratio: 2.928267e-02	ci left: 6.323123e-01	ci right 6.512050e-01	k: 6418	n:10000
KS ci ratio: 4.674428e-02	ci left: 4.031269e-01	ci right 4.225239e-01	k: 4128	n:10000
DCP1A   10000 perm   2 sec   (6520 perm/sec)   p_kst 4.128000e-01   p_cons 6.418000e-01   p_joint 8.152000e-01

Outputting figure to mutsig2_images.part000000000048/DCP1A.2_1789_10000_0.4128_0.6418_0.8152.png
                gene_name: DCP1A
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.82 

Current progress: 40 percent done.
DDHD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.148972e-01	ci left: 2.873209e-02	ci right 3.574387e-02	k: 321	n:10000
Cons ci ratio: 3.187220e-01	ci left: 1.252543e-02	ci right 1.736316e-02	k: 148	n:10000
KS ci ratio: 3.329911e-02	ci left: 5.710566e-01	ci right 5.904963e-01	k: 5808	n:10000
DDHD1   10000 perm   2 sec   (5796 perm/sec)   p_kst 5.808000e-01   p_cons 1.480000e-02   p_joint 3.210000e-02

Joint ci ratio: 9.201059e-02	ci left: 7.935919e-02	ci right 8.706249e-02	k: 1663	n:20000
Cons ci ratio: 2.269270e-01	ci left: 1.303072e-02	ci right 1.641252e-02	k: 293	n:20000
KS ci ratio: 2.300044e-02	ci left: 5.853513e-01	ci right 5.990219e-01	k: 11844	n:20000
DDHD1   20000 perm   4 sec   (5098 perm/sec)   p_kst 5.922000e-01   p_cons 1.465000e-02   p_joint 8.315000e-02

Joint ci ratio: 7.263172e-02	ci left: 8.527657e-02	ci right 9.173671e-02	k: 2654	n:30000
Cons ci ratio: 1.838116e-01	ci left: 1.355952e-02	ci right 1.633558e-02	k: 447	n:30000
KS ci ratio: 1.869084e-02	ci left: 5.889184e-01	ci right 6.000632e-01	k: 17835	n:30000
DDHD1   30000 perm   6 sec   (4800 perm/sec)   p_kst 5.945000e-01   p_cons 1.490000e-02   p_joint 8.846667e-02

Joint ci ratio: 6.945997e-02	ci left: 7.118259e-02	ci right 7.632949e-02	k: 2949	n:40000
Cons ci ratio: 1.588266e-01	ci left: 1.380760e-02	ci right 1.621357e-02	k: 599	n:40000
KS ci ratio: 1.610645e-02	ci left: 5.920736e-01	ci right 6.017123e-01	k: 23876	n:40000
DDHD1   40000 perm   9 sec   (4651 perm/sec)   p_kst 5.969000e-01   p_cons 1.497500e-02   p_joint 7.372500e-02

Joint ci ratio: 6.380043e-02	ci left: 6.795592e-02	ci right 7.245413e-02	k: 3509	n:50000
Cons ci ratio: 1.442219e-01	ci left: 1.350904e-02	ci right 1.562787e-02	k: 727	n:50000
KS ci ratio: 1.443968e-02	ci left: 5.914631e-01	ci right 6.000858e-01	k: 29789	n:50000
DDHD1   50000 perm   11 sec   (4480 perm/sec)   p_kst 5.957800e-01   p_cons 1.454000e-02   p_joint 7.018000e-02

Joint ci ratio: 9.997418e-02	ci left: 2.373293e-02	ci right 2.624664e-02	k: 1498	n:60000
Cons ci ratio: 1.317021e-01	ci left: 1.359095e-02	ci right 1.552309e-02	k: 872	n:60000
KS ci ratio: 1.313277e-02	ci left: 5.936298e-01	ci right 6.014941e-01	k: 35854	n:60000
DDHD1   60000 perm   14 sec   (4363 perm/sec)   p_kst 5.975667e-01   p_cons 1.453333e-02   p_joint 2.496667e-02

Joint ci ratio: 5.327697e-02	ci left: 6.987000e-02	ci right 7.370844e-02	k: 5024	n:70000
Cons ci ratio: 1.215396e-01	ci left: 1.375218e-02	ci right 1.554552e-02	k: 1024	n:70000
KS ci ratio: 1.218813e-02	ci left: 5.927544e-01	ci right 6.000376e-01	k: 41748	n:70000
DDHD1   70000 perm   16 sec   (4275 perm/sec)   p_kst 5.964000e-01   p_cons 1.462857e-02   p_joint 7.177143e-02

Joint ci ratio: 4.928291e-02	ci left: 7.147850e-02	ci right 7.510252e-02	k: 5862	n:80000
Cons ci ratio: 1.145580e-01	ci left: 1.359801e-02	ci right 1.526248e-02	k: 1153	n:80000
KS ci ratio: 1.140364e-02	ci left: 5.928779e-01	ci right 5.996901e-01	k: 47703	n:80000
DDHD1   80000 perm   19 sec   (4189 perm/sec)   p_kst 5.962875e-01   p_cons 1.441250e-02   p_joint 7.327500e-02

Joint ci ratio: 7.971327e-02	ci left: 2.512261e-02	ci right 2.721919e-02	k: 2354	n:90000
Cons ci ratio: 1.078064e-01	ci left: 1.369670e-02	ci right 1.526816e-02	k: 1302	n:90000
KS ci ratio: 1.074573e-02	ci left: 5.933307e-01	ci right 5.997520e-01	k: 53689	n:90000
DDHD1   90000 perm   22 sec   (4112 perm/sec)   p_kst 5.965444e-01   p_cons 1.446667e-02   p_joint 2.615556e-02

Joint ci ratio: 4.289088e-02	ci left: 7.543418e-02	ci right 7.875040e-02	k: 7708	n:100000
Cons ci ratio: 1.024099e-01	ci left: 1.369997e-02	ci right 1.518839e-02	k: 1443	n:100000
KS ci ratio: 1.019038e-02	ci left: 5.936818e-01	ci right 5.997726e-01	k: 59673	n:100000
DDHD1   100000 perm   25 sec   (4040 perm/sec)   p_kst 5.967300e-01   p_cons 1.443000e-02   p_joint 7.708000e-02

Joint ci ratio: 6.710204e-02	ci left: 2.908026e-02	ci right 3.110825e-02	k: 3309	n:110000
Cons ci ratio: 9.844577e-02	ci left: 1.350910e-02	ci right 1.491668e-02	k: 1562	n:110000
KS ci ratio: 9.727041e-03	ci left: 5.932843e-01	ci right 5.990924e-01	k: 65581	n:110000
DDHD1   110000 perm   28 sec   (3974 perm/sec)   p_kst 5.961909e-01   p_cons 1.420000e-02   p_joint 3.008182e-02

Outputting figure to mutsig2_images.part000000000048/DDHD1.2_2780_110000_0.59619_0.0142_0.030082.png
                gene_name: DDHD1
               theta_stop: 0.098 
                    nperm: 110000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.014 
      ci_cons_bounds_left: 0.014 
     ci_cons_bounds_right: 0.015 
                  p_joint: 0.030 
     ci_joint_bounds_left: 0.029 
    ci_joint_bounds_right: 0.031 

Current progress: 60 percent done.
DDX3X
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.021741e-01	ci left: 1.217066e-01	ci right 1.349108e-01	k: 1282	n:10000
Cons ci ratio: 1.190559e-01	ci left: 9.194847e-02	ci right 1.036870e-01	k: 977	n:10000
KS ci ratio: 2.689535e-02	ci left: 6.706551e-01	ci right 6.890400e-01	k: 6799	n:10000
DDX3X   10000 perm   2 sec   (5884 perm/sec)   p_kst 6.799000e-01   p_cons 9.770000e-02   p_joint 1.282000e-01

Joint ci ratio: 8.114045e-02	ci left: 1.002440e-01	ci right 1.087714e-01	k: 2089	n:20000
Cons ci ratio: 8.326984e-02	ci left: 9.558124e-02	ci right 1.039355e-01	k: 1994	n:20000
KS ci ratio: 1.899887e-02	ci left: 6.738361e-01	ci right 6.868114e-01	k: 13607	n:20000
DDX3X   20000 perm   4 sec   (5241 perm/sec)   p_kst 6.803500e-01   p_cons 9.970000e-02   p_joint 1.044500e-01

Outputting figure to mutsig2_images.part000000000048/DDX3X.2_2057_20000_0.68035_0.0997_0.10445.png
                gene_name: DDX3X
               theta_stop: 0.083 
                    nperm: 20000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.100 
      ci_cons_bounds_left: 0.096 
     ci_cons_bounds_right: 0.10 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 80 percent done.
DDX42
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.320499e-02	ci left: 7.317890e-01	ci right 7.490707e-01	k: 7405	n:10000
KS ci ratio: 4.315524e-02	ci left: 4.422106e-01	ci right 4.618174e-01	k: 4520	n:10000
DDX42   10000 perm   2 sec   (5644 perm/sec)   p_kst 4.520000e-01   p_cons 7.405000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000048/DDX42.2_2885_10000_0.452_0.7405_1.png
                gene_name: DDX42
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.75 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000048
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 48 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1428>
Subject: Job 4397946: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000049> was used as the working directory.
Started at Wed Oct 24 16:11:08 2012
Results reported at Wed Oct 24 16:13:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000049.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000049.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 49  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000049.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    259.50 sec.
    Max Memory :      1440 MB
    Max Swap   :      4016 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
49
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 49
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 49: processing genes 4307 - 4396
Calculating significance of each gene.
Using projection method.
4307	DEFA5	1
4308	DEFA6	1
4309	DEFB1	1
4310	DEFB104A	1
4311	DEFB104B	1
4312	DEFB106A	1
4313	DEFB106B	1
4314	DEFB108B	1
4315	DEFB110	1
4316	DEFB112	1
4317	DEFB113	1
4318	DEFB114	1
4319	DEFB115	1
4320	DEFB116	1
4321	DEFB118	1
4322	DEFB119	1
4323	DEFB121	1
4324	DEFB123	1
4325	DEFB124	1
4326	DEFB125	1
4327	DEFB126	1
4328	DEFB127	1
4329	DEFB128	1
4330	DEFB129	1
4331	DEFB131	1
4332	DEFB132	1
4333	DEFB134	1
4334	DEFB135	1
4335	DEFB136	1
4336	DEFB4A	1
4337	DEGS1	1
4338	DEGS2	1
4339	DEK	1.075505e-01
4340	DEM1	1
4341	DENND1A	1
4342	DENND1B	1
4343	DENND1C	1
4344	DENND2A	1
4345	DENND2C	2.546149e-03
4346	DENND2D	1
4347	DENND3	1
4348	DENND4A	4.574625e-01
4349	DENND4B	3.659677e-02
4350	DENND4C	1
4351	DENND5A	4.456317e-01
4352	DENND5B	1.623093e-01
4353	DENR	1
4354	DEPDC1	1
4355	DEPDC1B	1
4356	DEPDC4	5.811565e-03
4357	DEPDC5	1
4358	DEPDC6	1
4359	DEPDC7	1
4360	DERA	1
In gene DERL1 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 788     n = 1	mu =   4.43e-07
4361	DERL1	2.170106e-02
4362	DERL2	1
4363	DERL3	1
4364	DES	1
4365	DET1	1
4366	DEXI	1
4367	DFFA	1
4368	DFFB	1
4369	DFNA5	1
4370	DFNB31	1
4371	DFNB59	1
4372	DGAT1	1
4373	DGAT2	1
4374	DGAT2L6	1
4375	DGCR14	1
4376	DGCR2	9.422682e-02
4377	DGCR6	8.348920e-02
4378	DGCR6L	1
4379	DGCR8	2.898453e-01
4380	DGKA	1
4381	DGKB	1
4382	DGKD	1
4383	DGKE	1
4384	DGKG	1
4385	DGKH	1
4386	DGKI	4.565170e-02
4387	DGKK	4.921661e-01
4388	DGKQ	1
4389	DGKZ	1
4390	DGUOK	3.301056e-02
4391	DHCR24	1.685056e-01
4392	DHCR7	1
4393	DHDDS	1
4394	DHDH	1
4395	DHDPSL	1
4396	DHFR	1
Done

Running MutSig 2:
Scatter job 49: processing genes 4307 - 4396
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DENND2C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.215091e-02	ci left: 2.196098e-01	ci right 2.361490e-01	k: 2278	n:10000
Cons ci ratio: 2.255936e-02	ci left: 7.426043e-01	ci right 7.596492e-01	k: 7512	n:10000
KS ci ratio: 1.031915e-01	ci left: 1.195555e-01	ci right 1.326632e-01	k: 1260	n:10000
DENND2C   10000 perm   2 sec   (4833 perm/sec)   p_kst 1.260000e-01   p_cons 7.512000e-01   p_joint 2.278000e-01

Joint ci ratio: 5.472764e-02	ci left: 1.985325e-01	ci right 2.097536e-01	k: 4082	n:20000
Cons ci ratio: 1.542058e-02	ci left: 7.576991e-01	ci right 7.695242e-01	k: 15273	n:20000
KS ci ratio: 7.236256e-02	ci left: 1.233007e-01	ci right 1.326078e-01	k: 2558	n:20000
DENND2C   20000 perm   7 sec   (2798 perm/sec)   p_kst 1.279000e-01   p_cons 7.636500e-01   p_joint 2.041000e-01

Outputting figure to mutsig2_images.part000000000049/DENND2C.3_2684_20000_0.1279_0.76365_0.2041.png
                gene_name: DENND2C
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

Current progress: 25 percent done.
DENND4B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.356648e-02	ci left: 5.671455e-01	ci right 5.866096e-01	k: 5769	n:10000
KS ci ratio: 1.526929e-02	ci left: 8.615148e-01	ci right 8.748699e-01	k: 8683	n:10000
DENND4B   10000 perm   2 sec   (4552 perm/sec)   p_kst 8.683000e-01   p_cons 5.769000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000049/DENND4B.2_4599_10000_0.8683_0.5769_1.png
                gene_name: DENND4B
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
DEPDC4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.659224e-02	ci left: 1.345280e-01	ci right 1.482816e-01	k: 1413	n:10000
Cons ci ratio: 1.342318e-02	ci left: 8.889287e-01	ci right 9.010401e-01	k: 8951	n:10000
KS ci ratio: 2.458026e-01	ci left: 2.174701e-02	ci right 2.793403e-02	k: 247	n:10000
DEPDC4   10000 perm   2 sec   (6433 perm/sec)   p_kst 2.470000e-02   p_cons 8.951000e-01   p_joint 1.413000e-01

Joint ci ratio: 3.554546e-02	ci left: 3.713727e-01	ci right 3.848628e-01	k: 7562	n:20000
Cons ci ratio: 9.419466e-03	ci left: 8.921956e-01	ci right 9.006888e-01	k: 17930	n:20000
KS ci ratio: 1.745358e-01	ci left: 2.244966e-02	ci right 2.679005e-02	k: 491	n:20000
DEPDC4   20000 perm   4 sec   (5647 perm/sec)   p_kst 2.455000e-02   p_cons 8.965000e-01   p_joint 3.781000e-01

Joint ci ratio: 3.094438e-02	ci left: 3.430731e-01	ci right 3.538896e-01	k: 10454	n:30000
Cons ci ratio: 7.682318e-03	ci left: 8.932008e-01	ci right 9.001221e-01	k: 26901	n:30000
KS ci ratio: 1.436101e-01	ci left: 2.249062e-02	ci right 2.600234e-02	k: 726	n:30000
DEPDC4   30000 perm   5 sec   (5490 perm/sec)   p_kst 2.420000e-02   p_cons 8.967000e-01   p_joint 3.484667e-01

Joint ci ratio: 2.615040e-02	ci left: 3.549698e-01	ci right 3.644005e-01	k: 14387	n:40000
Cons ci ratio: 6.685196e-03	ci left: 8.927647e-01	ci right 8.987777e-01	k: 35832	n:40000
KS ci ratio: 1.233527e-01	ci left: 2.310407e-02	ci right 2.616548e-02	k: 984	n:40000
DEPDC4   40000 perm   7 sec   (5338 perm/sec)   p_kst 2.460000e-02   p_cons 8.958000e-01   p_joint 3.596750e-01

Joint ci ratio: 2.472177e-02	ci left: 3.304439e-01	ci right 3.387353e-01	k: 16729	n:50000
Cons ci ratio: 5.964598e-03	ci left: 8.935542e-01	ci right 8.989197e-01	k: 44813	n:50000
KS ci ratio: 1.109905e-01	ci left: 2.298747e-02	ci right 2.570814e-02	k: 1216	n:50000
DEPDC4   50000 perm   10 sec   (5199 perm/sec)   p_kst 2.432000e-02   p_cons 8.962600e-01   p_joint 3.345800e-01

Joint ci ratio: 2.259315e-02	ci left: 3.303090e-01	ci right 3.378737e-01	k: 20045	n:60000
Cons ci ratio: 5.428547e-03	ci left: 8.943551e-01	ci right 8.992398e-01	k: 53809	n:60000
KS ci ratio: 1.008049e-01	ci left: 2.334273e-02	ci right 2.583688e-02	k: 1474	n:60000
DEPDC4   60000 perm   12 sec   (5076 perm/sec)   p_kst 2.456667e-02   p_cons 8.968167e-01   p_joint 3.340833e-01

Joint ci ratio: 2.095283e-02	ci left: 3.298363e-01	ci right 3.368347e-01	k: 23333	n:70000
Cons ci ratio: 5.035581e-03	ci left: 8.941766e-01	ci right 8.987048e-01	k: 62752	n:70000
KS ci ratio: 9.335050e-02	ci left: 2.342320e-02	ci right 2.573072e-02	k: 1719	n:70000
DEPDC4   70000 perm   14 sec   (4949 perm/sec)   p_kst 2.455714e-02   p_cons 8.964571e-01   p_joint 3.333286e-01

Outputting figure to mutsig2_images.part000000000049/DEPDC4.2_905_70000_0.024557_0.89646_0.33333.png
                gene_name: DEPDC4
               theta_stop: 0.093 
                    nperm: 70000 
                     p_ks: 0.025 
        ci_ks_bounds_left: 0.023 
       ci_ks_bounds_right: 0.026 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.34 

Current progress: 75 percent done.
DGKI
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.352525e-02	ci left: 5.677472e-01	ci right 5.872076e-01	k: 5775	n:10000
Cons ci ratio: 4.246508e-02	ci left: 4.501944e-01	ci right 4.698289e-01	k: 4600	n:10000
KS ci ratio: 1.648870e-02	ci left: 8.425440e-01	ci right 8.566516e-01	k: 8497	n:10000
DGKI   10000 perm   2 sec   (5159 perm/sec)   p_kst 8.497000e-01   p_cons 4.600000e-01   p_joint 5.775000e-01

Outputting figure to mutsig2_images.part000000000049/DGKI.2_3334_10000_0.8497_0.46_0.5775.png
                gene_name: DGKI
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000049
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 49 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4397948: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000050> was used as the working directory.
Started at Wed Oct 24 16:11:18 2012
Results reported at Wed Oct 24 16:13:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000050.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000050.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 50  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000050.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    151.45 sec.
    Max Memory :      1591 MB
    Max Swap   :      4056 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
50
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 50
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 50: processing genes 4397 - 4486
Calculating significance of each gene.
Using projection method.
4397	DHFRL1	1
4398	DHH	1
4399	DHODH	1
4400	DHPS	1
4401	DHRS1	1.514707e-01
4402	DHRS11	1
4403	DHRS12	2.578733e-03
4404	DHRS13	1
4405	DHRS2	1
4406	DHRS3	9.875055e-02
4407	DHRS4	1
4408	DHRS4L1	1
4409	DHRS4L2	1
4410	DHRS7	1
4411	DHRS7B	1
4412	DHRS7C	1
4413	DHRS9	1
4414	DHRSX	1
4415	DHTKD1	1
4416	DHX15	1
4417	DHX16	3.943109e-01
4418	DHX29	3.827432e-01
4419	DHX30	1
4420	DHX32	1
4421	DHX33	6.304847e-02
4422	DHX34	4.406544e-01
4423	DHX35	1
4424	DHX36	1
4425	DHX37	2.303962e-01
4426	DHX38	1
4427	DHX40	2.629885e-01
4428	DHX57	3.833880e-01
4429	DHX58	1
4430	DHX8	1
4431	DHX9	1
4432	DIABLO	5.102166e-02
4433	DIAPH1	1
4434	DIAPH2	1
4435	DIAPH3	5.762016e-02
4436	DICER1	5.712309e-01
4437	DIDO1	1
4438	DIMT1L	1
4439	DIO1	8.699359e-02
4440	DIO2	1
4441	DIO3	1
4442	DIP2A	1
4443	DIP2B	1
4444	DIP2C	1
4445	DIRAS1	2.992756e-03
4446	DIRAS2	1
4447	DIRAS3	1.117635e-01
4448	DIRC1	1
4449	DIRC2	1.244794e-01
4450	DIS3	1
4451	DIS3L	4.199214e-01
4452	DIS3L2	1
4453	DISC1	1
4454	DISP1	3.603478e-02
4455	DISP2	1
4456	DIXDC1	2.882078e-01
4457	DKC1	1.665055e-01
4458	DKFZp761E198	1
4459	DKK1	1
4460	DKK2	1
4461	DKK3	1
4462	DKK4	1
4463	DKKL1	1
4464	DLAT	1
4465	DLC1	1
4466	DLD	1
4467	DLEC1	1
4468	DLG1	3.452279e-01
4469	DLG2	1
4470	DLG3	2.665030e-01
4471	DLG4	1.433511e-01
4472	DLG5	1
4473	DLGAP1	1
4474	DLGAP2	1
4475	DLGAP3	1.218499e-01
4476	DLGAP4	4.258300e-01
4477	DLGAP5	1.737317e-01
4478	DLK1	1
4479	DLK2	1
4480	DLL1	9.280878e-02
4481	DLL3	1
4482	DLL4	1
4483	DLST	1
4484	DLX1	1
4485	DLX2	1
4486	DLX3	1
Done

Running MutSig 2:
Scatter job 50: processing genes 4397 - 4486
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DHRS12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.168419e-02	ci left: 5.951385e-01	ci right 6.144005e-01	k: 6048	n:10000
Cons ci ratio: 7.047050e-02	ci left: 2.279029e-01	ci right 2.446510e-01	k: 2362	n:10000
KS ci ratio: 7.262567e-02	ci left: 2.173399e-01	ci right 2.338202e-01	k: 2255	n:10000
DHRS12   10000 perm   2 sec   (6486 perm/sec)   p_kst 2.255000e-01   p_cons 2.362000e-01   p_joint 6.048000e-01

Outputting figure to mutsig2_images.part000000000050/DHRS12.2_1018_10000_0.2255_0.2362_0.6048.png
                gene_name: DHRS12
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.61 

Current progress: 20 percent done.
DHX57
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.338240e-02	ci left: 4.396164e-01	ci right 4.592131e-01	k: 4494	n:10000
KS ci ratio: 1.153651e-01	ci left: 9.749841e-02	ci right 1.095337e-01	k: 1034	n:10000
DHX57   10000 perm   2 sec   (5474 perm/sec)   p_kst 1.034000e-01   p_cons 4.494000e-01   p_joint 1

Joint ci ratio: 2.870982e-02	ci left: 4.754528e-01	ci right 4.893524e-01	k: 9648	n:20000
Cons ci ratio: 3.066311e-02	ci left: 4.427384e-01	ci right 4.565762e-01	k: 8993	n:20000
KS ci ratio: 8.181969e-02	ci left: 9.872217e-02	ci right 1.071937e-01	k: 2058	n:20000
DHX57   20000 perm   4 sec   (4849 perm/sec)   p_kst 1.029000e-01   p_cons 4.496500e-01   p_joint 4.824000e-01

Outputting figure to mutsig2_images.part000000000050/DHX57.2_4253_20000_0.1029_0.44965_0.4824.png
                gene_name: DHX57
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.099 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.49 

Current progress: 40 percent done.
DIAPH3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.071047e-02	ci left: 9.254425e-01	ci right 9.355050e-01	k: 9306	n:10000
Cons ci ratio: 1.926953e-02	ci left: 7.975022e-01	ci right 8.131196e-01	k: 8054	n:10000
KS ci ratio: 1.994303e-02	ci left: 7.863438e-01	ci right 8.022844e-01	k: 7944	n:10000
DIAPH3   10000 perm   2 sec   (5370 perm/sec)   p_kst 7.944000e-01   p_cons 8.054000e-01   p_joint 9.306000e-01

Outputting figure to mutsig2_images.part000000000050/DIAPH3.2_3714_10000_0.7944_0.8054_0.9306.png
                gene_name: DIAPH3
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 60 percent done.
DIRAS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.090368e-02	ci left: 7.703319e-01	ci right 7.867055e-01	k: 7786	n:10000
Cons ci ratio: 4.094976e-02	ci left: 4.682672e-01	ci right 4.879456e-01	k: 4781	n:10000
KS ci ratio: 4.711256e-02	ci left: 3.993415e-01	ci right 4.187115e-01	k: 4090	n:10000
DIRAS1   10000 perm   1 sec   (7097 perm/sec)   p_kst 4.090000e-01   p_cons 4.781000e-01   p_joint 7.786000e-01

Outputting figure to mutsig2_images.part000000000050/DIRAS1.2_601_10000_0.409_0.4781_0.7786.png
                gene_name: DIRAS1
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 80 percent done.
DISP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.927855e-01	ci left: 3.586235e-02	ci right 4.360871e-02	k: 396	n:10000
Cons ci ratio: 4.162861e-02	ci left: 4.600779e-01	ci right 4.797396e-01	k: 4699	n:10000
KS ci ratio: 2.177074e-01	ci left: 2.797424e-02	ci right 3.490226e-02	k: 313	n:10000
DISP1   10000 perm   2 sec   (5162 perm/sec)   p_kst 3.130000e-02   p_cons 4.699000e-01   p_joint 3.960000e-02

Joint ci ratio: 3.343070e-02	ci left: 4.005294e-01	ci right 4.141976e-01	k: 8147	n:20000
Cons ci ratio: 2.916493e-02	ci left: 4.676086e-01	ci right 4.814988e-01	k: 9491	n:20000
KS ci ratio: 1.558784e-01	ci left: 2.825647e-02	ci right 3.308125e-02	k: 612	n:20000
DISP1   20000 perm   4 sec   (4662 perm/sec)   p_kst 3.060000e-02   p_cons 4.745500e-01   p_joint 4.073500e-01

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 2.397907e-02	ci left: 4.654379e-01	ci right 4.767677e-01	k: 14133	n:30000
KS ci ratio: 1.275976e-01	ci left: 2.855075e-02	ci right 3.247421e-02	k: 914	n:30000
DISP1   30000 perm   7 sec   (4466 perm/sec)   p_kst 3.046667e-02   p_cons 4.711000e-01   p_joint 1

Joint ci ratio: 2.323494e-02	ci left: 4.108890e-01	ci right 4.205733e-01	k: 16629	n:40000
Cons ci ratio: 2.072514e-02	ci left: 4.671974e-01	ci right 4.770067e-01	k: 18884	n:40000
KS ci ratio: 1.099928e-01	ci left: 2.907980e-02	ci right 3.248877e-02	k: 1230	n:40000
DISP1   40000 perm   9 sec   (4338 perm/sec)   p_kst 3.075000e-02   p_cons 4.721000e-01   p_joint 4.157250e-01

Joint ci ratio: 2.320191e-02	ci left: 3.591821e-01	ci right 3.676337e-01	k: 18170	n:50000
Cons ci ratio: 1.855811e-02	ci left: 4.671563e-01	ci right 4.759271e-01	k: 23577	n:50000
KS ci ratio: 9.814249e-02	ci left: 2.940049e-02	ci right 3.245429e-02	k: 1545	n:50000
DISP1   50000 perm   12 sec   (4240 perm/sec)   p_kst 3.090000e-02   p_cons 4.715400e-01   p_joint 3.634000e-01

Outputting figure to mutsig2_images.part000000000050/DISP1.2_4603_50000_0.0309_0.47154_0.3634.png
                gene_name: DISP1
               theta_stop: 0.098 
                    nperm: 50000 
                     p_ks: 0.031 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000050
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 50 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4397951: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000051> was used as the working directory.
Started at Wed Oct 24 16:11:18 2012
Results reported at Wed Oct 24 16:14:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000051.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000051.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 51  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000051.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    175.67 sec.
    Max Memory :      1535 MB
    Max Swap   :      4044 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
51
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 51
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 51: processing genes 4487 - 4575
Calculating significance of each gene.
Using projection method.
4487	DLX4	1
4488	DLX5	1
4489	DLX6	1
4490	DMAP1	1.612591e-01
4491	DMBT1	3.165831e-01
4492	DMBX1	1
4493	DMC1	1
4494	DMD	5.449582e-02
4495	DMGDH	1
4496	DMKN	1
4497	DMP1	1
4498	DMPK	1
4499	DMRT1	1
4500	DMRT2	1
4501	DMRT3	1
4502	DMRTA1	1
4503	DMRTB1	1
4504	DMRTC2	1
4505	DMTF1	1
4506	DMWD	1
4507	DMXL1	6.963453e-01
4508	DMXL2	2.540631e-01
4509	DNA2	1
4510	DNAH1	1
In gene DNAH10 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 12175   n = 1	mu =   4.43e-07
4511	DNAH10	6.056073e-01
4512	DNAH11	1
4513	DNAH17	7.025426e-01
4514	DNAH2	8.139200e-02
4515	DNAH3	1.321202e-01
4516	DNAH5	9.224872e-01
4517	DNAH7	1
4518	DNAH8	9.132522e-01
4519	DNAH9	7.436651e-01
4520	DNAI1	1
4521	DNAI2	4.505400e-02
4522	DNAJA1	1
4523	DNAJA2	1
4524	DNAJA3	1
4525	DNAJA4	1
4526	DNAJB1	1.765465e-04
4527	DNAJB11	6.152740e-02
4528	DNAJB12	1
4529	DNAJB13	1
4530	DNAJB14	1
4531	DNAJB2	1
4532	DNAJB3	1
4533	DNAJB4	1
4534	DNAJB5	1
4535	DNAJB6	1.009721e-01
4536	DNAJB7	1.263746e-01
4537	DNAJB8	1
4538	DNAJB9	1
4539	DNAJC1	2.452668e-01
4540	DNAJC10	1
4541	DNAJC11	1
4542	DNAJC12	1
4543	DNAJC13	1
4544	DNAJC14	1.409784e-02
4545	DNAJC15	1
4546	DNAJC16	1.440620e-01
4547	DNAJC17	1
4548	DNAJC18	1
4549	DNAJC19	1
4550	DNAJC2	1
4551	DNAJC21	1
4552	DNAJC22	1
4553	DNAJC24	1
4554	DNAJC25	1
4555	DNAJC25-GNG10	1
4556	DNAJC27	1
4557	DNAJC28	1.000830e-01
4558	DNAJC3	1
4559	DNAJC30	1
4560	DNAJC4	6.115024e-02
4561	DNAJC5	3.915359e-02
4562	DNAJC5B	1
4563	DNAJC5G	1.018393e-01
4564	DNAJC6	2.192565e-01
4565	DNAJC7	1
4566	DNAJC8	8.689243e-02
4567	DNAJC9	1
4568	DNAL1	1
4569	DNAL4	1
4570	DNALI1	1
4571	DNASE1	1
4572	DNASE1L1	1
4573	DNASE1L2	1
4574	DNASE1L3	1
4575	DNASE2	1
Done

Running MutSig 2:
Scatter job 51: processing genes 4487 - 4575
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DNAH5
Processing conservation and coverage...
70% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.703829e-02	ci left: 3.115552e-01	ci right 3.299493e-01	k: 3207	n:10000
Cons ci ratio: 7.686376e-02	ci left: 1.984054e-01	ci right 2.143660e-01	k: 2063	n:10000
KS ci ratio: 5.329191e-02	ci left: 3.416399e-01	ci right 3.604469e-01	k: 3510	n:10000
DNAH5   10000 perm   3 sec   (2959 perm/sec)   p_kst 3.510000e-01   p_cons 2.063000e-01   p_joint 3.207000e-01

Outputting figure to mutsig2_images.part000000000051/DNAH5.5_14191_10000_0.351_0.2063_0.3207.png
                gene_name: DNAH5
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 9 percent done.
DNAJB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.603282e-02	ci left: 3.192957e-01	ci right 3.378043e-01	k: 3285	n:10000
Cons ci ratio: 9.711277e-02	ci left: 1.332547e-01	ci right 1.469557e-01	k: 1400	n:10000
KS ci ratio: 4.365513e-02	ci left: 4.365237e-01	ci right 4.561076e-01	k: 4463	n:10000
DNAJB1   10000 perm   2 sec   (5728 perm/sec)   p_kst 4.463000e-01   p_cons 1.400000e-01   p_joint 3.285000e-01

Outputting figure to mutsig2_images.part000000000051/DNAJB1.5_1035_10000_0.4463_0.14_0.3285.png
                gene_name: DNAJB1
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 18 percent done.
DMD
Processing conservation and coverage...
85% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.005765e-02	ci left: 6.201489e-01	ci right 6.391755e-01	k: 6297	n:10000
Cons ci ratio: 2.524022e-02	ci left: 6.978692e-01	ci right 7.158101e-01	k: 7069	n:10000
KS ci ratio: 5.084582e-02	ci left: 3.632113e-01	ci right 3.822629e-01	k: 3727	n:10000
DMD   10000 perm   3 sec   (3446 perm/sec)   p_kst 3.727000e-01   p_cons 7.069000e-01   p_joint 6.297000e-01

Outputting figure to mutsig2_images.part000000000051/DMD.4_11651_10000_0.3727_0.7069_0.6297.png
                gene_name: DMD
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 27 percent done.
DNAH2
Processing conservation and coverage...
73% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.024951e-01	ci left: 1.210221e-01	ci right 1.341957e-01	k: 1275	n:10000
Cons ci ratio: 1.500300e-01	ci left: 5.908749e-02	ci right 6.876845e-02	k: 638	n:10000
KS ci ratio: 7.250119e-02	ci left: 2.179321e-01	ci right 2.344277e-01	k: 2261	n:10000
DNAH2   10000 perm   3 sec   (3200 perm/sec)   p_kst 2.261000e-01   p_cons 6.380000e-02   p_joint 1.275000e-01

Joint ci ratio: 7.124930e-02	ci left: 1.267467e-01	ci right 1.361607e-01	k: 2628	n:20000
Cons ci ratio: 1.060009e-01	ci left: 6.059777e-02	ci right 6.742966e-02	k: 1279	n:20000
KS ci ratio: 5.096823e-02	ci left: 2.223986e-01	ci right 2.340805e-01	k: 4564	n:20000
DNAH2   20000 perm   7 sec   (2945 perm/sec)   p_kst 2.282000e-01   p_cons 6.395000e-02   p_joint 1.314000e-01

Joint ci ratio: 6.040408e-02	ci left: 1.193692e-01	ci right 1.268373e-01	k: 3692	n:30000
Cons ci ratio: 8.676748e-02	ci left: 6.092949e-02	ci right 6.648870e-02	k: 1910	n:30000
KS ci ratio: 4.163325e-02	ci left: 2.233285e-01	ci right 2.328575e-01	k: 6842	n:30000
DNAH2   30000 perm   10 sec   (2862 perm/sec)   p_kst 2.280667e-01   p_cons 6.366667e-02   p_joint 1.230667e-01

Outputting figure to mutsig2_images.part000000000051/DNAH2.4_13624_30000_0.22807_0.063667_0.12307.png
                gene_name: DNAH2
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.064 
      ci_cons_bounds_left: 0.061 
     ci_cons_bounds_right: 0.066 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 36 percent done.
DNAH3
Processing conservation and coverage...
79% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.745527e-02	ci left: 3.958555e-01	ci right 4.151996e-01	k: 4055	n:10000
Cons ci ratio: 1.874557e-02	ci left: 8.061311e-01	ci right 8.214857e-01	k: 8139	n:10000
KS ci ratio: 8.366514e-02	ci left: 1.724157e-01	ci right 1.875712e-01	k: 1799	n:10000
DNAH3   10000 perm   3 sec   (3594 perm/sec)   p_kst 1.799000e-01   p_cons 8.139000e-01   p_joint 4.055000e-01

Outputting figure to mutsig2_images.part000000000051/DNAH3.4_12598_10000_0.1799_0.8139_0.4055.png
                gene_name: DNAH3
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.82 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 45 percent done.
DMBT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.664856e-02	ci left: 6.746845e-01	ci right 6.930083e-01	k: 6839	n:10000
KS ci ratio: 3.448967e-02	ci left: 5.538124e-01	ci right 5.733505e-01	k: 5636	n:10000
DMBT1   10000 perm   2 sec   (4334 perm/sec)   p_kst 5.636000e-01   p_cons 6.839000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000051/DMBT1.3_7454_10000_0.5636_0.6839_1.png
                gene_name: DMBT1
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 55 percent done.
DMXL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.399040e-02	ci left: 7.186579e-01	ci right 7.362094e-01	k: 7275	n:10000
Cons ci ratio: 5.742002e-02	ci left: 3.086781e-01	ci right 3.270281e-01	k: 3178	n:10000
KS ci ratio: 2.008330e-02	ci left: 7.840118e-01	ci right 8.000177e-01	k: 7921	n:10000
DMXL2   10000 perm   2 sec   (4053 perm/sec)   p_kst 7.921000e-01   p_cons 3.178000e-01   p_joint 7.275000e-01

Outputting figure to mutsig2_images.part000000000051/DMXL2.3_9286_10000_0.7921_0.3178_0.7275.png
                gene_name: DMXL2
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.73 
     ci_joint_bounds_left: 0.72 
    ci_joint_bounds_right: 0.74 

Current progress: 64 percent done.
DNAH11
Processing conservation and coverage...
71% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.881357e-02	ci left: 8.050140e-01	ci right 8.204033e-01	k: 8128	n:10000
Cons ci ratio: 7.621287e-02	ci left: 2.011651e-01	ci right 2.172047e-01	k: 2091	n:10000
KS ci ratio: 7.625897e-02	ci left: 2.009680e-01	ci right 2.170019e-01	k: 2089	n:10000
DNAH11   10000 perm   3 sec   (3396 perm/sec)   p_kst 2.089000e-01   p_cons 2.091000e-01   p_joint 8.128000e-01

Outputting figure to mutsig2_images.part000000000051/DNAH11.2_13901_10000_0.2089_0.2091_0.8128.png
                gene_name: DNAH11
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.82 

Current progress: 73 percent done.
DNAH17
Processing conservation and coverage...
72% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.361654e-02	ci left: 2.127026e-01	ci right 2.290604e-01	k: 2208	n:10000
Cons ci ratio: 1.715849e-01	ci left: 4.533038e-02	ci right 5.393440e-02	k: 495	n:10000
KS ci ratio: 2.251109e-02	ci left: 7.434132e-01	ci right 7.604398e-01	k: 7520	n:10000
DNAH17   10000 perm   3 sec   (3446 perm/sec)   p_kst 7.520000e-01   p_cons 4.950000e-02   p_joint 2.208000e-01

Joint ci ratio: 2.901042e-02	ci left: 4.702564e-01	ci right 4.841502e-01	k: 9544	n:20000
Cons ci ratio: 1.213959e-01	ci left: 4.653451e-02	ci right 5.259730e-02	k: 990	n:20000
KS ci ratio: 1.577705e-02	ci left: 7.492800e-01	ci right 7.612457e-01	k: 15106	n:20000
DNAH17   20000 perm   6 sec   (3112 perm/sec)   p_kst 7.553000e-01   p_cons 4.950000e-02   p_joint 4.772000e-01

Joint ci ratio: 8.954202e-03	ci left: 8.607438e-01	ci right 8.685188e-01	k: 25940	n:30000
Cons ci ratio: 9.813429e-02	ci left: 4.801652e-02	ci right 5.300432e-02	k: 1514	n:30000
KS ci ratio: 1.282966e-02	ci left: 7.519039e-01	ci right 7.616463e-01	k: 22704	n:30000
DNAH17   30000 perm   10 sec   (3006 perm/sec)   p_kst 7.568000e-01   p_cons 5.046667e-02   p_joint 8.646667e-01

Outputting figure to mutsig2_images.part000000000051/DNAH17.2_13709_30000_0.7568_0.050467_0.86467.png
                gene_name: DNAH17
               theta_stop: 0.098 
                    nperm: 30000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.050 
      ci_cons_bounds_left: 0.048 
     ci_cons_bounds_right: 0.053 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 82 percent done.
DNAI2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.073223e-01	ci left: 1.113483e-01	ci right 1.240753e-01	k: 1176	n:10000
Cons ci ratio: 3.277544e-02	ci left: 5.787803e-01	ci right 5.981681e-01	k: 5885	n:10000
KS ci ratio: 2.076755e-01	ci left: 3.081908e-02	ci right 3.805543e-02	k: 343	n:10000
DNAI2   10000 perm   2 sec   (6235 perm/sec)   p_kst 3.430000e-02   p_cons 5.885000e-01   p_joint 1.176000e-01

Joint ci ratio: 5.246706e-02	ci left: 2.124426e-01	ci right 2.239394e-01	k: 4363	n:20000
Cons ci ratio: 2.340265e-02	ci left: 5.769317e-01	ci right 5.906439e-01	k: 11676	n:20000
KS ci ratio: 1.472962e-01	ci left: 3.167591e-02	ci right 3.676068e-02	k: 683	n:20000
DNAI2   20000 perm   4 sec   (5616 perm/sec)   p_kst 3.415000e-02   p_cons 5.838000e-01   p_joint 2.181500e-01

Joint ci ratio: 7.249699e-02	ci left: 8.557163e-02	ci right 9.204160e-02	k: 2663	n:30000
Cons ci ratio: 1.904702e-02	ci left: 5.797671e-01	ci right 5.909497e-01	k: 17561	n:30000
KS ci ratio: 1.210024e-01	ci left: 3.175129e-02	ci right 3.587297e-02	k: 1013	n:30000
DNAI2   30000 perm   6 sec   (5317 perm/sec)   p_kst 3.376667e-02   p_cons 5.853667e-01   p_joint 8.876667e-02

Joint ci ratio: 5.961420e-02	ci left: 9.463446e-02	ci right 1.004741e-01	k: 3901	n:40000
Cons ci ratio: 1.643229e-02	ci left: 5.823815e-01	ci right 5.920558e-01	k: 23489	n:40000
KS ci ratio: 1.051138e-01	ci left: 3.183116e-02	ci right 3.538697e-02	k: 1343	n:40000
DNAI2   40000 perm   8 sec   (5187 perm/sec)   p_kst 3.357500e-02   p_cons 5.872250e-01   p_joint 9.752500e-02

Joint ci ratio: 4.662933e-02	ci left: 1.209448e-01	ci right 1.267389e-01	k: 6191	n:50000
Cons ci ratio: 1.466864e-02	ci left: 5.838511e-01	ci right 5.924987e-01	k: 29409	n:50000
KS ci ratio: 9.344286e-02	ci left: 3.240904e-02	ci right 3.560536e-02	k: 1699	n:50000
DNAI2   50000 perm   10 sec   (5056 perm/sec)   p_kst 3.398000e-02   p_cons 5.881800e-01   p_joint 1.238200e-01

Outputting figure to mutsig2_images.part000000000051/DNAI2.2_1866_50000_0.03398_0.58818_0.12382.png
                gene_name: DNAI2
               theta_stop: 0.093 
                    nperm: 50000 
                     p_ks: 0.034 
        ci_ks_bounds_left: 0.032 
       ci_ks_bounds_right: 0.036 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 91 percent done.
DNAJC14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.241456e-02	ci left: 7.450311e-01	ci right 7.620210e-01	k: 7536	n:10000
Cons ci ratio: 1.812426e-02	ci left: 8.162904e-01	ci right 8.313205e-01	k: 8239	n:10000
KS ci ratio: 4.448599e-02	ci left: 4.272478e-01	ci right 4.467889e-01	k: 4370	n:10000
DNAJC14   10000 perm   2 sec   (5991 perm/sec)   p_kst 4.370000e-01   p_cons 8.239000e-01   p_joint 7.536000e-01

Outputting figure to mutsig2_images.part000000000051/DNAJC14.2_2133_10000_0.437_0.8239_0.7536.png
                gene_name: DNAJC14
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.76 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000051
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 51 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4397956: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000052> was used as the working directory.
Started at Wed Oct 24 16:11:18 2012
Results reported at Wed Oct 24 16:12:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000052.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000052.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 52  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000052.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     79.79 sec.
    Max Memory :      1231 MB
    Max Swap   :      4048 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
52
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 52
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 52: processing genes 4576 - 4665
Calculating significance of each gene.
Using projection method.
4576	DNASE2B	1
4577	DND1	1
4578	DNER	1
4579	DNHD1	1
4580	DNLZ	1
4581	DNM1	1
4582	DNM1L	3.290655e-01
4583	DNM2	1
4584	DNM3	1
4585	DNMBP	3.398055e-02
4586	DNMT1	5.230573e-01
4587	DNMT3A	3.826531e-01
4588	DNMT3B	1
4589	DNMT3L	1
4590	DNPEP	1
4591	DNTT	1
4592	DNTTIP1	1
4593	DNTTIP2	1
4594	DOC2A	1
4595	DOCK1	1
4596	DOCK10	3.584774e-02
4597	DOCK11	1.476652e-02
4598	DOCK2	1
4599	DOCK3	4.250580e-01
4600	DOCK4	1
4601	DOCK5	2.153942e-01
4602	DOCK6	1
4603	DOCK7	4.564485e-01
4604	DOCK8	5.602942e-01
4605	DOCK9	1
4606	DOHH	1
4607	DOK1	1
4608	DOK2	1
4609	DOK3	1.708991e-01
4610	DOK4	1
4611	DOK5	1.641996e-01
4612	DOK6	1.708309e-01
4613	DOK7	1
4614	DOLK	1
4615	DOLPP1	1
4616	DOM3Z	1
4617	DONSON	1
4618	DOPEY1	1
4619	DOPEY2	7.321136e-01
4620	DOT1L	1
4621	DPAGT1	1
4622	DPCD	1
4623	DPEP1	1
4624	DPEP2	9.455305e-02
4625	DPEP3	1
4626	DPF1	1
4627	DPF2	1
4628	DPF3	1.826718e-01
4629	DPH1	1
4630	DPH2	1
4631	DPH3	1
4632	DPH5	1
4633	DPM1	1
4634	DPM2	1
4635	DPM3	1
4636	DPP10	1
4637	DPP3	1
4638	DPP4	1
4639	DPP6	1
4640	DPP7	1
4641	DPP8	1
4642	DPP9	1.530525e-01
4643	DPPA2	1
4644	DPPA3	1
4645	DPPA4	1
4646	DPPA5	1
4647	DPRX	1
4648	DPT	1
4649	DPY19L1	1
4650	DPY19L2	1
4651	DPY19L3	6.093874e-02
4652	DPY19L4	1
4653	DPY30	1
4654	DPYD	1
4655	DPYS	1
4656	DPYSL2	1
4657	DPYSL3	1
4658	DPYSL4	1
4659	DPYSL5	1
4660	DQX1	1.358802e-01
4661	DR1	5.230545e-02
4662	DRAM1	1
4663	DRAM2	1
4664	DRAP1	1
4665	DRD1	1
Done

Running MutSig 2:
Scatter job 52: processing genes 4576 - 4665
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DNMBP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.583164e-02	ci left: 8.528403e-01	ci right 8.665494e-01	k: 8598	n:10000
Cons ci ratio: 1.060242e-02	ci left: 9.267855e-01	ci right 9.367612e-01	k: 9319	n:10000
KS ci ratio: 3.613146e-02	ci left: 5.307719e-01	ci right 5.504044e-01	k: 5406	n:10000
DNMBP   10000 perm   2 sec   (5527 perm/sec)   p_kst 5.406000e-01   p_cons 9.319000e-01   p_joint 8.598000e-01

Outputting figure to mutsig2_images.part000000000052/DNMBP.4_4798_10000_0.5406_0.9319_0.8598.png
                gene_name: DNMBP
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.87 

Current progress: 25 percent done.
DOCK10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.673487e-02	ci left: 6.732741e-01	ci right 6.916195e-01	k: 6825	n:10000
KS ci ratio: 7.915936e-03	ci left: 9.569143e-01	ci right 9.646143e-01	k: 9609	n:10000
DOCK10   10000 perm   2 sec   (5436 perm/sec)   p_kst 9.609000e-01   p_cons 6.825000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000052/DOCK10.4_6785_10000_0.9609_0.6825_1.png
                gene_name: DOCK10
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
DOCK11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.062465e-02	ci left: 7.749918e-01	ci right 7.912430e-01	k: 7832	n:10000
Cons ci ratio: 4.251639e-02	ci left: 4.495956e-01	ci right 4.692281e-01	k: 4594	n:10000
KS ci ratio: 2.978118e-02	ci left: 6.244707e-01	ci right 6.434512e-01	k: 6340	n:10000
DOCK11   10000 perm   2 sec   (5257 perm/sec)   p_kst 6.340000e-01   p_cons 4.594000e-01   p_joint 7.832000e-01

Outputting figure to mutsig2_images.part000000000052/DOCK11.3_6434_10000_0.634_0.4594_0.7832.png
                gene_name: DOCK11
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 75 percent done.
DR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.601716e-03	ci left: 9.840410e-01	ci right 9.886693e-01	k: 9865	n:10000
Cons ci ratio: 1.182134e-02	ci left: 9.111117e-01	ci right 9.220441e-01	k: 9167	n:10000
KS ci ratio: 6.452096e-02	ci left: 2.608218e-01	ci right 2.783127e-01	k: 2695	n:10000
DR1   10000 perm   1 sec   (8343 perm/sec)   p_kst 2.695000e-01   p_cons 9.167000e-01   p_joint 9.865000e-01

Outputting figure to mutsig2_images.part000000000052/DR1.2_543_10000_0.2695_0.9167_0.9865.png
                gene_name: DR1
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000052
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 52 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1654>
Subject: Job 4397959: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1654>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000053> was used as the working directory.
Started at Wed Oct 24 16:11:20 2012
Results reported at Wed Oct 24 16:14:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000053.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000053.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 53  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000053.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    213.16 sec.
    Max Memory :      1611 MB
    Max Swap   :      3979 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
53
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 53
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 53: processing genes 4666 - 4755
Calculating significance of each gene.
Using projection method.
4666	DRD2	1
4667	DRD3	1
4668	DRD4	1
4669	DRD5	1
4670	DRG1	9.508003e-02
4671	DRG2	1
4672	DRGX	1
4673	DRP2	1
4674	DSC1	1
4675	DSC2	1
4676	DSC3	1
4677	DSCAM	1.749672e-01
4678	DSCAML1	2.491063e-01
4679	DSCC1	1
4680	DSCR3	1
4681	DSCR4	1
4682	DSCR6	1
4683	DSE	1.902940e-01
4684	DSEL	1.811578e-01
4685	DSG1	1
4686	DSG2	1
4687	DSG3	4.192239e-01
4688	DSG4	2.776863e-02
4689	DSN1	1
4690	DSP	8.787848e-02
4691	DSPP	1
4692	DST	1
4693	DSTN	1
4694	DSTYK	1
4695	DTD1	1
4696	DTL	1
4697	DTNA	1.584610e-01
4698	DTNB	1
4699	DTNBP1	1
4700	DTWD1	1
4701	DTWD2	1
4702	DTX1	1
4703	DTX2	1
4704	DTX3	1
4705	DTX3L	1.827548e-01
4706	DTX4	1
4707	DTYMK	1
4708	DULLARD	1
4709	DUOX1	1
4710	DUOX2	3.250792e-01
4711	DUOXA1	6.538451e-02
4712	DUOXA2	1
4713	DUPD1	1
4714	DUS1L	1
4715	DUS2L	1
4716	DUS3L	1
4717	DUS4L	1
4718	DUSP1	1
4719	DUSP10	1
4720	DUSP11	1
4721	DUSP12	1
4722	DUSP13	1
4723	DUSP14	1
4724	DUSP15	3.242396e-02
4725	DUSP16	1
4726	DUSP18	1
4727	DUSP19	1
4728	DUSP2	1
4729	DUSP21	1
4730	DUSP22	1
4731	DUSP23	1
4732	DUSP26	1
4733	DUSP27	3.409928e-01
4734	DUSP28	1
4735	DUSP3	1
4736	DUSP4	1
4737	DUSP5	1.202808e-01
4738	DUSP6	1
4739	DUSP7	1
4740	DUSP8	1.286185e-02
4741	DUSP9	1
4742	DUT	1
4743	DUXA	1
4744	DVL1	1
4745	DVL2	1
4746	DVL3	1
4747	DYDC1	1
4748	DYDC2	1
4749	DYM	2.087671e-02
4750	DYNC1H1	1.279082e-01
4751	DYNC1I1	1
4752	DYNC1I2	1
4753	DYNC1LI1	7.874672e-02
4754	DYNC1LI2	1
4755	DYNC2H1	2.261354e-01
Done

Running MutSig 2:
Scatter job 53: processing genes 4666 - 4755
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DYNC1H1
Processing conservation and coverage...
70% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.160559e-02	ci left: 7.585873e-01	ci right 7.752569e-01	k: 7670	n:10000
KS ci ratio: 2.594843e-02	ci left: 6.861727e-01	ci right 7.043134e-01	k: 6953	n:10000
DYNC1H1   10000 perm   3 sec   (3158 perm/sec)   p_kst 6.953000e-01   p_cons 7.670000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000053/DYNC1H1.4_14253_10000_0.6953_0.767_1.png
                gene_name: DYNC1H1
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 11 percent done.
DSP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.147477e-01	ci left: 9.847268e-02	ci right 1.105588e-01	k: 1044	n:10000
Cons ci ratio: 1.022202e-02	ci left: 9.314385e-01	ci right 9.411054e-01	k: 9364	n:10000
KS ci ratio: 1.597330e-01	ci left: 5.224686e-02	ci right 6.141345e-02	k: 567	n:10000
DSP   10000 perm   3 sec   (3987 perm/sec)   p_kst 5.670000e-02   p_cons 9.364000e-01   p_joint 1.044000e-01

Joint ci ratio: 5.993394e-02	ci left: 1.708928e-01	ci right 1.815015e-01	k: 3523	n:20000
Cons ci ratio: 7.107013e-03	ci left: 9.349274e-01	ci right 9.416445e-01	k: 18767	n:20000
KS ci ratio: 1.107455e-01	ci left: 5.567637e-02	ci right 6.225258e-02	k: 1178	n:20000
DSP   20000 perm   5 sec   (3642 perm/sec)   p_kst 5.890000e-02   p_cons 9.383500e-01   p_joint 1.761500e-01

Joint ci ratio: 5.258844e-02	ci left: 1.521416e-01	ci right 1.603918e-01	k: 4687	n:30000
Cons ci ratio: 5.746087e-03	ci left: 9.367087e-01	ci right 9.421392e-01	k: 28184	n:30000
KS ci ratio: 9.073788e-02	ci left: 5.590313e-02	ci right 6.124943e-02	k: 1756	n:30000
DSP   30000 perm   9 sec   (3512 perm/sec)   p_kst 5.853333e-02   p_cons 9.394667e-01   p_joint 1.562333e-01

Outputting figure to mutsig2_images.part000000000053/DSP.3_8712_30000_0.058533_0.93947_0.15623.png
                gene_name: DSP
               theta_stop: 0.091 
                    nperm: 30000 
                     p_ks: 0.059 
        ci_ks_bounds_left: 0.056 
       ci_ks_bounds_right: 0.061 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.16 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.16 

Current progress: 22 percent done.
DST
Processing conservation and coverage...
48% 97% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.903667e-02	ci left: 2.353112e-01	ci right 2.522383e-01	k: 2437	n:10000
Cons ci ratio: 2.510420e-01	ci left: 2.080800e-02	ci right 2.687375e-02	k: 237	n:10000
KS ci ratio: 5.379860e-02	ci left: 3.373679e-01	ci right 3.561214e-01	k: 3467	n:10000
DST   10000 perm   4 sec   (2686 perm/sec)   p_kst 3.467000e-01   p_cons 2.370000e-02   p_joint 2.437000e-01

Joint ci ratio: 3.023006e-02	ci left: 4.497782e-01	ci right 4.636344e-01	k: 9134	n:20000
Cons ci ratio: 1.845928e-01	ci left: 2.001183e-02	ci right 2.412875e-02	k: 440	n:20000
KS ci ratio: 3.801193e-02	ci left: 3.405001e-01	ci right 3.537444e-01	k: 6942	n:20000
DST   20000 perm   8 sec   (2506 perm/sec)   p_kst 3.471000e-01   p_cons 2.200000e-02   p_joint 4.567000e-01

Joint ci ratio: 2.583369e-02	ci left: 4.285812e-01	ci right 4.398315e-01	k: 13026	n:30000
Cons ci ratio: 1.490585e-01	ci left: 2.085152e-02	ci right 2.424182e-02	k: 675	n:30000
KS ci ratio: 3.105829e-02	ci left: 3.414126e-01	ci right 3.522171e-01	k: 10404	n:30000
DST   30000 perm   12 sec   (2434 perm/sec)   p_kst 3.468000e-01   p_cons 2.250000e-02   p_joint 4.342000e-01

Joint ci ratio: 3.372100e-02	ci left: 2.482481e-01	ci right 2.567879e-01	k: 10100	n:40000
Cons ci ratio: 1.279559e-01	ci left: 2.145631e-02	ci right 2.441351e-02	k: 916	n:40000
KS ci ratio: 2.689033e-02	ci left: 3.422591e-01	ci right 3.516131e-01	k: 13877	n:40000
DST   40000 perm   17 sec   (2385 perm/sec)   p_kst 3.469250e-01   p_cons 2.290000e-02   p_joint 2.525000e-01

Joint ci ratio: 3.326717e-02	ci left: 2.137115e-01	ci right 2.209613e-01	k: 10866	n:50000
Cons ci ratio: 1.146652e-01	ci left: 2.152885e-02	ci right 2.416695e-02	k: 1141	n:50000
KS ci ratio: 2.404773e-02	ci left: 3.428266e-01	ci right 3.511912e-01	k: 17350	n:50000
DST   50000 perm   21 sec   (2351 perm/sec)   p_kst 3.470000e-01   p_cons 2.282000e-02   p_joint 2.173200e-01

Joint ci ratio: 3.130211e-02	ci left: 2.039629e-01	ci right 2.104655e-01	k: 12432	n:60000
Cons ci ratio: 1.048078e-01	ci left: 2.158796e-02	ci right 2.399184e-02	k: 1366	n:60000
KS ci ratio: 2.191313e-02	ci left: 3.440048e-01	ci right 3.516432e-01	k: 20869	n:60000
DST   60000 perm   26 sec   (2320 perm/sec)   p_kst 3.478167e-01   p_cons 2.276667e-02   p_joint 2.072000e-01

Joint ci ratio: 3.033832e-02	ci left: 1.896418e-01	ci right 1.954980e-01	k: 13479	n:70000
Cons ci ratio: 9.638083e-02	ci left: 2.197193e-02	ci right 2.421070e-02	k: 1615	n:70000
KS ci ratio: 2.026995e-02	ci left: 3.446843e-01	ci right 3.517569e-01	k: 24375	n:70000
DST   70000 perm   31 sec   (2294 perm/sec)   p_kst 3.482143e-01   p_cons 2.307143e-02   p_joint 1.925571e-01

Outputting figure to mutsig2_images.part000000000053/DST.3_20492_70000_0.34821_0.023071_0.19256.png
                gene_name: DST
               theta_stop: 0.096 
                    nperm: 70000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.023 
      ci_cons_bounds_left: 0.022 
     ci_cons_bounds_right: 0.024 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 33 percent done.
DSCAM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.350728e-03	ci left: 9.789852e-01	ci right 9.843289e-01	k: 9818	n:10000
Cons ci ratio: 1.639828e-02	ci left: 8.439706e-01	ci right 8.580243e-01	k: 8511	n:10000
KS ci ratio: 7.695773e-02	ci left: 1.980113e-01	ci right 2.139604e-01	k: 2059	n:10000
DSCAM   10000 perm   2 sec   (4827 perm/sec)   p_kst 2.059000e-01   p_cons 8.511000e-01   p_joint 9.818000e-01

Outputting figure to mutsig2_images.part000000000053/DSCAM.2_6171_10000_0.2059_0.8511_0.9818.png
                gene_name: DSCAM
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 44 percent done.
DSCAML1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.909827e-02	ci left: 6.352285e-01	ci right 6.540872e-01	k: 6447	n:10000
Cons ci ratio: 1.526929e-02	ci left: 8.615148e-01	ci right 8.748699e-01	k: 8683	n:10000
KS ci ratio: 3.375245e-02	ci left: 5.644382e-01	ci right 5.839185e-01	k: 5742	n:10000
DSCAML1   10000 perm   2 sec   (4616 perm/sec)   p_kst 5.742000e-01   p_cons 8.683000e-01   p_joint 6.447000e-01

Outputting figure to mutsig2_images.part000000000053/DSCAML1.2_6474_10000_0.5742_0.8683_0.6447.png
                gene_name: DSCAML1
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.65 

Current progress: 56 percent done.
DSG3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.293946e-02	ci left: 7.362356e-01	ci right 7.534215e-01	k: 7449	n:10000
Cons ci ratio: 5.829190e-02	ci left: 3.022309e-01	ci right 3.204791e-01	k: 3113	n:10000
KS ci ratio: 4.924285e-02	ci left: 3.782339e-01	ci right 3.974315e-01	k: 3878	n:10000
DSG3   10000 perm   2 sec   (5969 perm/sec)   p_kst 3.878000e-01   p_cons 3.113000e-01   p_joint 7.449000e-01

Outputting figure to mutsig2_images.part000000000053/DSG3.2_3064_10000_0.3878_0.3113_0.7449.png
                gene_name: DSG3
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.74 
    ci_joint_bounds_right: 0.75 

Current progress: 67 percent done.
DSG4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.209730e-02	ci left: 3.519757e-01	ci right 3.709051e-01	k: 3614	n:10000
Cons ci ratio: 5.699905e-02	ci left: 3.118529e-01	ci right 3.302514e-01	k: 3210	n:10000
KS ci ratio: 4.279990e-02	ci left: 4.463020e-01	ci right 4.659236e-01	k: 4561	n:10000
DSG4   10000 perm   2 sec   (5655 perm/sec)   p_kst 4.561000e-01   p_cons 3.210000e-01   p_joint 3.614000e-01

Outputting figure to mutsig2_images.part000000000053/DSG4.2_3308_10000_0.4561_0.321_0.3614.png
                gene_name: DSG4
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 78 percent done.
DYM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.049357e-02	ci left: 9.281291e-01	ci right 9.380168e-01	k: 9332	n:10000
Cons ci ratio: 1.015846e-01	ci left: 1.229780e-01	ci right 1.362386e-01	k: 1295	n:10000
KS ci ratio: 1.341604e-02	ci left: 8.890312e-01	ci right 9.011376e-01	k: 8952	n:10000
DYM   10000 perm   2 sec   (6399 perm/sec)   p_kst 8.952000e-01   p_cons 1.295000e-01   p_joint 9.332000e-01

Joint ci ratio: 7.886088e-03	ci left: 9.214158e-01	ci right 9.287600e-01	k: 18503	n:20000
Cons ci ratio: 7.262314e-02	ci left: 1.225132e-01	ci right 1.317955e-01	k: 2542	n:20000
KS ci ratio: 9.538260e-03	ci left: 8.898039e-01	ci right 8.983812e-01	k: 17883	n:20000
DYM   20000 perm   4 sec   (5696 perm/sec)   p_kst 8.941500e-01   p_cons 1.271000e-01   p_joint 9.251500e-01

Outputting figure to mutsig2_images.part000000000053/DYM.2_2074_20000_0.89415_0.1271_0.92515.png
                gene_name: DYM
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 89 percent done.
DYNC2H1
Processing conservation and coverage...
75% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.013191e-03	ci left: 9.813449e-01	ci right 9.863675e-01	k: 9840	n:10000
Cons ci ratio: 2.107331e-02	ci left: 7.674962e-01	ci right 7.839429e-01	k: 7758	n:10000
KS ci ratio: 2.814575e-02	ci left: 6.504187e-01	ci right 6.690882e-01	k: 6598	n:10000
DYNC2H1   10000 perm   3 sec   (3401 perm/sec)   p_kst 6.598000e-01   p_cons 7.758000e-01   p_joint 9.840000e-01

Outputting figure to mutsig2_images.part000000000053/DYNC2H1.2_13305_10000_0.6598_0.7758_0.984.png
                gene_name: DYNC2H1
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000053
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 53 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1424>
Subject: Job 4397961: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1424>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000054> was used as the working directory.
Started at Wed Oct 24 16:11:23 2012
Results reported at Wed Oct 24 16:13:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000054.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000054.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 54  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000054.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    167.00 sec.
    Max Memory :      1264 MB
    Max Swap   :      4001 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
54
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 54
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 54: processing genes 4756 - 4844
Calculating significance of each gene.
Using projection method.
4756	DYNC2LI1	1
4757	DYNLL1	1
4758	DYNLL2	1
4759	DYNLRB1	1
4760	DYNLRB2	1
4761	DYNLT1	1
4762	DYNLT3	1
4763	DYRK1A	3.479297e-01
4764	DYRK1B	2.875943e-02
4765	DYRK2	1
4766	DYRK3	1
4767	DYRK4	2.646535e-01
4768	DYSF	1
4769	DYSFIP1	1
4770	DYTN	1
4771	DYX1C1	1
4772	DZIP1	3.559632e-02
4773	DZIP1L	2.063618e-01
4774	DZIP3	1
4775	E2F1	1
4776	E2F2	1
4777	E2F3	9.171973e-02
4778	E2F4	1
4779	E2F5	7.461200e-02
4780	E2F6	1.414318e-01
4781	E2F7	1
4782	E2F8	3.662838e-02
4783	E4F1	1
4784	EAF1	1
4785	EAF2	1
4786	EAPP	1
4787	EARS2	1
4788	EBAG9	7.410335e-02
4789	EBF1	1
4790	EBF2	1
4791	EBF3	1
4792	EBI3	1
4793	EBLN2	1
4794	EBNA1BP2	1
4795	EBP	1
4796	EBPL	1
4797	ECD	1
4798	ECE1	1
4799	ECE2	3.753324e-01
4800	ECEL1	1
4801	ECH1	1
4802	ECHDC1	2.419715e-02
4803	ECHDC2	1
4804	ECHDC3	1
4805	ECHS1	1
4806	ECM1	1
4807	ECM2	2.726362e-01
4808	ECSCR	1
4809	ECSIT	1
4810	ECT2	1
4811	ECT2L	1.450150e-01
4812	EDA	1
4813	EDA2R	1
4814	EDAR	3.131602e-02
4815	EDARADD	1
4816	EDC3	1.488847e-02
4817	EDC4	5.200144e-01
4818	EDDM3A	4.227611e-02
4819	EDDM3B	1
4820	EDEM1	1.490168e-01
4821	EDEM2	1
4822	EDEM3	1
4823	EDF1	1
4824	EDIL3	2.262097e-01
4825	EDN1	1
4826	EDN2	1
4827	EDN3	1
4828	EDNRA	1
4829	EDNRB	1
4830	EEA1	1
4831	EED	1
4832	EEF1A1	1
4833	EEF1A2	2.232290e-02
4834	EEF1B2	1
4835	EEF1D	1
4836	EEF1E1	1
4837	EEF1G	1
4838	EEF2	1
4839	EEF2K	1
4840	EEFSEC	1
4841	EEPD1	1
4842	EFCAB1	1
4843	EFCAB2	1
4844	EFCAB3	2.116994e-01
Done

Running MutSig 2:
Scatter job 54: processing genes 4756 - 4844
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DZIP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.109888e-01	ci left: 1.047120e-01	ci right 1.171157e-01	k: 1108	n:10000
Cons ci ratio: 9.572663e-02	ci left: 1.366833e-01	ci right 1.505251e-01	k: 1435	n:10000
KS ci ratio: 4.374355e-02	ci left: 4.355261e-01	ci right 4.551058e-01	k: 4453	n:10000
DZIP1   10000 perm   2 sec   (5420 perm/sec)   p_kst 4.453000e-01   p_cons 1.435000e-01   p_joint 1.108000e-01

Joint ci ratio: 8.049680e-02	ci left: 1.017171e-01	ci right 1.102979e-01	k: 2119	n:20000
Cons ci ratio: 6.680972e-02	ci left: 1.419218e-01	ci right 1.517811e-01	k: 2936	n:20000
KS ci ratio: 3.084340e-02	ci left: 4.398431e-01	ci right 4.536724e-01	k: 8935	n:20000
DZIP1   20000 perm   7 sec   (2960 perm/sec)   p_kst 4.467500e-01   p_cons 1.468000e-01   p_joint 1.059500e-01

Outputting figure to mutsig2_images.part000000000054/DZIP1.2_2684_20000_0.44675_0.1468_0.10595.png
                gene_name: DZIP1
               theta_stop: 0.080 
                    nperm: 20000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 33 percent done.
E2F8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.149680e-02	ci left: 7.604092e-01	ci right 7.770340e-01	k: 7688	n:10000
KS ci ratio: 3.098618e-02	ci left: 6.057823e-01	ci right 6.249505e-01	k: 6154	n:10000
E2F8   10000 perm   2 sec   (6009 perm/sec)   p_kst 6.154000e-01   p_cons 7.688000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000054/E2F8.2_2652_10000_0.6154_0.7688_1.png
                gene_name: E2F8
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
EDC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.516717e-02	ci left: 6.990796e-01	ci right 7.169991e-01	k: 7081	n:10000
Cons ci ratio: 5.457943e-02	ci left: 3.309118e-01	ci right 3.495813e-01	k: 3402	n:10000
KS ci ratio: 5.486017e-02	ci left: 3.286278e-01	ci right 3.472667e-01	k: 3379	n:10000
EDC3   10000 perm   2 sec   (6361 perm/sec)   p_kst 3.379000e-01   p_cons 3.402000e-01   p_joint 7.081000e-01

Outputting figure to mutsig2_images.part000000000054/EDC3.2_1551_10000_0.3379_0.3402_0.7081.png
                gene_name: EDC3
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000054
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 54 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1418>
Subject: Job 4397964: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1418>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000055> was used as the working directory.
Started at Wed Oct 24 16:11:28 2012
Results reported at Wed Oct 24 16:15:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000055.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000055.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 55  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000055.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    236.64 sec.
    Max Memory :      1421 MB
    Max Swap   :      3985 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
55
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 55
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 55: processing genes 4845 - 4934
Calculating significance of each gene.
Using projection method.
4845	EFCAB4A	1
4846	EFCAB4B	1
4847	EFCAB5	1
4848	EFCAB6	5.751941e-01
4849	EFCAB7	1
4850	EFEMP1	1
4851	EFEMP2	5.516651e-02
4852	EFHA1	1
4853	EFHA2	1
4854	EFHB	1
4855	EFHC1	1
4856	EFHC2	1
4857	EFHD1	1
4858	EFHD2	1
4859	EFNA1	1
4860	EFNA2	1
4861	EFNA3	1
4862	EFNA4	1
4863	EFNA5	1
4864	EFNB1	1
4865	EFNB2	1
4866	EFNB3	1
4867	EFR3A	1
4868	EFS	1
4869	EFTUD1	3.380580e-01
4870	EFTUD2	1.799029e-01
4871	EGF	1
4872	EGFL6	1
4873	EGFL7	1
4874	EGFL8	1
4875	EGFLAM	4.324971e-01
4876	EGFR	3.476829e-01
4877	EGLN1	6.036229e-02
4878	EGLN2	1
4879	EGLN3	1
4880	EGR1	1
4881	EGR2	1
4882	EGR3	1
4883	EGR4	1
4884	EHBP1	1
4885	EHBP1L1	3.336624e-01
4886	EHD1	1
4887	EHD2	1
4888	EHD3	1
4889	EHD4	1
4890	EHF	1
4891	EHHADH	1
4892	EHMT1	2.692250e-01
4893	EHMT2	4.792010e-02
4894	EI24	1
4895	EID1	1
4896	EID2	1
4897	EID2B	1
4898	EID3	1
4899	EIF1	1
4900	EIF1AD	1
4901	EIF1AX	1
4902	EIF1B	1
4903	EIF2A	1.355526e-01
4904	EIF2AK1	1
4905	EIF2AK2	1
4906	EIF2AK3	1
4907	EIF2AK4	1
4908	EIF2B1	1
4909	EIF2B2	1
4910	EIF2B3	1
4911	EIF2B4	1.136314e-01
4912	EIF2B5	3.225471e-01
4913	EIF2C1	1.709924e-01
4914	EIF2C2	1.144505e-01
4915	EIF2C3	1
4916	EIF2C4	3.595720e-01
4917	EIF2S1	1.170371e-03
4918	EIF2S2	1
4919	EIF2S3	1.620323e-01
4920	EIF3A	1
4921	EIF3B	1
4922	EIF3D	1.357005e-01
4923	EIF3E	2.499186e-03
4924	EIF3F	1
4925	EIF3G	1
4926	EIF3H	1
4927	EIF3I	1.708783e-01
4928	EIF3J	1
4929	EIF3K	1
4930	EIF3L	1
4931	EIF3M	1
4932	EIF4A1	1
4933	EIF4A2	1
4934	EIF4A3	1
Done

Running MutSig 2:
Scatter job 55: processing genes 4845 - 4934
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EHMT2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.270890e-02	ci left: 2.169452e-01	ci right 2.334152e-01	k: 2251	n:10000
Cons ci ratio: 1.420057e-01	ci left: 6.575174e-02	ci right 7.590000e-02	k: 707	n:10000
KS ci ratio: 4.517969e-02	ci left: 4.196701e-01	ci right 4.391710e-01	k: 4294	n:10000
EHMT2   10000 perm   2 sec   (4537 perm/sec)   p_kst 4.294000e-01   p_cons 7.070000e-02   p_joint 2.251000e-01

Joint ci ratio: 7.129614e-02	ci left: 1.265990e-01	ci right 1.360085e-01	k: 2625	n:20000
Cons ci ratio: 1.001113e-01	ci left: 6.762471e-02	ci right 7.480055e-02	k: 1423	n:20000
KS ci ratio: 3.210340e-02	ci left: 4.201807e-01	ci right 4.339406e-01	k: 8541	n:20000
EHMT2   20000 perm   8 sec   (2439 perm/sec)   p_kst 4.270500e-01   p_cons 7.115000e-02   p_joint 1.312500e-01

Joint ci ratio: 4.810954e-02	ci left: 1.768227e-01	ci right 1.855725e-01	k: 5435	n:30000
Cons ci ratio: 8.114953e-02	ci left: 6.923069e-02	ci right 7.511915e-02	k: 2164	n:30000
KS ci ratio: 2.628017e-02	ci left: 4.201955e-01	ci right 4.314189e-01	k: 12774	n:30000
EHMT2   30000 perm   11 sec   (2767 perm/sec)   p_kst 4.258000e-01   p_cons 7.213333e-02   p_joint 1.811667e-01

Outputting figure to mutsig2_images.part000000000055/EHMT2.3_3745_30000_0.4258_0.072133_0.18117.png
                gene_name: EHMT2
               theta_stop: 0.081 
                    nperm: 30000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.072 
      ci_cons_bounds_left: 0.069 
     ci_cons_bounds_right: 0.075 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 25 percent done.
EIF2S1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.913147e-02	ci left: 2.961823e-01	ci right 3.143313e-01	k: 3052	n:10000
Cons ci ratio: 1.831749e-02	ci left: 8.131401e-01	ci right 8.282726e-01	k: 8208	n:10000
KS ci ratio: 6.108332e-02	ci left: 2.827037e-01	ci right 3.006178e-01	k: 2916	n:10000
EIF2S1   10000 perm   1 sec   (6947 perm/sec)   p_kst 2.916000e-01   p_cons 8.208000e-01   p_joint 3.052000e-01

Outputting figure to mutsig2_images.part000000000055/EIF2S1.3_976_10000_0.2916_0.8208_0.3052.png
                gene_name: EIF2S1
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.31 

Current progress: 50 percent done.
EGFR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.571106e-01	ci left: 5.397934e-02	ci right 6.327985e-02	k: 585	n:10000
Cons ci ratio: 3.979435e-02	ci left: 4.825547e-01	ci right 5.022497e-01	k: 4924	n:10000
KS ci ratio: 2.195183e-01	ci left: 2.750089e-02	ci right 3.437595e-02	k: 308	n:10000
EGFR   10000 perm   2 sec   (5155 perm/sec)   p_kst 3.080000e-02   p_cons 4.924000e-01   p_joint 5.850000e-02

Joint ci ratio: 7.932974e-02	ci left: 1.044674e-01	ci right 1.131467e-01	k: 2175	n:20000
Cons ci ratio: 2.791956e-02	ci left: 4.893966e-01	ci right 5.033044e-01	k: 9927	n:20000
KS ci ratio: 1.538196e-01	ci left: 2.902635e-02	ci right 3.391111e-02	k: 628	n:20000
EGFR   20000 perm   4 sec   (4607 perm/sec)   p_kst 3.140000e-02   p_cons 4.963500e-01   p_joint 1.087500e-01

Joint ci ratio: 9.799316e-03	ci left: 8.379576e-01	ci right 8.462427e-01	k: 25264	n:30000
Cons ci ratio: 2.273988e-02	ci left: 4.919259e-01	ci right 5.032745e-01	k: 14928	n:30000
KS ci ratio: 1.249461e-01	ci left: 2.977857e-02	ci right 3.377945e-02	k: 952	n:30000
EGFR   30000 perm   7 sec   (4373 perm/sec)   p_kst 3.173333e-02   p_cons 4.976000e-01   p_joint 8.421333e-01

Joint ci ratio: 9.799510e-05	ci left: 9.999078e-01	ci right 1	k: 40000	n:40000
Cons ci ratio: 1.969849e-02	ci left: 4.925630e-01	ci right 5.023874e-01	k: 19899	n:40000
KS ci ratio: 1.073233e-01	ci left: 3.054025e-02	ci right 3.402808e-02	k: 1290	n:40000
EGFR   40000 perm   9 sec   (4231 perm/sec)   p_kst 3.225000e-02   p_cons 4.974750e-01   p_joint 1

Joint ci ratio: 7.839686e-05	ci left: 9.999262e-01	ci right 1	k: 50000	n:50000
Cons ci ratio: 1.763574e-02	ci left: 4.926077e-01	ci right 5.013926e-01	k: 24850	n:50000
KS ci ratio: 9.598538e-02	ci left: 3.072848e-02	ci right 3.384613e-02	k: 1613	n:50000
EGFR   50000 perm   12 sec   (4125 perm/sec)   p_kst 3.226000e-02   p_cons 4.970000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000055/EGFR.2_4009_50000_0.03226_0.497_1.png
                gene_name: EGFR
               theta_stop: 0.096 
                    nperm: 50000 
                     p_ks: 0.032 
        ci_ks_bounds_left: 0.031 
       ci_ks_bounds_right: 0.034 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.50 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
EIF3E
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.208994e-02	ci left: 9.075108e-01	ci right 9.186472e-01	k: 9132	n:10000
Cons ci ratio: 5.290849e-03	ci left: 9.794135e-01	ci right 9.847004e-01	k: 9822	n:10000
KS ci ratio: 6.513262e-02	ci left: 2.571609e-01	ci right 2.745757e-01	k: 2658	n:10000
EIF3E   10000 perm   2 sec   (6360 perm/sec)   p_kst 2.658000e-01   p_cons 9.822000e-01   p_joint 9.132000e-01

Outputting figure to mutsig2_images.part000000000055/EIF3E.2_1390_10000_0.2658_0.9822_0.9132.png
                gene_name: EIF3E
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000055
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 55 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4397968: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000056> was used as the working directory.
Started at Wed Oct 24 16:11:28 2012
Results reported at Wed Oct 24 16:13:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000056.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000056.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 56  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000056.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    143.84 sec.
    Max Memory :      1172 MB
    Max Swap   :      3877 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
56
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 56
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 56: processing genes 4935 - 5024
Calculating significance of each gene.
Using projection method.
4935	EIF4B	8.008021e-02
4936	EIF4E	1
4937	EIF4E1B	1
4938	EIF4E2	1
4939	EIF4E3	1
4940	EIF4EBP1	1
4941	EIF4EBP2	1
4942	EIF4EBP3	1
4943	EIF4ENIF1	5.834811e-02
4944	EIF4G1	1.941904e-01
4945	EIF4G2	1
4946	EIF4G3	1
4947	EIF4H	1
4948	EIF5	1.155483e-01
4949	EIF5A	1
4950	EIF5A2	1
4951	EIF5AL1	5.482828e-02
4952	EIF5B	3.964420e-01
4953	EIF6	2.602251e-02
4954	ELAC1	1
4955	ELAC2	9.614315e-02
4956	ELANE	1
4957	ELAVL1	1
4958	ELAVL2	1
4959	ELAVL3	1
4960	ELAVL4	1
4961	ELF1	1
4962	ELF2	1
4963	ELF3	1.651028e-01
4964	ELF4	1
4965	ELF5	1
4966	ELFN2	1
4967	ELK1	1
4968	ELK3	9.672077e-02
4969	ELK4	6.378278e-02
4970	ELL	1
4971	ELL2	1
4972	ELL3	2.003580e-01
4973	ELMO1	1.594476e-01
4974	ELMO2	1
4975	ELMO3	5.894452e-02
4976	ELMOD1	1
4977	ELMOD2	2.335906e-02
4978	ELMOD3	1
4979	ELN	1
4980	ELOF1	1
4981	ELOVL1	1
4982	ELOVL2	1
4983	ELOVL3	1
4984	ELOVL4	1.066647e-01
4985	ELOVL5	4.146005e-02
4986	ELOVL6	1
4987	ELOVL7	1
4988	ELP2	1
4989	ELP3	1
4990	ELP4	1
4991	ELSPBP1	1
4992	ELTD1	1
4993	EMB	1
4994	EMCN	1
4995	EMD	7.141028e-02
4996	EME1	1
4997	EME2	1
4998	EMG1	1
4999	EMID1	1
5000/17942 5000	EMID2	1
5001	EMILIN1	1
5002	EMILIN2	1
5003	EMILIN3	1
5004	EML1	1
5005	EML2	4.133252e-02
5006	EML3	1
5007	EML4	1
5008	EML5	1
5009	EMP1	1
5010	EMP2	1
5011	EMP3	1
5012	EMR1	1
5013	EMR2	1
5014	EMR3	1
5015	EMX1	1
5016	EMX2	1
5017	EN1	1
5018	EN2	1
5019	ENAH	7.296872e-02
5020	ENAM	3.802300e-02
5021	ENC1	1
5022	ENDOD1	4.731997e-02
5023	ENDOU	1
5024	ENG	1.926494e-01
Done

Running MutSig 2:
Scatter job 56: processing genes 4935 - 5024
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EIF4G1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.639033e-02	ci left: 2.498415e-01	ci right 2.670994e-01	k: 2584	n:10000
Cons ci ratio: 1.487901e-01	ci left: 6.005239e-02	ci right 6.980294e-02	k: 648	n:10000
KS ci ratio: 4.521658e-02	ci left: 4.192713e-01	ci right 4.387700e-01	k: 4290	n:10000
EIF4G1   10000 perm   2 sec   (4399 perm/sec)   p_kst 4.290000e-01   p_cons 6.480000e-02   p_joint 2.584000e-01

Joint ci ratio: 7.313472e-02	ci left: 1.209876e-01	ci right 1.302216e-01	k: 2511	n:20000
Cons ci ratio: 1.067604e-01	ci left: 5.976897e-02	ci right 6.655871e-02	k: 1262	n:20000
KS ci ratio: 3.258694e-02	ci left: 4.128974e-01	ci right 4.266259e-01	k: 8395	n:20000
EIF4G1   20000 perm   7 sec   (3002 perm/sec)   p_kst 4.197500e-01   p_cons 6.310000e-02   p_joint 1.255500e-01

Joint ci ratio: 4.021146e-02	ci left: 2.357055e-01	ci right 2.454115e-01	k: 7216	n:30000
Cons ci ratio: 8.691329e-02	ci left: 6.073356e-02	ci right 6.628467e-02	k: 1904	n:30000
KS ci ratio: 2.657065e-02	ci left: 4.148388e-01	ci right 4.260433e-01	k: 12613	n:30000
EIF4G1   30000 perm   9 sec   (3272 perm/sec)   p_kst 4.204333e-01   p_cons 6.346667e-02   p_joint 2.405333e-01

Outputting figure to mutsig2_images.part000000000056/EIF4G1.3_4924_30000_0.42043_0.063467_0.24053.png
                gene_name: EIF4G1
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.063 
      ci_cons_bounds_left: 0.061 
     ci_cons_bounds_right: 0.066 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

Current progress: 25 percent done.
EIF4ENIF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.528263e-02	ci left: 8.613106e-01	ci right 8.746743e-01	k: 8681	n:10000
KS ci ratio: 1.635299e-02	ci left: 8.446839e-01	ci right 8.587105e-01	k: 8518	n:10000
EIF4ENIF1   10000 perm   2 sec   (4327 perm/sec)   p_kst 8.518000e-01   p_cons 8.681000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000056/EIF4ENIF1.2_3033_10000_0.8518_0.8681_1.png
                gene_name: EIF4ENIF1
               theta_stop: 0.016 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
ELMO3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.623483e-02	ci left: 2.507315e-01	ci right 2.680089e-01	k: 2593	n:10000
KS ci ratio: 3.202320e-02	ci left: 5.900191e-01	ci right 6.093228e-01	k: 5997	n:10000
ELMO3   10000 perm   2 sec   (5097 perm/sec)   p_kst 5.997000e-01   p_cons 2.593000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000056/ELMO3.2_2402_10000_0.5997_0.2593_1.png
                gene_name: ELMO3
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
ENAM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.775073e-02	ci left: 2.422288e-01	ci right 2.593166e-01	k: 2507	n:10000
Cons ci ratio: 3.633558e-02	ci left: 5.279684e-01	ci right 5.476096e-01	k: 5378	n:10000
KS ci ratio: 1.397872e-01	ci left: 6.778282e-02	ci right 7.806763e-02	k: 728	n:10000
ENAM   10000 perm   2 sec   (5751 perm/sec)   p_kst 7.280000e-02   p_cons 5.378000e-01   p_joint 2.507000e-01

Joint ci ratio: 4.595010e-02	ci left: 2.606299e-01	ci right 2.729379e-01	k: 5335	n:20000
Cons ci ratio: 2.559168e-02	ci left: 5.328621e-01	ci right 5.467263e-01	k: 10796	n:20000
KS ci ratio: 9.988490e-02	ci left: 6.791774e-02	ci right 7.510743e-02	k: 1429	n:20000
ENAM   20000 perm   4 sec   (4609 perm/sec)   p_kst 7.145000e-02   p_cons 5.398000e-01   p_joint 2.667500e-01

Outputting figure to mutsig2_images.part000000000056/ENAM.2_3461_20000_0.07145_0.5398_0.26675.png
                gene_name: ENAM
               theta_stop: 0.100 
                    nperm: 20000 
                     p_ks: 0.071 
        ci_ks_bounds_left: 0.068 
       ci_ks_bounds_right: 0.075 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.27 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000056
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 56 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4397974: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000057> was used as the working directory.
Started at Wed Oct 24 16:11:28 2012
Results reported at Wed Oct 24 16:13:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000057.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000057.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 57  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000057.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    102.47 sec.
    Max Memory :      1615 MB
    Max Swap   :      4093 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
57
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 57
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 57: processing genes 5025 - 5113
Calculating significance of each gene.
Using projection method.
5025	ENGASE	1.634264e-01
5026	ENHO	1
5027	ENKUR	1
5028	ENO1	1
5029	ENO2	1
5030	ENO3	1
5031	ENOPH1	1.024156e-01
5032	ENOSF1	1
5033	ENOX1	1
5034	ENOX2	1
5035	ENPEP	1
5036	ENPP1	1
5037	ENPP2	1.718951e-01
5038	ENPP3	1.723970e-01
5039	ENPP4	1
5040	ENPP5	1
5041	ENPP6	1
5042	ENPP7	1
5043	ENSA	1
5044	ENTHD1	1
5045	ENTPD1	1
5046	ENTPD2	1
5047	ENTPD3	1
5048	ENTPD4	1
5049	ENTPD5	1
5050	ENTPD6	7.138108e-02
5051	ENTPD7	2.860315e-01
5052	ENTPD8	1
5053	ENY2	1
5054	EOMES	1
5055	EP300	1.335969e-01
5056	EP400	1.944237e-01
5057	EPAS1	3.927899e-02
5058	EPB41	3.917167e-01
5059	EPB41L1	3.310889e-01
5060	EPB41L2	1
5061	EPB41L3	1
5062	EPB41L4A	2.585597e-01
5063	EPB41L4B	1
5064	EPB41L5	1
5065	EPB42	1
5066	EPB49	1
5067	EPC1	1.621417e-02
5068	EPC2	1
5069	EPCAM	1
5070	EPDR1	1
5071	EPGN	1
5072	EPHA1	1
5073	EPHA10	1.750480e-01
5074	EPHA2	8.608612e-02
5075	EPHA3	1
5076	EPHA4	2.882736e-01
5077	EPHA5	1.897120e-02
5078	EPHA6	1
5079	EPHA7	1
5080	EPHA8	2.702942e-01
5081	EPHB1	1.573780e-01
5082	EPHB2	2.120222e-01
5083	EPHB3	1
5084	EPHB4	1
5085	EPHB6	9.901771e-02
5086	EPHX1	1
5087	EPHX2	2.004412e-01
5088	EPHX3	1
5089	EPHX4	7.131353e-02
5090	EPM2A	1
5091	EPM2AIP1	9.956683e-02
5092	EPN1	1
5093	EPN2	1
5094	EPN3	1
5095	EPO	5.768232e-02
5096	EPOR	1
5097	EPPK1	5.524549e-01
5098	EPRS	1
5099	EPS15	2.715429e-01
5100	EPS15L1	1
5101	EPS8	1
5102	EPS8L1	1
5103	EPS8L2	1
5104	EPS8L3	1
5105	EPSTI1	1
5106	EPT1	1
5107	EPX	1
5108	EPYC	1
5109	ERAL1	1
5110	ERAP1	1
5111	ERAP2	1
5112	ERAS	1
5113	ERBB2	2.348276e-01
Done

Running MutSig 2:
Scatter job 57: processing genes 5025 - 5113
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EP300
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.204255e-01	ci left: 9.000254e-02	ci right 1.016341e-01	k: 957	n:10000
KS ci ratio: 2.871829e-02	ci left: 6.412631e-01	ci right 6.600491e-01	k: 6507	n:10000
EP300   10000 perm   2 sec   (4829 perm/sec)   p_kst 6.507000e-01   p_cons 9.570000e-02   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 8.466752e-02	ci left: 9.268686e-02	ci right 1.009308e-01	k: 1935	n:20000
KS ci ratio: 2.044641e-02	ci left: 6.409332e-01	ci right 6.542239e-01	k: 12952	n:20000
EP300   20000 perm   6 sec   (3223 perm/sec)   p_kst 6.476000e-01   p_cons 9.675000e-02   p_joint 1

Outputting figure to mutsig2_images.part000000000057/EP300.2_7369_20000_0.6476_0.09675_1.png
                gene_name: EP300
               theta_stop: 0.085 
                    nperm: 20000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.097 
      ci_cons_bounds_left: 0.093 
     ci_cons_bounds_right: 0.10 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 14 percent done.
EP400
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.507522e-02	ci left: 8.644763e-01	ci right 8.777067e-01	k: 8712	n:10000
Cons ci ratio: 4.218414e-02	ci left: 4.534885e-01	ci right 4.731329e-01	k: 4633	n:10000
KS ci ratio: 2.923175e-02	ci left: 6.331167e-01	ci right 6.520002e-01	k: 6426	n:10000
EP400   10000 perm   2 sec   (4603 perm/sec)   p_kst 6.426000e-01   p_cons 4.633000e-01   p_joint 8.712000e-01

Outputting figure to mutsig2_images.part000000000057/EP400.2_9577_10000_0.6426_0.4633_0.8712.png
                gene_name: EP400
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.88 

Current progress: 29 percent done.
EPAS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.296339e-02	ci left: 1.748744e-01	ci right 1.901110e-01	k: 1824	n:10000
Cons ci ratio: 7.669991e-02	ci left: 1.990953e-01	ci right 2.150757e-01	k: 2070	n:10000
KS ci ratio: 9.072868e-02	ci left: 1.501165e-01	ci right 1.644837e-01	k: 1572	n:10000
EPAS1   10000 perm   1 sec   (6699 perm/sec)   p_kst 1.572000e-01   p_cons 2.070000e-01   p_joint 1.824000e-01

Outputting figure to mutsig2_images.part000000000057/EPAS1.2_2677_10000_0.1572_0.207_0.1824.png
                gene_name: EPAS1
               theta_stop: 0.091 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.19 

Current progress: 43 percent done.
EPC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.235470e-02	ci left: 9.039125e-01	ci right 9.152476e-01	k: 9097	n:10000
Cons ci ratio: 5.268928e-02	ci left: 3.468072e-01	ci right 3.656766e-01	k: 3562	n:10000
KS ci ratio: 2.585051e-02	ci left: 6.877856e-01	ci right 7.058996e-01	k: 6969	n:10000
EPC1   10000 perm   1 sec   (6721 perm/sec)   p_kst 6.969000e-01   p_cons 3.562000e-01   p_joint 9.097000e-01

Outputting figure to mutsig2_images.part000000000057/EPC1.2_2571_10000_0.6969_0.3562_0.9097.png
                gene_name: EPC1
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.92 

Current progress: 57 percent done.
EPHA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.339316e-01	ci left: 7.359257e-02	ci right 8.425426e-02	k: 788	n:10000
Cons ci ratio: 3.589212e-02	ci left: 5.340764e-01	ci right 5.536980e-01	k: 5439	n:10000
KS ci ratio: 1.650363e-01	ci left: 4.897794e-02	ci right 5.788448e-02	k: 533	n:10000
EPHA2   10000 perm   1 sec   (6944 perm/sec)   p_kst 5.330000e-02   p_cons 5.439000e-01   p_joint 7.880000e-02

Joint ci ratio: 1.130035e-01	ci left: 5.353447e-02	ci right 5.999515e-02	k: 1134	n:20000
Cons ci ratio: 2.477590e-02	ci left: 5.489311e-01	ci right 5.627526e-01	k: 11117	n:20000
KS ci ratio: 1.179902e-01	ci left: 4.920621e-02	ci right 5.542476e-02	k: 1045	n:20000
EPHA2   20000 perm   3 sec   (6159 perm/sec)   p_kst 5.225000e-02   p_cons 5.558500e-01   p_joint 5.670000e-02

Joint ci ratio: 9.202437e-02	ci left: 5.440283e-02	ci right 5.968336e-02	k: 1710	n:30000
Cons ci ratio: 2.016917e-02	ci left: 5.516907e-01	ci right 5.629648e-01	k: 16720	n:30000
KS ci ratio: 9.620999e-02	ci left: 4.990524e-02	ci right 5.498188e-02	k: 1572	n:30000
EPHA2   30000 perm   5 sec   (5848 perm/sec)   p_kst 5.240000e-02   p_cons 5.573333e-01   p_joint 5.700000e-02

Outputting figure to mutsig2_images.part000000000057/EPHA2.2_2999_30000_0.0524_0.55733_0.057.png
                gene_name: EPHA2
               theta_stop: 0.096 
                    nperm: 30000 
                     p_ks: 0.052 
        ci_ks_bounds_left: 0.050 
       ci_ks_bounds_right: 0.055 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.057 
     ci_joint_bounds_left: 0.054 
    ci_joint_bounds_right: 0.060 

Current progress: 71 percent done.
EPHA5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.624658e-02	ci left: 4.083079e-01	ci right 4.277399e-01	k: 4180	n:10000
KS ci ratio: 3.664360e-02	ci left: 5.237637e-01	ci right 5.434167e-01	k: 5336	n:10000
EPHA5   10000 perm   1 sec   (6786 perm/sec)   p_kst 5.336000e-01   p_cons 4.180000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000057/EPHA5.2_3186_10000_0.5336_0.418_1.png
                gene_name: EPHA5
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 86 percent done.
EPHB6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.299120e-02	ci left: 1.747761e-01	ci right 1.900094e-01	k: 1823	n:10000
Cons ci ratio: 6.668601e-02	ci left: 2.481605e-01	ci right 2.653814e-01	k: 2567	n:10000
KS ci ratio: 1.694391e-01	ci left: 4.648153e-02	ci right 5.518251e-02	k: 507	n:10000
EPHB6   10000 perm   1 sec   (6861 perm/sec)   p_kst 5.070000e-02   p_cons 2.567000e-01   p_joint 1.823000e-01

Joint ci ratio: 7.080039e-02	ci left: 1.281747e-01	ci right 1.376323e-01	k: 2657	n:20000
Cons ci ratio: 4.700057e-02	ci left: 2.519467e-01	ci right 2.641237e-01	k: 5160	n:20000
KS ci ratio: 1.178714e-01	ci left: 4.930341e-02	ci right 5.552753e-02	k: 1047	n:20000
EPHB6   20000 perm   3 sec   (6102 perm/sec)   p_kst 5.235000e-02   p_cons 2.580000e-01   p_joint 1.328500e-01

Joint ci ratio: 4.822877e-02	ci left: 1.760963e-01	ci right 1.848324e-01	k: 5413	n:30000
Cons ci ratio: 3.843445e-02	ci left: 2.524928e-01	ci right 2.624209e-01	k: 7723	n:30000
KS ci ratio: 9.627460e-02	ci left: 4.984009e-02	ci right 5.491370e-02	k: 1570	n:30000
EPHB6   30000 perm   5 sec   (5790 perm/sec)   p_kst 5.233333e-02   p_cons 2.574333e-01   p_joint 1.804333e-01

Outputting figure to mutsig2_images.part000000000057/EPHB6.2_3130_30000_0.052333_0.25743_0.18043.png
                gene_name: EPHB6
               theta_stop: 0.096 
                    nperm: 30000 
                     p_ks: 0.052 
        ci_ks_bounds_left: 0.050 
       ci_ks_bounds_right: 0.055 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.18 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000057
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 57 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4397978: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000058> was used as the working directory.
Started at Wed Oct 24 16:11:33 2012
Results reported at Wed Oct 24 16:14:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000058.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000058.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 58  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000058.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    108.52 sec.
    Max Memory :      1679 MB
    Max Swap   :      4031 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
58
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 58
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 58: processing genes 5114 - 5203
Calculating significance of each gene.
Using projection method.
5114	ERBB2IP	1
5115	ERBB3	5.411796e-02
5116	ERBB4	1.830967e-01
5117	ERC1	2.971604e-01
5118	ERC2	1
5119	ERCC1	1
5120	ERCC2	1
5121	ERCC3	1
5122	ERCC4	3.352249e-01
5123	ERCC5	7.599400e-02
5124	ERCC6	3.060532e-01
5125	ERCC6L	1.008340e-01
5126	ERCC8	1
5127	EREG	1
5128	ERF	1.750422e-01
5129	ERG	1
5130	ERGIC1	1
5131	ERGIC2	1
5132	ERGIC3	1
5133	ERH	1
5134	ERI1	1
5135	ERI2	1
5136	ERI3	1
5137	ERICH1	1
5138	ERLEC1	1
5139	ERLIN1	1
5140	ERLIN2	1
5141	ERMAP	1
5142	ERMN	1
5143	ERMP1	1
5144	ERN1	1
5145	ERN2	1
5146	ERO1L	1
5147	ERO1LB	1
5148	ERP27	1.770478e-03
5149	ERP29	3.448063e-02
5150	ERP44	1.428806e-01
5151	ERRFI1	1
5152	ERV3	1
5153	ERVFRDE1	1
5154	ESAM	1
5155	ESCO1	1
5156	ESCO2	2.736167e-01
5157	ESD	1
5158	ESF1	1
5159	ESM1	1
5160	ESPL1	1
5161	ESPN	2.079248e-02
5162	ESPNL	1
5163	ESR1	1
5164	ESR2	1
5165	ESRP1	1
5166	ESRP2	7.409809e-02
5167	ESRRA	1
5168	ESRRB	1
5169	ESRRG	1
5170	ESX1	1
5171	ESYT1	2.228784e-01
5172	ESYT2	3.490791e-01
5173	ESYT3	1
5174	ETAA1	1
5175	ETF1	1
5176	ETFA	1
5177	ETFB	1
5178	ETFDH	1
5179	ETHE1	1
5180	ETNK1	1
5181	ETNK2	1
5182	ETS1	1
5183	ETS2	1
5184	ETV1	1
5185	ETV2	1
5186	ETV3	1
5187	ETV3L	1
5188	ETV4	1
5189	ETV5	2.551954e-01
5190	ETV6	1
5191	ETV7	1
5192	EVC	1
5193	EVC2	1.272920e-01
5194	EVI2A	1
5195	EVI2B	1.263671e-01
5196	EVI5	1.456247e-01
5197	EVI5L	1
5198	EVL	2.130876e-01
5199	EVPL	9.927659e-02
5200	EVX1	1
5201	EVX2	1
5202	EWSR1	1
5203	EXD1	1
Done

Running MutSig 2:
Scatter job 58: processing genes 5114 - 5203
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ERBB3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.244799e-02	ci left: 4.503941e-01	ci right 4.700291e-01	k: 4602	n:10000
Cons ci ratio: 5.764585e-02	ci left: 3.069917e-01	ci right 3.253155e-01	k: 3161	n:10000
KS ci ratio: 3.128802e-02	ci left: 6.011627e-01	ci right 6.203727e-01	k: 6108	n:10000
ERBB3   10000 perm   2 sec   (4397 perm/sec)   p_kst 6.108000e-01   p_cons 3.161000e-01   p_joint 4.602000e-01

Outputting figure to mutsig2_images.part000000000058/ERBB3.2_4272_10000_0.6108_0.3161_0.4602.png
                gene_name: ERBB3
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 14 percent done.
ERC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.699584e-02	ci left: 4.005369e-01	ci right 4.199155e-01	k: 4102	n:10000
Cons ci ratio: 1.066050e-01	ci left: 1.127155e-01	ci right 1.255073e-01	k: 1190	n:10000
KS ci ratio: 2.301068e-01	ci left: 2.494902e-02	ci right 3.152965e-02	k: 281	n:10000
ERC1   10000 perm   2 sec   (6303 perm/sec)   p_kst 2.810000e-02   p_cons 1.190000e-01   p_joint 4.102000e-01

Joint ci ratio: 3.342032e-02	ci left: 4.006790e-01	ci right 4.143479e-01	k: 8150	n:20000
Cons ci ratio: 7.587147e-02	ci left: 1.132647e-01	ci right 1.222468e-01	k: 2354	n:20000
KS ci ratio: 1.589819e-01	ci left: 2.715054e-02	ci right 3.188756e-02	k: 589	n:20000
ERC1   20000 perm   4 sec   (5676 perm/sec)   p_kst 2.945000e-02   p_cons 1.177000e-01   p_joint 4.075000e-01

Joint ci ratio: 3.946993e-02	ci left: 2.425252e-01	ci right 2.523238e-01	k: 7422	n:30000
Cons ci ratio: 6.128736e-02	ci left: 1.163101e-01	ci right 1.236970e-01	k: 3599	n:30000
KS ci ratio: 1.300365e-01	ci left: 2.748520e-02	ci right 3.133998e-02	k: 881	n:30000
ERC1   30000 perm   6 sec   (5433 perm/sec)   p_kst 2.936667e-02   p_cons 1.199667e-01   p_joint 2.474000e-01

Joint ci ratio: 1.275624e-02	ci left: 6.979426e-01	ci right 7.069280e-01	k: 28098	n:40000
Cons ci ratio: 5.328492e-02	ci left: 1.159904e-01	ci right 1.223650e-01	k: 4766	n:40000
KS ci ratio: 1.126153e-01	ci left: 2.774198e-02	ci right 3.107680e-02	k: 1175	n:40000
ERC1   40000 perm   8 sec   (5274 perm/sec)   p_kst 2.937500e-02   p_cons 1.191500e-01   p_joint 7.024500e-01

Joint ci ratio: 3.793986e-02	ci left: 1.725915e-01	ci right 1.792862e-01	k: 8796	n:50000
Cons ci ratio: 4.783633e-02	ci left: 1.155605e-01	ci right 1.212438e-01	k: 5919	n:50000
KS ci ratio: 1.007618e-01	ci left: 2.789769e-02	ci right 3.087729e-02	k: 1468	n:50000
ERC1   50000 perm   10 sec   (5138 perm/sec)   p_kst 2.936000e-02   p_cons 1.183800e-01   p_joint 1.759200e-01

Joint ci ratio: 3.466092e-02	ci left: 1.726623e-01	ci right 1.787691e-01	k: 10542	n:60000
Cons ci ratio: 4.368240e-02	ci left: 1.157425e-01	ci right 1.209278e-01	k: 7099	n:60000
KS ci ratio: 9.224713e-02	ci left: 2.786729e-02	ci right 3.057851e-02	k: 1752	n:60000
ERC1   60000 perm   12 sec   (5020 perm/sec)   p_kst 2.920000e-02   p_cons 1.183167e-01   p_joint 1.757000e-01

Outputting figure to mutsig2_images.part000000000058/ERC1.2_3423_60000_0.0292_0.11832_0.1757.png
                gene_name: ERC1
               theta_stop: 0.092 
                    nperm: 60000 
                     p_ks: 0.029 
        ci_ks_bounds_left: 0.028 
       ci_ks_bounds_right: 0.031 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 29 percent done.
ERCC5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.319059e-03	ci left: 9.857766e-01	ci right 9.901322e-01	k: 9881	n:10000
Cons ci ratio: 4.525351e-02	ci left: 4.188726e-01	ci right 4.383690e-01	k: 4286	n:10000
KS ci ratio: 1.643060e-02	ci left: 8.434611e-01	ci right 8.575341e-01	k: 8506	n:10000
ERCC5   10000 perm   2 sec   (5988 perm/sec)   p_kst 8.506000e-01   p_cons 4.286000e-01   p_joint 9.881000e-01

Outputting figure to mutsig2_images.part000000000058/ERCC5.2_3621_10000_0.8506_0.4286_0.9881.png
                gene_name: ERCC5
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 43 percent done.
ERCC6L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.966194e-02	ci left: 7.910089e-01	ci right 8.068166e-01	k: 7990	n:10000
Cons ci ratio: 4.555035e-02	ci left: 4.156828e-01	ci right 4.351607e-01	k: 4254	n:10000
KS ci ratio: 4.069629e-02	ci left: 4.713638e-01	ci right 4.910472e-01	k: 4812	n:10000
ERCC6L   10000 perm   2 sec   (6285 perm/sec)   p_kst 4.812000e-01   p_cons 4.254000e-01   p_joint 7.990000e-01

Outputting figure to mutsig2_images.part000000000058/ERCC6L.2_3761_10000_0.4812_0.4254_0.799.png
                gene_name: ERCC6L
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.80 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.81 

Current progress: 57 percent done.
ERP27
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.902845e-02	ci left: 6.363347e-01	ci right 6.551803e-01	k: 6458	n:10000
Cons ci ratio: 2.118833e-02	ci left: 7.655723e-01	ci right 7.820679e-01	k: 7739	n:10000
KS ci ratio: 1.222691e-01	ci left: 8.747398e-02	ci right 9.896426e-02	k: 931	n:10000
ERP27   10000 perm   1 sec   (7910 perm/sec)   p_kst 9.310000e-02   p_cons 7.739000e-01   p_joint 6.458000e-01

Joint ci ratio: 2.927334e-02	ci left: 4.657602e-01	ci right 4.796477e-01	k: 9454	n:20000
Cons ci ratio: 1.499306e-02	ci left: 7.677859e-01	ci right 7.794345e-01	k: 15473	n:20000
KS ci ratio: 8.789646e-02	ci left: 8.646061e-02	ci right 9.445892e-02	k: 1808	n:20000
ERP27   20000 perm   3 sec   (6891 perm/sec)   p_kst 9.040000e-02   p_cons 7.736500e-01   p_joint 4.727000e-01

Outputting figure to mutsig2_images.part000000000058/ERP27.2_850_20000_0.0904_0.77365_0.4727.png
                gene_name: ERP27
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.090 
        ci_ks_bounds_left: 0.086 
       ci_ks_bounds_right: 0.094 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.48 

Current progress: 71 percent done.
ESPN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.382843e-02	ci left: 5.633354e-01	ci right 5.828220e-01	k: 5731	n:10000
Cons ci ratio: 9.035409e-02	ci left: 1.511960e-01	ci right 1.656036e-01	k: 1583	n:10000
KS ci ratio: 2.968502e-02	ci left: 6.259785e-01	ci right 6.449425e-01	k: 6355	n:10000
ESPN   10000 perm   1 sec   (6859 perm/sec)   p_kst 6.355000e-01   p_cons 1.583000e-01   p_joint 5.731000e-01

Outputting figure to mutsig2_images.part000000000058/ESPN.2_2617_10000_0.6355_0.1583_0.5731.png
                gene_name: ESPN
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 86 percent done.
EVPL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.290595e-02	ci left: 2.708188e-01	ci right 2.885097e-01	k: 2796	n:10000
Cons ci ratio: 8.624746e-02	ci left: 1.637654e-01	ci right 1.786266e-01	k: 1711	n:10000
KS ci ratio: 2.634093e-02	ci left: 6.797224e-01	ci right 6.979674e-01	k: 6889	n:10000
EVPL   10000 perm   2 sec   (5485 perm/sec)   p_kst 6.889000e-01   p_cons 1.711000e-01   p_joint 2.796000e-01

Outputting figure to mutsig2_images.part000000000058/EVPL.2_6190_10000_0.6889_0.1711_0.2796.png
                gene_name: EVPL
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.29 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000058
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 58 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4397981: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000059> was used as the working directory.
Started at Wed Oct 24 16:11:36 2012
Results reported at Wed Oct 24 16:13:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000059.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000059.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 59  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000059.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    132.75 sec.
    Max Memory :      1249 MB
    Max Swap   :      4039 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
59
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 59
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 59: processing genes 5204 - 5293
Calculating significance of each gene.
Using projection method.
5204	EXD2	1
5205	EXD3	1
5206	EXO1	1
5207	EXOC1	3.863515e-01
5208	EXOC2	1
5209	EXOC3	1
5210	EXOC3L	1
5211	EXOC3L2	1
5212	EXOC4	1
5213	EXOC5	1
5214	EXOC6	3.515444e-01
5215	EXOC6B	1
5216	EXOC7	1
5217	EXOC8	3.365858e-01
5218	EXOG	1
5219	EXOSC1	7.892697e-02
5220	EXOSC10	1
5221	EXOSC2	1
5222	EXOSC3	1
5223	EXOSC4	6.941192e-02
5224	EXOSC5	1
5225	EXOSC7	1
5226	EXOSC8	1
5227	EXOSC9	2.376829e-02
5228	EXPH5	5.954588e-01
5229	EXT1	1
5230	EXT2	1
5231	EXTL1	1
5232	EXTL2	1
5233	EXTL3	1
5234	EYA1	1
5235	EYA2	1
5236	EYA3	1
5237	EYA4	1
5238	EZH1	1
5239	EZH2	8.352453e-02
5240	EZR	5.736214e-02
5241	F10	1
5242	F11	1
5243	F11R	1.603626e-01
5244	F12	1
5245	F13A1	1
5246	F13B	2.963138e-01
5247	F2	1
5248	F2R	4.241847e-02
5249	F2RL1	1
5250	F2RL2	1
5251	F2RL3	8.734657e-04
5252	F3	1
5253	F5	5.273153e-01
5254	F7	1
5255	F8	3.459787e-01
5256	F9	1
5257	FA2H	3.945721e-02
5258	FAAH	1
5259	FAAH2	1
5260	FABP1	1
5261	FABP12	1
5262	FABP2	1
5263	FABP3	1
5264	FABP4	1
5265	FABP5	1
5266	FABP6	1
5267	FABP7	1
5268	FABP9	1
5269	FADD	1
5270	FADS1	1
5271	FADS2	1
5272	FADS3	1
5273	FADS6	1
5274	FAF1	1
5275	FAF2	1.784193e-01
5276	FAH	1
5277	FAHD1	1
5278	FAHD2A	1.597569e-01
5279	FAHD2B	1
5280	FAIM	5.848467e-02
5281	FAIM2	1
5282	FAIM3	1
5283	FAM100A	1
5284	FAM100B	1
5285	FAM101A	1
5286	FAM101B	1
5287	FAM102A	1.625301e-01
5288	FAM102B	1
5289	FAM103A1	1
5290	FAM104A	1
5291	FAM104B	1
5292	FAM105A	1
5293	FAM105B	1
Done

Running MutSig 2:
Scatter job 59: processing genes 5204 - 5293
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EXOC8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.782306e-02	ci left: 5.079524e-01	ci right 5.276372e-01	k: 5178	n:10000
Cons ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
KS ci ratio: 1.319447e-01	ci left: 7.572512e-02	ci right 8.652038e-02	k: 810	n:10000
EXOC8   10000 perm   2 sec   (6153 perm/sec)   p_kst 8.100000e-02   p_cons 1   p_joint 5.178000e-01

Joint ci ratio: 5.435154e-02	ci left: 2.007595e-01	ci right 2.120260e-01	k: 4127	n:20000
Cons ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
KS ci ratio: 9.234391e-02	ci left: 7.882080e-02	ci right 8.650104e-02	k: 1652	n:20000
EXOC8   20000 perm   5 sec   (3711 perm/sec)   p_kst 8.260000e-02   p_cons 1   p_joint 2.063500e-01

Outputting figure to mutsig2_images.part000000000059/EXOC8.2_2182_20000_0.0826_1_0.20635.png
                gene_name: EXOC8
               theta_stop: 0.092 
                    nperm: 20000 
                     p_ks: 0.083 
        ci_ks_bounds_left: 0.079 
       ci_ks_bounds_right: 0.087 
                   p_cons: 1 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

Current progress: 33 percent done.
EXOSC9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.532262e-02	ci left: 8.606980e-01	ci right 8.740872e-01	k: 8675	n:10000
Cons ci ratio: 3.698355e-02	ci left: 5.191594e-01	ci right 5.388237e-01	k: 5290	n:10000
KS ci ratio: 2.115807e-02	ci left: 7.660785e-01	ci right 7.825614e-01	k: 7744	n:10000
EXOSC9   10000 perm   2 sec   (4866 perm/sec)   p_kst 7.744000e-01   p_cons 5.290000e-01   p_joint 8.675000e-01

Outputting figure to mutsig2_images.part000000000059/EXOSC9.2_1423_10000_0.7744_0.529_0.8675.png
                gene_name: EXOSC9
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 67 percent done.
F2RL3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.722332e-02	ci left: 6.653172e-01	ci right 6.837810e-01	k: 6746	n:10000
Cons ci ratio: 1.828014e-02	ci left: 8.137498e-01	ci right 8.288626e-01	k: 8214	n:10000
KS ci ratio: 9.110698e-02	ci left: 1.490372e-01	ci right 1.633637e-01	k: 1561	n:10000
F2RL3   10000 perm   2 sec   (4644 perm/sec)   p_kst 1.561000e-01   p_cons 8.214000e-01   p_joint 6.746000e-01

Outputting figure to mutsig2_images.part000000000059/F2RL3.2_1166_10000_0.1561_0.8214_0.6746.png
                gene_name: F2RL3
               theta_stop: 0.091 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.68 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000059
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 59 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 4397986: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000060> was used as the working directory.
Started at Wed Oct 24 16:11:45 2012
Results reported at Wed Oct 24 16:14:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000060.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000060.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 60  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000060.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    167.67 sec.
    Max Memory :      1024 MB
    Max Swap   :      3807 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
60
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 60
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 60: processing genes 5294 - 5383
Calculating significance of each gene.
Using projection method.
5294	FAM107A	1
5295	FAM107B	1
5296	FAM108A1	1
5297	FAM108B1	1
5298	FAM108C1	1
5299	FAM109A	1
5300	FAM109B	7.658405e-02
5301	FAM110A	1
5302	FAM110B	1
5303	FAM110C	1
5304	FAM111A	1.720413e-02
5305	FAM111B	1
5306	FAM113A	1
5307	FAM113B	1
5308	FAM114A1	1
5309	FAM114A2	1
5310	FAM115A	1
5311	FAM115C	1
5312	FAM116A	1
5313	FAM116B	1
5314	FAM117A	1
5315	FAM117B	1
5316	FAM118A	1
5317	FAM118B	1
5318	FAM119A	9.411130e-02
5319	FAM119B	1
5320	FAM120A	1
5321	FAM120AOS	1
5322	FAM120B	1.666614e-01
5323	FAM120C	1
5324	FAM122A	1
5325	FAM122B	1
5326	FAM122C	1
5327	FAM123A	1
5328	FAM123B	1
5329	FAM123C	1
5330	FAM124A	1
5331	FAM124B	1
5332	FAM125A	1
5333	FAM125B	6.707447e-02
5334	FAM126A	1
5335	FAM126B	1
5336	FAM127A	1
5337	FAM127B	1.319114e-02
5338	FAM127C	1
5339	FAM128A	1
5340	FAM128B	1
5341	FAM129A	4.260176e-01
5342	FAM129B	1
5343	FAM129C	1.750736e-01
5344	FAM131A	1
5345	FAM131B	1
5346	FAM131C	1
5347	FAM132A	1
5348	FAM133A	1
5349	FAM133B	1
5350	FAM134A	1
5351	FAM134B	1
5352	FAM134C	1
5353	FAM135A	1
5354	FAM135B	1
5355	FAM136A	1
5356	FAM13A	3.313728e-01
5357	FAM13B	1
5358	FAM13C	1
5359	FAM149A	1
5360	FAM150A	1
5361	FAM150B	1
5362	FAM151A	1
5363	FAM151B	1
5364	FAM153A	1
5365	FAM153B	1
5366	FAM153C	1
5367	FAM154A	1
5368	FAM154B	1
5369	FAM155A	1
5370	FAM155B	1
5371	FAM158A	5.969244e-02
5372	FAM159A	1
5373	FAM160A2	1
5374	FAM160B1	1
5375	FAM160B2	1
5376	FAM161A	1.170722e-01
5377	FAM161B	5.339725e-02
5378	FAM162A	1
5379	FAM162B	1
5380	FAM163A	1
5381	FAM164A	4.726257e-02
5382	FAM164C	1
5383	FAM165B	1
Done

Running MutSig 2:
Scatter job 60: processing genes 5294 - 5383
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FAM111A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.327272e-02	ci left: 8.910815e-01	ci right 9.030861e-01	k: 8972	n:10000
KS ci ratio: 2.150889e-02	ci left: 7.602067e-01	ci right 7.768366e-01	k: 7686	n:10000
FAM111A   10000 perm   2 sec   (5671 perm/sec)   p_kst 7.686000e-01   p_cons 8.972000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000060/FAM111A.2_1844_10000_0.7686_0.8972_1.png
                gene_name: FAM111A
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
FAM161B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.962467e-03	ci left: 9.345442e-01	ci right 9.439979e-01	k: 9394	n:10000
Cons ci ratio: 1.926339e-02	ci left: 7.976037e-01	ci right 8.132180e-01	k: 8055	n:10000
KS ci ratio: 2.351292e-02	ci left: 7.266365e-01	ci right 7.440262e-01	k: 7354	n:10000
FAM161B   10000 perm   2 sec   (5916 perm/sec)   p_kst 7.354000e-01   p_cons 8.055000e-01   p_joint 9.394000e-01

Outputting figure to mutsig2_images.part000000000060/FAM161B.2_1980_10000_0.7354_0.8055_0.9394.png
                gene_name: FAM161B
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000060
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 60 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4397988: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000061> was used as the working directory.
Started at Wed Oct 24 16:11:45 2012
Results reported at Wed Oct 24 16:13:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000061.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000061.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 61  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000061.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    194.16 sec.
    Max Memory :      1125 MB
    Max Swap   :      3865 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
61
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 61
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 61: processing genes 5384 - 5472
Calculating significance of each gene.
Using projection method.
5384	FAM166A	1
5385	FAM166B	1
5386	FAM167A	1
5387	FAM167B	1
5388	FAM168A	1
5389	FAM168B	1
5390	FAM169A	1
5391	FAM169B	1
5392	FAM170A	1
5393	FAM171A1	7.190173e-02
5394	FAM171B	1
5395	FAM172A	1
5396	FAM173A	1
5397	FAM173B	1
5398	FAM174A	1
5399	FAM174B	1
5400	FAM175A	1
5401	FAM175B	1
5402	FAM176A	1
5403	FAM176B	1
5404	FAM177A1	1
5405	FAM177B	1
5406	FAM178A	1
5407	FAM179A	2.855669e-01
5408	FAM179B	1
5409	FAM180A	1
5410	FAM181A	9.519895e-02
5411	FAM183A	1
5412	FAM184A	1.236247e-01
5413	FAM186B	1
5414	FAM187B	1
5415	FAM188A	1
5416	FAM188B	1
5417	FAM189A2	1
5418	FAM189B	1
5419	FAM18A	1
5420	FAM18B	1.043415e-01
5421	FAM18B2	1
5422	FAM190A	1
5423	FAM190B	1
5424	FAM192A	1
5425	FAM193A	1
5426	FAM193B	1
5427	FAM194A	1
5428	FAM195A	1
5429	FAM196A	1
5430	FAM198B	1
5431	FAM199X	6.397631e-02
5432	FAM19A1	1
5433	FAM19A2	1
5434	FAM19A3	1
5435	FAM19A4	1
5436	FAM19A5	1
5437	FAM20A	1
5438	FAM20B	1
5439	FAM21A	1
5440	FAM21B	1
5441	FAM21C	1.296738e-01
5442	FAM22A	1.284316e-01
5443	FAM22D	1
5444	FAM22F	1
5445	FAM22G	1
5446	FAM24A	1
5447	FAM24B	1
5448	FAM26D	1
5449	FAM26E	1
5450	FAM26F	1
5451	FAM32A	1
5452	FAM35A	1
5453	FAM36A	1
5454	FAM3A	1
5455	FAM3B	1
5456	FAM3C	1
5457	FAM3D	1
5458	FAM40A	3.461318e-01
5459	FAM40B	1
5460	FAM43A	1
5461	FAM43B	1
5462	FAM45A	1
5463	FAM46A	1
5464	FAM46B	1.113940e-01
5465	FAM46C	1
5466	FAM46D	1
5467	FAM47A	2.574034e-01
5468	FAM47B	1
5469	FAM47C	2.623112e-01
5470	FAM48A	3.331058e-01
5471	FAM48B1	1
5472	FAM48B2	4.831295e-02
Done

Running MutSig 2:
Scatter job 61: processing genes 5384 - 5472
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FAM171A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.453122e-02	ci left: 4.267492e-01	ci right 4.462878e-01	k: 4365	n:10000
Cons ci ratio: 5.529198e-02	ci left: 3.251526e-01	ci right 3.437439e-01	k: 3344	n:10000
KS ci ratio: 5.283892e-02	ci left: 3.455153e-01	ci right 3.643693e-01	k: 3549	n:10000
FAM171A1   10000 perm   2 sec   (5350 perm/sec)   p_kst 3.549000e-01   p_cons 3.344000e-01   p_joint 4.365000e-01

Outputting figure to mutsig2_images.part000000000061/FAM171A1.2_2705_10000_0.3549_0.3344_0.4365.png
                gene_name: FAM171A1
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000061
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 61 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1644>
Subject: Job 4397991: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000062> was used as the working directory.
Started at Wed Oct 24 16:11:45 2012
Results reported at Wed Oct 24 16:20:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000062.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000062.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 62  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000062.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    565.39 sec.
    Max Memory :      1287 MB
    Max Swap   :      4103 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
62
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 62
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 62: processing genes 5473 - 5562
Calculating significance of each gene.
Using projection method.
5473	FAM49A	1.419094e-03
5474	FAM49B	1
5475	FAM50A	1
5476	FAM50B	1.648199e-01
5477	FAM53A	1
5478	FAM53B	1.934782e-01
5479	FAM53C	1
5480	FAM54A	1
5481	FAM54B	1
5482	FAM55A	1
5483	FAM55C	1
5484	FAM55D	1
5485	FAM57A	1
5486	FAM57B	1
5487	FAM58A	1
5488	FAM58B	1
5489	FAM59A	1
5490	FAM5B	2.100844e-01
5491	FAM5C	8.643599e-02
5492	FAM60A	1
5493	FAM63A	1
5494	FAM63B	1
5495	FAM64A	1
5496	FAM65A	1
5497	FAM65B	2.895097e-01
5498	FAM65C	1
5499	FAM69B	1
5500	FAM69C	1
5501	FAM70A	1
5502	FAM70B	1
5503	FAM71A	1.043766e-01
5504	FAM71B	1.026989e-01
5505	FAM71C	1
5506	FAM71D	1
5507	FAM71E1	1
5508	FAM71F1	1
5509	FAM71F2	1.330838e-01
5510	FAM72A	1
5511	FAM72B	1
5512	FAM73A	1
5513	FAM73B	1
5514	FAM75A3	1
5515	FAM76A	1
5516	FAM76B	1.353467e-02
5517	FAM78A	1
5518	FAM78B	1
5519	FAM81A	1
5520	FAM81B	2.239543e-01
5521	FAM82A1	1
5522	FAM82A2	1
5523	FAM82B	1
5524	FAM83A	1
5525	FAM83B	4.119344e-01
5526	FAM83C	1
5527	FAM83D	1
5528	FAM83E	1
5529	FAM83F	1
5530	FAM83G	1
5531	FAM83H	2.710701e-01
5532	FAM84A	1
5533	FAM84B	1
5534	FAM86A	1
5535	FAM86B1	1
5536	FAM86C	1
5537	FAM89A	1
5538	FAM89B	1
5539	FAM8A1	1
5540	FAM90A1	1
5541	FAM91A1	1
5542	FAM92A1	1
5543	FAM92B	5.603302e-02
5544	FAM96A	1
5545	FAM96B	1
5546	FAM98A	1
5547	FAM98B	1
5548	FAM98C	1
5549	FAM9A	1
5550	FAM9B	1
5551	FAM9C	1
5552	FANCA	1.667858e-01
5553	FANCB	1
5554	FANCC	1
5555	FANCD2	3.139049e-01
5556	FANCE	1
5557	FANCF	1
5558	FANCG	1
5559	FANCI	4.443260e-01
5560	FANCL	1.237999e-01
5561	FANCM	1
5562	FANK1	3.317226e-02
Done

Running MutSig 2:
Scatter job 62: processing genes 5473 - 5562
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FAM49A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.163954e-01	ci left: 1.379226e-03	ci right 3.328943e-03	k: 22	n:10000
Cons ci ratio: 3.800521e-02	ci left: 5.055515e-01	ci right 5.252395e-01	k: 5154	n:10000
KS ci ratio: 8.163954e-01	ci left: 1.379226e-03	ci right 3.328943e-03	k: 22	n:10000
FAM49A   10000 perm   2 sec   (6439 perm/sec)   p_kst 2.200000e-03   p_cons 5.154000e-01   p_joint 2.200000e-03

Joint ci ratio: 5.971366e-01	ci left: 1.513902e-03	ci right 2.837541e-03	k: 42	n:20000
Cons ci ratio: 2.668800e-02	ci left: 5.119481e-01	ci right 5.258464e-01	k: 10378	n:20000
KS ci ratio: 5.971366e-01	ci left: 1.513902e-03	ci right 2.837541e-03	k: 42	n:20000
FAM49A   20000 perm   5 sec   (3695 perm/sec)   p_kst 2.100000e-03   p_cons 5.189000e-01   p_joint 2.100000e-03

Joint ci ratio: 4.933466e-01	ci left: 1.584857e-03	ci right 2.648601e-03	k: 62	n:30000
Cons ci ratio: 2.181592e-02	ci left: 5.126610e-01	ci right 5.240021e-01	k: 15550	n:30000
KS ci ratio: 4.933466e-01	ci left: 1.584857e-03	ci right 2.648601e-03	k: 62	n:30000
FAM49A   30000 perm   7 sec   (4068 perm/sec)   p_kst 2.066667e-03   p_cons 5.183333e-01   p_joint 2.066667e-03

Joint ci ratio: 4.272524e-01	ci left: 1.653054e-03	ci right 2.571635e-03	k: 83	n:40000
Cons ci ratio: 1.890882e-02	ci left: 5.130146e-01	ci right 5.228328e-01	k: 20717	n:40000
KS ci ratio: 4.272524e-01	ci left: 1.653054e-03	ci right 2.571635e-03	k: 83	n:40000
FAM49A   40000 perm   9 sec   (4261 perm/sec)   p_kst 2.075000e-03   p_cons 5.179250e-01   p_joint 2.075000e-03

Joint ci ratio: 3.877379e-01	ci left: 1.645615e-03	ci right 2.453950e-03	k: 101	n:50000
Cons ci ratio: 1.693183e-02	ci left: 5.129691e-01	ci right 5.217489e-01	k: 25868	n:50000
KS ci ratio: 3.877379e-01	ci left: 1.645615e-03	ci right 2.453950e-03	k: 101	n:50000
FAM49A   50000 perm   12 sec   (4338 perm/sec)   p_kst 2.020000e-03   p_cons 5.173600e-01   p_joint 2.020000e-03

Joint ci ratio: 3.589863e-01	ci left: 1.628124e-03	ci right 2.354734e-03	k: 118	n:60000
Cons ci ratio: 1.547812e-02	ci left: 5.126591e-01	ci right 5.206726e-01	k: 31000	n:60000
KS ci ratio: 3.589863e-01	ci left: 1.628124e-03	ci right 2.354734e-03	k: 118	n:60000
FAM49A   60000 perm   14 sec   (4367 perm/sec)   p_kst 1.966667e-03   p_cons 5.166667e-01   p_joint 1.966667e-03

Joint ci ratio: 3.383097e-01	ci left: 1.591065e-03	ci right 2.251319e-03	k: 133	n:70000
Cons ci ratio: 1.429548e-02	ci left: 5.141620e-01	ci right 5.215794e-01	k: 36251	n:70000
KS ci ratio: 3.383097e-01	ci left: 1.591065e-03	ci right 2.251319e-03	k: 133	n:70000
FAM49A   70000 perm   16 sec   (4371 perm/sec)   p_kst 1.900000e-03   p_cons 5.178714e-01   p_joint 1.900000e-03

Joint ci ratio: 3.166081e-01	ci left: 1.610181e-03	ci right 2.226838e-03	k: 152	n:80000
Cons ci ratio: 1.340128e-02	ci left: 5.133179e-01	ci right 5.202559e-01	k: 41343	n:80000
KS ci ratio: 3.166081e-01	ci left: 1.610181e-03	ci right 2.226838e-03	k: 152	n:80000
FAM49A   80000 perm   18 sec   (4360 perm/sec)   p_kst 1.900000e-03   p_cons 5.167875e-01   p_joint 1.900000e-03

Joint ci ratio: 3.058199e-01	ci left: 1.543943e-03	ci right 2.111162e-03	k: 163	n:90000
Cons ci ratio: 1.290915e-02	ci left: 5.027835e-01	ci right 5.093272e-01	k: 45545	n:90000
KS ci ratio: 3.058199e-01	ci left: 1.543943e-03	ci right 2.111162e-03	k: 163	n:90000
FAM49A   90000 perm   21 sec   (4334 perm/sec)   p_kst 1.811111e-03   p_cons 5.060556e-01   p_joint 1.811111e-03

Joint ci ratio: 2.879360e-01	ci left: 1.583927e-03	ci right 2.125621e-03	k: 184	n:100000
Cons ci ratio: 1.224244e-02	ci left: 5.031261e-01	ci right 5.093335e-01	k: 50623	n:100000
KS ci ratio: 2.879360e-01	ci left: 1.583927e-03	ci right 2.125621e-03	k: 184	n:100000
FAM49A   100000 perm   23 sec   (4300 perm/sec)   p_kst 1.840000e-03   p_cons 5.062300e-01   p_joint 1.840000e-03

Joint ci ratio: 2.769325e-01	ci left: 1.566640e-03	ci right 2.078381e-03	k: 199	n:110000
Cons ci ratio: 1.166324e-02	ci left: 5.036772e-01	ci right 5.095952e-01	k: 55730	n:110000
KS ci ratio: 2.769325e-01	ci left: 1.566640e-03	ci right 2.078381e-03	k: 199	n:110000
FAM49A   110000 perm   26 sec   (4259 perm/sec)   p_kst 1.809091e-03   p_cons 5.066364e-01   p_joint 1.809091e-03

Joint ci ratio: 2.658651e-01	ci left: 1.568118e-03	ci right 2.056463e-03	k: 216	n:120000
Cons ci ratio: 1.116734e-02	ci left: 5.037753e-01	ci right 5.094410e-01	k: 60793	n:120000
KS ci ratio: 2.658651e-01	ci left: 1.568118e-03	ci right 2.056463e-03	k: 216	n:120000
FAM49A   120000 perm   28 sec   (4218 perm/sec)   p_kst 1.800000e-03   p_cons 5.066083e-01   p_joint 1.800000e-03

Joint ci ratio: 2.533296e-01	ci left: 1.605722e-03	ci right 2.078481e-03	k: 238	n:130000
Cons ci ratio: 1.072959e-02	ci left: 5.038706e-01	ci right 5.093137e-01	k: 65857	n:130000
KS ci ratio: 2.533296e-01	ci left: 1.605722e-03	ci right 2.078481e-03	k: 238	n:130000
FAM49A   130000 perm   31 sec   (4171 perm/sec)   p_kst 1.830769e-03   p_cons 5.065923e-01   p_joint 1.830769e-03

Joint ci ratio: 2.433507e-01	ci left: 1.624999e-03	ci right 2.081743e-03	k: 258	n:140000
Cons ci ratio: 1.034343e-02	ci left: 5.037703e-01	ci right 5.090152e-01	k: 70895	n:140000
KS ci ratio: 2.433507e-01	ci left: 1.624999e-03	ci right 2.081743e-03	k: 258	n:140000
FAM49A   140000 perm   34 sec   (4100 perm/sec)   p_kst 1.842857e-03   p_cons 5.063929e-01   p_joint 1.842857e-03

Joint ci ratio: 2.379070e-01	ci left: 1.591840e-03	ci right 2.027779e-03	k: 270	n:150000
Cons ci ratio: 9.993496e-03	ci left: 5.038198e-01	ci right 5.088866e-01	k: 75953	n:150000
KS ci ratio: 2.379070e-01	ci left: 1.591840e-03	ci right 2.027779e-03	k: 270	n:150000
FAM49A   150000 perm   37 sec   (4053 perm/sec)   p_kst 1.800000e-03   p_cons 5.063533e-01   p_joint 1.800000e-03

Joint ci ratio: 2.284082e-01	ci left: 1.627709e-03	ci right 2.053167e-03	k: 293	n:160000
Cons ci ratio: 9.673933e-03	ci left: 5.040158e-01	ci right 5.089215e-01	k: 81035	n:160000
KS ci ratio: 2.284082e-01	ci left: 1.627709e-03	ci right 2.053167e-03	k: 293	n:160000
FAM49A   160000 perm   40 sec   (4006 perm/sec)   p_kst 1.831250e-03   p_cons 5.064688e-01   p_joint 1.831250e-03

Joint ci ratio: 2.217219e-01	ci left: 1.631876e-03	ci right 2.044233e-03	k: 311	n:170000
Cons ci ratio: 9.388378e-03	ci left: 5.039145e-01	ci right 5.086736e-01	k: 86070	n:170000
KS ci ratio: 2.217219e-01	ci left: 1.631876e-03	ci right 2.044233e-03	k: 311	n:170000
FAM49A   170000 perm   43 sec   (3957 perm/sec)   p_kst 1.829412e-03   p_cons 5.062941e-01   p_joint 1.829412e-03

Joint ci ratio: 2.152639e-01	ci left: 1.640997e-03	ci right 2.041986e-03	k: 330	n:180000
Cons ci ratio: 9.122037e-03	ci left: 5.040819e-01	ci right 5.087068e-01	k: 91151	n:180000
KS ci ratio: 2.152639e-01	ci left: 1.640997e-03	ci right 2.041986e-03	k: 330	n:180000
FAM49A   180000 perm   46 sec   (3911 perm/sec)   p_kst 1.833333e-03   p_cons 5.063944e-01   p_joint 1.833333e-03

Joint ci ratio: 2.114684e-01	ci left: 1.614410e-03	ci right 2.001044e-03	k: 342	n:190000
Cons ci ratio: 8.879204e-03	ci left: 5.041177e-01	ci right 5.086190e-01	k: 96210	n:190000
KS ci ratio: 2.114684e-01	ci left: 1.614410e-03	ci right 2.001044e-03	k: 342	n:190000
FAM49A   190000 perm   49 sec   (3866 perm/sec)   p_kst 1.800000e-03   p_cons 5.063684e-01   p_joint 1.800000e-03

Joint ci ratio: 2.044340e-01	ci left: 1.647445e-03	ci right 2.027227e-03	k: 366	n:200000
Cons ci ratio: 8.657644e-03	ci left: 5.039863e-01	ci right 5.083735e-01	k: 101236	n:200000
KS ci ratio: 2.044340e-01	ci left: 1.647445e-03	ci right 2.027227e-03	k: 366	n:200000
FAM49A   200000 perm   52 sec   (3821 perm/sec)   p_kst 1.830000e-03   p_cons 5.061800e-01   p_joint 1.830000e-03

Joint ci ratio: 1.990806e-01	ci left: 1.659423e-03	ci right 2.030734e-03	k: 386	n:210000
Cons ci ratio: 8.442948e-03	ci left: 5.043973e-01	ci right 5.086787e-01	k: 106373	n:210000
KS ci ratio: 1.990806e-01	ci left: 1.659423e-03	ci right 2.030734e-03	k: 386	n:210000
FAM49A   210000 perm   56 sec   (3777 perm/sec)   p_kst 1.838095e-03   p_cons 5.065381e-01   p_joint 1.838095e-03

Joint ci ratio: 1.955765e-01	ci left: 1.644486e-03	ci right 2.005206e-03	k: 400	n:220000
Cons ci ratio: 8.251638e-03	ci left: 5.042767e-01	ci right 5.084595e-01	k: 111401	n:220000
KS ci ratio: 1.955765e-01	ci left: 1.644486e-03	ci right 2.005206e-03	k: 400	n:220000
FAM49A   220000 perm   59 sec   (3734 perm/sec)   p_kst 1.818182e-03   p_cons 5.063682e-01   p_joint 1.818182e-03

Joint ci ratio: 1.924836e-01	ci left: 1.626761e-03	ci right 1.977289e-03	k: 413	n:230000
Cons ci ratio: 8.070733e-03	ci left: 5.042936e-01	ci right 5.083845e-01	k: 116458	n:230000
KS ci ratio: 1.924836e-01	ci left: 1.626761e-03	ci right 1.977289e-03	k: 413	n:230000
FAM49A   230000 perm   62 sec   (3689 perm/sec)   p_kst 1.795652e-03   p_cons 5.063391e-01   p_joint 1.795652e-03

Joint ci ratio: 1.888694e-01	ci left: 1.622464e-03	ci right 1.964748e-03	k: 429	n:240000
Cons ci ratio: 7.900239e-03	ci left: 5.043726e-01	ci right 5.083772e-01	k: 121530	n:240000
KS ci ratio: 1.888694e-01	ci left: 1.622464e-03	ci right 1.964748e-03	k: 429	n:240000
FAM49A   240000 perm   66 sec   (3642 perm/sec)   p_kst 1.787500e-03   p_cons 5.063750e-01   p_joint 1.787500e-03

Joint ci ratio: 1.856600e-01	ci left: 1.614752e-03	ci right 1.948969e-03	k: 444	n:250000
Cons ci ratio: 7.743891e-03	ci left: 5.042021e-01	ci right 5.081257e-01	k: 126541	n:250000
KS ci ratio: 1.856600e-01	ci left: 1.614752e-03	ci right 1.948969e-03	k: 444	n:250000
FAM49A   250000 perm   70 sec   (3594 perm/sec)   p_kst 1.776000e-03   p_cons 5.061640e-01   p_joint 1.776000e-03

Joint ci ratio: 1.822125e-01	ci left: 1.615020e-03	ci right 1.942400e-03	k: 461	n:260000
Cons ci ratio: 7.594192e-03	ci left: 5.041955e-01	ci right 5.080428e-01	k: 131591	n:260000
KS ci ratio: 1.822125e-01	ci left: 1.615020e-03	ci right 1.942400e-03	k: 461	n:260000
FAM49A   260000 perm   73 sec   (3549 perm/sec)   p_kst 1.773077e-03   p_cons 5.061192e-01   p_joint 1.773077e-03

Joint ci ratio: 1.791375e-01	ci left: 1.611784e-03	ci right 1.932396e-03	k: 477	n:270000
Cons ci ratio: 7.451306e-03	ci left: 5.042937e-01	ci right 5.080691e-01	k: 136669	n:270000
KS ci ratio: 1.791375e-01	ci left: 1.611784e-03	ci right 1.932396e-03	k: 477	n:270000
FAM49A   270000 perm   77 sec   (3505 perm/sec)   p_kst 1.766667e-03   p_cons 5.061815e-01   p_joint 1.766667e-03

Joint ci ratio: 1.763921e-01	ci left: 1.605407e-03	ci right 1.919335e-03	k: 492	n:280000
Cons ci ratio: 7.318701e-03	ci left: 5.042142e-01	ci right 5.079214e-01	k: 141699	n:280000
KS ci ratio: 1.763921e-01	ci left: 1.605407e-03	ci right 1.919335e-03	k: 492	n:280000
FAM49A   280000 perm   81 sec   (3459 perm/sec)   p_kst 1.757143e-03   p_cons 5.060679e-01   p_joint 1.757143e-03

Joint ci ratio: 1.737692e-01	ci left: 1.599505e-03	ci right 1.907140e-03	k: 507	n:290000
Cons ci ratio: 7.191594e-03	ci left: 5.042337e-01	ci right 5.078765e-01	k: 146756	n:290000
KS ci ratio: 1.737692e-01	ci left: 1.599505e-03	ci right 1.907140e-03	k: 507	n:290000
FAM49A   290000 perm   85 sec   (3419 perm/sec)   p_kst 1.748276e-03   p_cons 5.060552e-01   p_joint 1.748276e-03

Joint ci ratio: 1.709328e-01	ci left: 1.600411e-03	ci right 1.902678e-03	k: 524	n:300000
Cons ci ratio: 7.070887e-03	ci left: 5.042526e-01	ci right 5.078340e-01	k: 151813	n:300000
KS ci ratio: 1.709328e-01	ci left: 1.600411e-03	ci right 1.902678e-03	k: 524	n:300000
FAM49A   300000 perm   89 sec   (3377 perm/sec)   p_kst 1.746667e-03   p_cons 5.060433e-01   p_joint 1.746667e-03

Joint ci ratio: 1.676124e-01	ci left: 1.613658e-03	ci right 1.911909e-03	k: 545	n:310000
Cons ci ratio: 6.954310e-03	ci left: 5.043964e-01	ci right 5.079196e-01	k: 156909	n:310000
KS ci ratio: 1.676124e-01	ci left: 1.613658e-03	ci right 1.911909e-03	k: 545	n:310000
FAM49A   310000 perm   93 sec   (3336 perm/sec)   p_kst 1.758065e-03   p_cons 5.061581e-01   p_joint 1.758065e-03

Joint ci ratio: 1.649160e-01	ci left: 1.617141e-03	ci right 1.910750e-03	k: 563	n:320000
Cons ci ratio: 6.846182e-03	ci left: 5.043224e-01	ci right 5.077900e-01	k: 161938	n:320000
KS ci ratio: 1.649160e-01	ci left: 1.617141e-03	ci right 1.910750e-03	k: 563	n:320000
FAM49A   320000 perm   97 sec   (3297 perm/sec)   p_kst 1.759375e-03   p_cons 5.060562e-01   p_joint 1.759375e-03

Joint ci ratio: 1.629074e-01	ci left: 1.608820e-03	ci right 1.897012e-03	k: 577	n:330000
Cons ci ratio: 6.737715e-03	ci left: 5.046411e-01	ci right 5.080557e-01	k: 167095	n:330000
KS ci ratio: 1.629074e-01	ci left: 1.608820e-03	ci right 1.897012e-03	k: 577	n:330000
FAM49A   330000 perm   101 sec   (3259 perm/sec)   p_kst 1.748485e-03   p_cons 5.063485e-01   p_joint 1.748485e-03

Joint ci ratio: 1.606988e-01	ci left: 1.606655e-03	ci right 1.890181e-03	k: 593	n:340000
Cons ci ratio: 6.634671e-03	ci left: 5.049091e-01	ci right 5.082731e-01	k: 172241	n:340000
KS ci ratio: 1.606988e-01	ci left: 1.606655e-03	ci right 1.890181e-03	k: 593	n:340000
FAM49A   340000 perm   106 sec   (3221 perm/sec)   p_kst 1.744118e-03   p_cons 5.065912e-01   p_joint 1.744118e-03

Joint ci ratio: 1.593646e-01	ci left: 1.588176e-03	ci right 1.865892e-03	k: 603	n:350000
Cons ci ratio: 6.539873e-03	ci left: 5.048822e-01	ci right 5.081977e-01	k: 177289	n:350000
KS ci ratio: 1.593646e-01	ci left: 1.588176e-03	ci right 1.865892e-03	k: 603	n:350000
FAM49A   350000 perm   110 sec   (3182 perm/sec)   p_kst 1.722857e-03   p_cons 5.065400e-01   p_joint 1.722857e-03

Joint ci ratio: 1.566636e-01	ci left: 1.600088e-03	ci right 1.874699e-03	k: 624	n:360000
Cons ci ratio: 6.451033e-03	ci left: 5.047015e-01	ci right 5.079706e-01	k: 182281	n:360000
KS ci ratio: 1.566636e-01	ci left: 1.600088e-03	ci right 1.874699e-03	k: 624	n:360000
FAM49A   360000 perm   114 sec   (3147 perm/sec)   p_kst 1.733333e-03   p_cons 5.063361e-01   p_joint 1.733333e-03

Joint ci ratio: 1.542150e-01	ci left: 1.608795e-03	ci right 1.880185e-03	k: 644	n:370000
Cons ci ratio: 6.363823e-03	ci left: 5.046795e-01	ci right 5.079041e-01	k: 187328	n:370000
KS ci ratio: 1.542150e-01	ci left: 1.608795e-03	ci right 1.880185e-03	k: 644	n:370000
FAM49A   370000 perm   119 sec   (3112 perm/sec)   p_kst 1.740541e-03   p_cons 5.062919e-01   p_joint 1.740541e-03

Joint ci ratio: 1.518778e-01	ci left: 1.617074e-03	ci right 1.885352e-03	k: 664	n:380000
Cons ci ratio: 6.278967e-03	ci left: 5.047459e-01	ci right 5.079277e-01	k: 192408	n:380000
KS ci ratio: 1.518778e-01	ci left: 1.617074e-03	ci right 1.885352e-03	k: 664	n:380000
FAM49A   380000 perm   124 sec   (3076 perm/sec)   p_kst 1.747368e-03   p_cons 5.063368e-01   p_joint 1.747368e-03

Joint ci ratio: 1.495344e-01	ci left: 1.627427e-03	ci right 1.892884e-03	k: 685	n:390000
Cons ci ratio: 6.197130e-03	ci left: 5.048321e-01	ci right 5.079729e-01	k: 197497	n:390000
KS ci ratio: 1.495344e-01	ci left: 1.627427e-03	ci right 1.892884e-03	k: 685	n:390000
FAM49A   390000 perm   128 sec   (3043 perm/sec)   p_kst 1.756410e-03   p_cons 5.064026e-01   p_joint 1.756410e-03

Joint ci ratio: 1.471920e-01	ci left: 1.639701e-03	ci right 1.902601e-03	k: 707	n:400000
Cons ci ratio: 6.121044e-03	ci left: 5.046993e-01	ci right 5.078006e-01	k: 202500	n:400000
KS ci ratio: 1.471920e-01	ci left: 1.639701e-03	ci right 1.902601e-03	k: 707	n:400000
FAM49A   400000 perm   133 sec   (3010 perm/sec)   p_kst 1.767500e-03   p_cons 5.062500e-01   p_joint 1.767500e-03

Joint ci ratio: 1.455568e-01	ci left: 1.637303e-03	ci right 1.896649e-03	k: 723	n:410000
Cons ci ratio: 6.043533e-03	ci left: 5.049172e-01	ci right 5.079803e-01	k: 207644	n:410000
KS ci ratio: 1.455568e-01	ci left: 1.637303e-03	ci right 1.896649e-03	k: 723	n:410000
FAM49A   410000 perm   138 sec   (2976 perm/sec)   p_kst 1.763415e-03   p_cons 5.064488e-01   p_joint 1.763415e-03

Joint ci ratio: 1.439749e-01	ci left: 1.635035e-03	ci right 1.890965e-03	k: 739	n:420000
Cons ci ratio: 5.970713e-03	ci left: 5.049725e-01	ci right 5.079989e-01	k: 212724	n:420000
KS ci ratio: 1.439749e-01	ci left: 1.635035e-03	ci right 1.890965e-03	k: 739	n:420000
FAM49A   420000 perm   143 sec   (2945 perm/sec)   p_kst 1.759524e-03   p_cons 5.064857e-01   p_joint 1.759524e-03

Joint ci ratio: 1.420675e-01	ci left: 1.641858e-03	ci right 1.895163e-03	k: 759	n:430000
Cons ci ratio: 5.901972e-03	ci left: 5.048975e-01	ci right 5.078885e-01	k: 217749	n:430000
KS ci ratio: 1.420675e-01	ci left: 1.641858e-03	ci right 1.895163e-03	k: 759	n:430000
FAM49A   430000 perm   147 sec   (2915 perm/sec)   p_kst 1.765116e-03   p_cons 5.063930e-01   p_joint 1.765116e-03

Joint ci ratio: 1.397858e-01	ci left: 1.659359e-03	ci right 1.910910e-03	k: 784	n:440000
Cons ci ratio: 5.834782e-03	ci left: 5.048920e-01	ci right 5.078488e-01	k: 222803	n:440000
KS ci ratio: 1.397858e-01	ci left: 1.659359e-03	ci right 1.910910e-03	k: 784	n:440000
FAM49A   440000 perm   153 sec   (2884 perm/sec)   p_kst 1.781818e-03   p_cons 5.063705e-01   p_joint 1.781818e-03

Joint ci ratio: 1.380381e-01	ci left: 1.665385e-03	ci right 1.914433e-03	k: 804	n:450000
Cons ci ratio: 5.769324e-03	ci left: 5.049314e-01	ci right 5.078552e-01	k: 227877	n:450000
KS ci ratio: 1.380381e-01	ci left: 1.665385e-03	ci right 1.914433e-03	k: 804	n:450000
FAM49A   450000 perm   158 sec   (2853 perm/sec)   p_kst 1.786667e-03   p_cons 5.063933e-01   p_joint 1.786667e-03

Joint ci ratio: 1.363543e-01	ci left: 1.671167e-03	ci right 1.917785e-03	k: 824	n:460000
Cons ci ratio: 5.707757e-03	ci left: 5.048171e-01	ci right 5.077089e-01	k: 232881	n:460000
KS ci ratio: 1.363543e-01	ci left: 1.671167e-03	ci right 1.917785e-03	k: 824	n:460000
FAM49A   460000 perm   163 sec   (2825 perm/sec)   p_kst 1.791304e-03   p_cons 5.062630e-01   p_joint 1.791304e-03

Joint ci ratio: 1.352124e-01	ci left: 1.664385e-03	ci right 1.907780e-03	k: 838	n:470000
Cons ci ratio: 5.646965e-03	ci left: 5.048100e-01	ci right 5.076708e-01	k: 237933	n:470000
KS ci ratio: 1.352124e-01	ci left: 1.664385e-03	ci right 1.907780e-03	k: 838	n:470000
FAM49A   470000 perm   168 sec   (2797 perm/sec)   p_kst 1.782979e-03   p_cons 5.062404e-01   p_joint 1.782979e-03

Joint ci ratio: 1.339416e-01	ci left: 1.661922e-03	ci right 1.902489e-03	k: 854	n:480000
Cons ci ratio: 5.588681e-03	ci left: 5.047491e-01	ci right 5.075800e-01	k: 242959	n:480000
KS ci ratio: 1.339416e-01	ci left: 1.661922e-03	ci right 1.902489e-03	k: 854	n:480000
FAM49A   480000 perm   173 sec   (2768 perm/sec)   p_kst 1.779167e-03   p_cons 5.061646e-01   p_joint 1.779167e-03

Joint ci ratio: 1.327823e-01	ci left: 1.657596e-03	ci right 1.895296e-03	k: 869	n:490000
Cons ci ratio: 5.530269e-03	ci left: 5.048623e-01	ci right 5.076641e-01	k: 248069	n:490000
KS ci ratio: 1.327823e-01	ci left: 1.657596e-03	ci right 1.895296e-03	k: 869	n:490000
FAM49A   490000 perm   179 sec   (2740 perm/sec)   p_kst 1.773469e-03   p_cons 5.062633e-01   p_joint 1.773469e-03

Joint ci ratio: 1.316526e-01	ci left: 1.653451e-03	ci right 1.888383e-03	k: 884	n:500000
Cons ci ratio: 5.474548e-03	ci left: 5.048892e-01	ci right 5.076628e-01	k: 253138	n:500000
KS ci ratio: 1.316526e-01	ci left: 1.653451e-03	ci right 1.888383e-03	k: 884	n:500000
FAM49A   500000 perm   184 sec   (2713 perm/sec)   p_kst 1.768000e-03   p_cons 5.062760e-01   p_joint 1.768000e-03

Joint ci ratio: 1.302615e-01	ci left: 1.657065e-03	ci right 1.889830e-03	k: 903	n:510000
Cons ci ratio: 5.419181e-03	ci left: 5.050347e-01	ci right 5.077809e-01	k: 258268	n:510000
KS ci ratio: 1.302615e-01	ci left: 1.657065e-03	ci right 1.889830e-03	k: 903	n:510000
FAM49A   510000 perm   190 sec   (2687 perm/sec)   p_kst 1.770588e-03   p_cons 5.064078e-01   p_joint 1.770588e-03

Joint ci ratio: 1.290538e-01	ci left: 1.656830e-03	ci right 1.887239e-03	k: 920	n:520000
Cons ci ratio: 5.366224e-03	ci left: 5.051036e-01	ci right 5.078233e-01	k: 263361	n:520000
KS ci ratio: 1.290538e-01	ci left: 1.656830e-03	ci right 1.887239e-03	k: 920	n:520000
FAM49A   520000 perm   195 sec   (2661 perm/sec)   p_kst 1.769231e-03   p_cons 5.064635e-01   p_joint 1.769231e-03

Joint ci ratio: 1.278791e-01	ci left: 1.656614e-03	ci right 1.884737e-03	k: 937	n:530000
Cons ci ratio: 5.315371e-03	ci left: 5.051153e-01	ci right 5.078092e-01	k: 268425	n:530000
KS ci ratio: 1.278791e-01	ci left: 1.656614e-03	ci right 1.884737e-03	k: 937	n:530000
FAM49A   530000 perm   201 sec   (2636 perm/sec)   p_kst 1.767925e-03   p_cons 5.064623e-01   p_joint 1.767925e-03

Joint ci ratio: 1.270026e-01	ci left: 1.649242e-03	ci right 1.874676e-03	k: 950	n:540000
Cons ci ratio: 5.266873e-03	ci left: 5.050378e-01	ci right 5.077066e-01	k: 273441	n:540000
KS ci ratio: 1.270026e-01	ci left: 1.649242e-03	ci right 1.874676e-03	k: 950	n:540000
FAM49A   540000 perm   207 sec   (2611 perm/sec)   p_kst 1.759259e-03   p_cons 5.063722e-01   p_joint 1.759259e-03

Joint ci ratio: 1.260130e-01	ci left: 1.645665e-03	ci right 1.868726e-03	k: 965	n:550000
Cons ci ratio: 5.217952e-03	ci left: 5.051287e-01	ci right 5.077731e-01	k: 278548	n:550000
KS ci ratio: 1.260130e-01	ci left: 1.645665e-03	ci right 1.868726e-03	k: 965	n:550000
FAM49A   550000 perm   213 sec   (2585 perm/sec)   p_kst 1.754545e-03   p_cons 5.064509e-01   p_joint 1.754545e-03

Joint ci ratio: 1.249187e-01	ci left: 1.645683e-03	ci right 1.866666e-03	k: 982	n:560000
Cons ci ratio: 5.170424e-03	ci left: 5.052111e-01	ci right 5.078317e-01	k: 283652	n:560000
KS ci ratio: 1.249187e-01	ci left: 1.645683e-03	ci right 1.866666e-03	k: 982	n:560000
FAM49A   560000 perm   219 sec   (2561 perm/sec)   p_kst 1.753571e-03   p_cons 5.065214e-01   p_joint 1.753571e-03

Joint ci ratio: 1.239766e-01	ci left: 1.642308e-03	ci right 1.861052e-03	k: 997	n:570000
Cons ci ratio: 5.122751e-03	ci left: 5.054293e-01	ci right 5.080268e-01	k: 288835	n:570000
KS ci ratio: 1.239766e-01	ci left: 1.642308e-03	ci right 1.861052e-03	k: 997	n:570000
FAM49A   570000 perm   225 sec   (2538 perm/sec)   p_kst 1.749123e-03   p_cons 5.067281e-01   p_joint 1.749123e-03

Joint ci ratio: 1.222721e-01	ci left: 1.660782e-03	ci right 1.878726e-03	k: 1025	n:580000
Cons ci ratio: 5.078542e-03	ci left: 5.054262e-01	ci right 5.080013e-01	k: 293894	n:580000
KS ci ratio: 1.222721e-01	ci left: 1.660782e-03	ci right 1.878726e-03	k: 1025	n:580000
FAM49A   580000 perm   231 sec   (2515 perm/sec)   p_kst 1.767241e-03   p_cons 5.067138e-01   p_joint 1.767241e-03

Joint ci ratio: 1.210394e-01	ci left: 1.667143e-03	ci right 1.883558e-03	k: 1046	n:590000
Cons ci ratio: 5.035067e-03	ci left: 5.054624e-01	ci right 5.080155e-01	k: 298976	n:590000
KS ci ratio: 1.210394e-01	ci left: 1.667143e-03	ci right 1.883558e-03	k: 1046	n:590000
FAM49A   590000 perm   237 sec   (2492 perm/sec)   p_kst 1.772881e-03   p_cons 5.067390e-01   p_joint 1.772881e-03

Joint ci ratio: 1.202385e-01	ci left: 1.661987e-03	ci right 1.876203e-03	k: 1060	n:600000
Cons ci ratio: 4.993571e-03	ci left: 5.054091e-01	ci right 5.079408e-01	k: 304005	n:600000
KS ci ratio: 1.202385e-01	ci left: 1.661987e-03	ci right 1.876203e-03	k: 1060	n:600000
FAM49A   600000 perm   243 sec   (2470 perm/sec)   p_kst 1.766667e-03   p_cons 5.066750e-01   p_joint 1.766667e-03

Joint ci ratio: 1.191761e-01	ci left: 1.664956e-03	ci right 1.877525e-03	k: 1079	n:610000
Cons ci ratio: 4.952321e-03	ci left: 5.054347e-01	ci right 5.079456e-01	k: 309081	n:610000
KS ci ratio: 1.191761e-01	ci left: 1.664956e-03	ci right 1.877525e-03	k: 1079	n:610000
FAM49A   610000 perm   249 sec   (2448 perm/sec)   p_kst 1.768852e-03   p_cons 5.066902e-01   p_joint 1.768852e-03

Joint ci ratio: 1.179265e-01	ci left: 1.674099e-03	ci right 1.885439e-03	k: 1102	n:620000
Cons ci ratio: 4.911411e-03	ci left: 5.055273e-01	ci right 5.080178e-01	k: 314199	n:620000
KS ci ratio: 1.179265e-01	ci left: 1.674099e-03	ci right 1.885439e-03	k: 1102	n:620000
FAM49A   620000 perm   255 sec   (2427 perm/sec)   p_kst 1.777419e-03   p_cons 5.067726e-01   p_joint 1.777419e-03

Joint ci ratio: 1.168194e-01	ci left: 1.679881e-03	ci right 1.889822e-03	k: 1123	n:630000
Cons ci ratio: 4.873509e-03	ci left: 5.054107e-01	ci right 5.078813e-01	k: 319187	n:630000
KS ci ratio: 1.168194e-01	ci left: 1.679881e-03	ci right 1.889822e-03	k: 1123	n:630000
FAM49A   630000 perm   262 sec   (2406 perm/sec)   p_kst 1.782540e-03   p_cons 5.066460e-01   p_joint 1.782540e-03

Joint ci ratio: 1.153900e-01	ci left: 1.696113e-03	ci right 1.905313e-03	k: 1151	n:640000
Cons ci ratio: 4.835126e-03	ci left: 5.054368e-01	ci right 5.078881e-01	k: 324264	n:640000
KS ci ratio: 1.153900e-01	ci left: 1.696113e-03	ci right 1.905313e-03	k: 1151	n:640000
FAM49A   640000 perm   268 sec   (2386 perm/sec)   p_kst 1.798437e-03   p_cons 5.066625e-01   p_joint 1.798437e-03

Joint ci ratio: 1.145480e-01	ci left: 1.695421e-03	ci right 1.902906e-03	k: 1168	n:650000
Cons ci ratio: 4.798964e-03	ci left: 5.053238e-01	ci right 5.077562e-01	k: 329251	n:650000
KS ci ratio: 1.145480e-01	ci left: 1.695421e-03	ci right 1.902906e-03	k: 1168	n:650000
FAM49A   650000 perm   275 sec   (2364 perm/sec)   p_kst 1.796923e-03   p_cons 5.065400e-01   p_joint 1.796923e-03

Joint ci ratio: 1.138686e-01	ci left: 1.690339e-03	ci right 1.895892e-03	k: 1182	n:660000
Cons ci ratio: 4.763500e-03	ci left: 5.052249e-01	ci right 5.076387e-01	k: 334245	n:660000
KS ci ratio: 1.138686e-01	ci left: 1.690339e-03	ci right 1.895892e-03	k: 1182	n:660000
FAM49A   660000 perm   282 sec   (2343 perm/sec)   p_kst 1.790909e-03   p_cons 5.064318e-01   p_joint 1.790909e-03

Joint ci ratio: 1.131064e-01	ci left: 1.688312e-03	ci right 1.892154e-03	k: 1198	n:670000
Cons ci ratio: 4.726482e-03	ci left: 5.053752e-01	ci right 5.077710e-01	k: 339404	n:670000
KS ci ratio: 1.131064e-01	ci left: 1.688312e-03	ci right 1.892154e-03	k: 1198	n:670000
FAM49A   670000 perm   288 sec   (2323 perm/sec)   p_kst 1.788060e-03   p_cons 5.065731e-01   p_joint 1.788060e-03

Joint ci ratio: 1.121745e-01	ci left: 1.692067e-03	ci right 1.894568e-03	k: 1218	n:680000
Cons ci ratio: 4.692038e-03	ci left: 5.053374e-01	ci right 5.077155e-01	k: 344438	n:680000
KS ci ratio: 1.121745e-01	ci left: 1.692067e-03	ci right 1.894568e-03	k: 1218	n:680000
FAM49A   680000 perm   295 sec   (2303 perm/sec)   p_kst 1.791176e-03   p_cons 5.065265e-01   p_joint 1.791176e-03

Joint ci ratio: 1.114005e-01	ci left: 1.691493e-03	ci right 1.892436e-03	k: 1235	n:690000
Cons ci ratio: 4.657269e-03	ci left: 5.054152e-01	ci right 5.077760e-01	k: 349551	n:690000
KS ci ratio: 1.114005e-01	ci left: 1.691493e-03	ci right 1.892436e-03	k: 1235	n:690000
FAM49A   690000 perm   302 sec   (2284 perm/sec)   p_kst 1.789855e-03   p_cons 5.065957e-01   p_joint 1.789855e-03

Joint ci ratio: 1.105098e-01	ci left: 1.695108e-03	ci right 1.894766e-03	k: 1255	n:700000
Cons ci ratio: 4.622562e-03	ci left: 5.055666e-01	ci right 5.079105e-01	k: 354717	n:700000
KS ci ratio: 1.105098e-01	ci left: 1.695108e-03	ci right 1.894766e-03	k: 1255	n:700000
FAM49A   700000 perm   309 sec   (2265 perm/sec)   p_kst 1.792857e-03   p_cons 5.067386e-01   p_joint 1.792857e-03

Joint ci ratio: 1.097264e-01	ci left: 1.695887e-03	ci right 1.894129e-03	k: 1273	n:710000
Cons ci ratio: 4.589510e-03	ci left: 5.056166e-01	ci right 5.079439e-01	k: 359814	n:710000
KS ci ratio: 1.097264e-01	ci left: 1.695887e-03	ci right 1.894129e-03	k: 1273	n:710000
FAM49A   710000 perm   316 sec   (2246 perm/sec)   p_kst 1.792958e-03   p_cons 5.067803e-01   p_joint 1.792958e-03

Joint ci ratio: 1.090863e-01	ci left: 1.692596e-03	ci right 1.889225e-03	k: 1288	n:720000
Cons ci ratio: 4.558677e-03	ci left: 5.054986e-01	ci right 5.078096e-01	k: 364791	n:720000
KS ci ratio: 1.090863e-01	ci left: 1.692596e-03	ci right 1.889225e-03	k: 1288	n:720000
FAM49A   720000 perm   323 sec   (2226 perm/sec)   p_kst 1.788889e-03   p_cons 5.066542e-01   p_joint 1.788889e-03

Joint ci ratio: 1.080431e-01	ci left: 1.702727e-03	ci right 1.898521e-03	k: 1313	n:730000
Cons ci ratio: 4.527328e-03	ci left: 5.055086e-01	ci right 5.078037e-01	k: 369859	n:730000
KS ci ratio: 1.080431e-01	ci left: 1.702727e-03	ci right 1.898521e-03	k: 1313	n:730000
FAM49A   730000 perm   331 sec   (2208 perm/sec)   p_kst 1.798630e-03   p_cons 5.066562e-01   p_joint 1.798630e-03

Joint ci ratio: 1.073509e-01	ci left: 1.702071e-03	ci right 1.896457e-03	k: 1330	n:740000
Cons ci ratio: 4.496556e-03	ci left: 5.055251e-01	ci right 5.078046e-01	k: 374932	n:740000
KS ci ratio: 1.073509e-01	ci left: 1.702071e-03	ci right 1.896457e-03	k: 1330	n:740000
FAM49A   740000 perm   338 sec   (2190 perm/sec)   p_kst 1.797297e-03   p_cons 5.066649e-01   p_joint 1.797297e-03

Joint ci ratio: 1.065532e-01	ci left: 1.705330e-03	ci right 1.898550e-03	k: 1350	n:750000
Cons ci ratio: 4.465938e-03	ci left: 5.055932e-01	ci right 5.078575e-01	k: 380044	n:750000
KS ci ratio: 1.065532e-01	ci left: 1.705330e-03	ci right 1.898550e-03	k: 1350	n:750000
FAM49A   750000 perm   345 sec   (2173 perm/sec)   p_kst 1.800000e-03   p_cons 5.067253e-01   p_joint 1.800000e-03

Joint ci ratio: 1.058504e-01	ci left: 1.705947e-03	ci right 1.897882e-03	k: 1368	n:760000
Cons ci ratio: 4.435692e-03	ci left: 5.056871e-01	ci right 5.079365e-01	k: 385177	n:760000
KS ci ratio: 1.058504e-01	ci left: 1.705947e-03	ci right 1.897882e-03	k: 1368	n:760000
FAM49A   760000 perm   353 sec   (2156 perm/sec)   p_kst 1.800000e-03   p_cons 5.068118e-01   p_joint 1.800000e-03

Joint ci ratio: 1.047460e-01	ci left: 1.720463e-03	ci right 1.911887e-03	k: 1397	n:770000
Cons ci ratio: 4.407426e-03	ci left: 5.056229e-01	ci right 5.078576e-01	k: 390190	n:770000
KS ci ratio: 1.047460e-01	ci left: 1.720463e-03	ci right 1.911887e-03	k: 1397	n:770000
FAM49A   770000 perm   360 sec   (2139 perm/sec)   p_kst 1.814286e-03   p_cons 5.067403e-01   p_joint 1.814286e-03

Joint ci ratio: 1.042998e-01	ci left: 1.713388e-03	ci right 1.903163e-03	k: 1409	n:780000
Cons ci ratio: 4.378907e-03	ci left: 5.056501e-01	ci right 5.078704e-01	k: 395273	n:780000
KS ci ratio: 1.042998e-01	ci left: 1.713388e-03	ci right 1.903163e-03	k: 1409	n:780000
FAM49A   780000 perm   367 sec   (2123 perm/sec)   p_kst 1.806410e-03   p_cons 5.067603e-01   p_joint 1.806410e-03

Joint ci ratio: 1.035314e-01	ci left: 1.717591e-03	ci right 1.906345e-03	k: 1430	n:790000
Cons ci ratio: 4.351551e-03	ci left: 5.056057e-01	ci right 5.078119e-01	k: 400300	n:790000
KS ci ratio: 1.035314e-01	ci left: 1.717591e-03	ci right 1.906345e-03	k: 1430	n:790000
FAM49A   790000 perm   375 sec   (2107 perm/sec)   p_kst 1.810127e-03   p_cons 5.067089e-01   p_joint 1.810127e-03

Joint ci ratio: 1.031363e-01	ci left: 1.709515e-03	ci right 1.896621e-03	k: 1441	n:800000
Cons ci ratio: 4.323372e-03	ci left: 5.057163e-01	ci right 5.079087e-01	k: 405450	n:800000
KS ci ratio: 1.031363e-01	ci left: 1.709515e-03	ci right 1.896621e-03	k: 1441	n:800000
FAM49A   800000 perm   383 sec   (2091 perm/sec)   p_kst 1.801250e-03   p_cons 5.068125e-01   p_joint 1.801250e-03

Joint ci ratio: 1.024985e-01	ci left: 1.710061e-03	ci right 1.896000e-03	k: 1459	n:810000
Cons ci ratio: 4.296826e-03	ci left: 5.056970e-01	ci right 5.078758e-01	k: 410497	n:810000
KS ci ratio: 1.024985e-01	ci left: 1.710061e-03	ci right 1.896000e-03	k: 1459	n:810000
FAM49A   810000 perm   390 sec   (2075 perm/sec)   p_kst 1.801235e-03   p_cons 5.067864e-01   p_joint 1.801235e-03

Joint ci ratio: 1.020109e-01	ci left: 1.705843e-03	ci right 1.890388e-03	k: 1473	n:820000
Cons ci ratio: 4.269919e-03	ci left: 5.057770e-01	ci right 5.079424e-01	k: 415625	n:820000
KS ci ratio: 1.020109e-01	ci left: 1.705843e-03	ci right 1.890388e-03	k: 1473	n:820000
FAM49A   820000 perm   398 sec   (2060 perm/sec)   p_kst 1.796341e-03   p_cons 5.068598e-01   p_joint 1.796341e-03

Joint ci ratio: 1.016328e-01	ci left: 1.698206e-03	ci right 1.881203e-03	k: 1484	n:830000
Cons ci ratio: 4.244361e-03	ci left: 5.057551e-01	ci right 5.079075e-01	k: 420670	n:830000
KS ci ratio: 1.016328e-01	ci left: 1.698206e-03	ci right 1.881203e-03	k: 1484	n:830000
FAM49A   830000 perm   406 sec   (2044 perm/sec)   p_kst 1.787952e-03   p_cons 5.068313e-01   p_joint 1.787952e-03

Joint ci ratio: 1.006873e-01	ci left: 1.710480e-03	ci right 1.892983e-03	k: 1512	n:840000
Cons ci ratio: 4.219104e-03	ci left: 5.057517e-01	ci right 5.078911e-01	k: 425730	n:840000
KS ci ratio: 1.006873e-01	ci left: 1.710480e-03	ci right 1.892983e-03	k: 1512	n:840000
FAM49A   840000 perm   414 sec   (2029 perm/sec)   p_kst 1.800000e-03   p_cons 5.068214e-01   p_joint 1.800000e-03

Joint ci ratio: 1.002578e-01	ci left: 1.705266e-03	ci right 1.886391e-03	k: 1525	n:850000
Cons ci ratio: 4.193524e-03	ci left: 5.058401e-01	ci right 5.079669e-01	k: 430868	n:850000
KS ci ratio: 1.002578e-01	ci left: 1.705266e-03	ci right 1.886391e-03	k: 1525	n:850000
FAM49A   850000 perm   422 sec   (2014 perm/sec)   p_kst 1.794118e-03   p_cons 5.069035e-01   p_joint 1.794118e-03

Joint ci ratio: 9.970407e-02	ci left: 1.704710e-03	ci right 1.884718e-03	k: 1542	n:860000
Cons ci ratio: 4.169082e-03	ci left: 5.058451e-01	ci right 5.079595e-01	k: 435936	n:860000
KS ci ratio: 9.970407e-02	ci left: 1.704710e-03	ci right 1.884718e-03	k: 1542	n:860000
FAM49A   860000 perm   430 sec   (1999 perm/sec)   p_kst 1.793023e-03   p_cons 5.069023e-01   p_joint 1.793023e-03

Outputting figure to mutsig2_images.part000000000062/FAM49A.2_1012_860000_0.001793_0.5069_0.001793.png
                gene_name: FAM49A
               theta_stop: 0.100 
                    nperm: 860000 
                     p_ks: 0.0018 
        ci_ks_bounds_left: 0.0017 
       ci_ks_bounds_right: 0.0019 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.0018 
     ci_joint_bounds_left: 0.0017 
    ci_joint_bounds_right: 0.0019 

Current progress: 33 percent done.
FANCA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.492635e-02	ci left: 5.475994e-01	ci right 5.671671e-01	k: 5574	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
FANCA   10000 perm   2 sec   (5455 perm/sec)   p_kst 1   p_cons 5.574000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000062/FANCA.2_4545_10000_1_0.5574_1.png
                gene_name: FANCA
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
FANK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.627496e-02	ci left: 3.174100e-01	ci right 3.358911e-01	k: 3266	n:10000
Cons ci ratio: 6.613156e-02	ci left: 2.513249e-01	ci right 2.686151e-01	k: 2599	n:10000
KS ci ratio: 6.994737e-02	ci left: 2.305695e-01	ci right 2.473828e-01	k: 2389	n:10000
FANK1   10000 perm   2 sec   (6470 perm/sec)   p_kst 2.389000e-01   p_cons 2.599000e-01   p_joint 3.266000e-01

Outputting figure to mutsig2_images.part000000000062/FANK1.2_1082_10000_0.2389_0.2599_0.3266.png
                gene_name: FANK1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000062
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 62 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1431>
Subject: Job 4397993: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1431>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000063> was used as the working directory.
Started at Wed Oct 24 16:11:45 2012
Results reported at Wed Oct 24 16:16:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000063.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000063.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 63  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000063.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    234.74 sec.
    Max Memory :      1587 MB
    Max Swap   :      4015 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
63
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 63
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 63: processing genes 5563 - 5652
Calculating significance of each gene.
Using projection method.
5563	FAP	1
5564	FAR1	1
5565	FAR2	1
5566	FARP1	1
5567	FARP2	4.451735e-01
5568	FARS2	1
5569	FARSA	1
5570	FARSB	1
5571	FAS	1.400643e-01
5572	FASLG	1.383943e-01
5573	FASN	4.985953e-01
5574	FASTK	1
5575	FASTKD1	3.527742e-01
5576	FASTKD2	1
5577	FASTKD3	1
5578	FASTKD5	1
5579	FAT1	6.565065e-01
5580	FAT2	8.010668e-01
5581	FAT3	4.712108e-01
5582	FAT4	8.942370e-02
5583	FATE1	1
5584	FAU	1
5585	FBF1	1
5586	FBL	1
5587	FBLIM1	1
5588	FBLN1	1
5589	FBLN2	1
5590	FBLN5	1
5591	FBLN7	1
5592	FBN1	8.193678e-02
5593	FBN2	4.669460e-01
5594	FBN3	1
5595	FBP1	1
5596	FBP2	1
5597	FBRS	1
5598	FBXL12	1
5599	FBXL13	1
5600	FBXL14	1
5601	FBXL15	1
5602	FBXL16	1
5603	FBXL17	1
5604	FBXL18	1
5605	FBXL19	1
5606	FBXL2	1
5607	FBXL20	2.108080e-01
5608	FBXL21	1
5609	FBXL22	1
5610	FBXL3	1
5611	FBXL4	1
5612	FBXL5	1
5613	FBXL6	1
5614	FBXL7	1
5615	FBXO10	1
5616	FBXO11	1
5617	FBXO15	1
5618	FBXO16	1
5619	FBXO17	1
5620	FBXO18	1
5621	FBXO2	1
5622	FBXO21	1
5623	FBXO22	1
5624	FBXO24	2.244834e-01
5625	FBXO25	5.384233e-03
5626	FBXO27	1.542205e-02
5627	FBXO28	1
5628	FBXO3	6.294668e-02
5629	FBXO30	1
5630	FBXO31	1
5631	FBXO32	1
5632	FBXO33	1.645411e-01
5633	FBXO34	1
5634	FBXO36	1
5635	FBXO38	1.973496e-01
5636	FBXO39	1
5637	FBXO4	1
5638	FBXO40	1
5639	FBXO41	1
5640	FBXO42	2.132857e-02
5641	FBXO43	2.229746e-01
5642	FBXO44	1
5643	FBXO45	1
5644	FBXO46	1
5645	FBXO47	1
5646	FBXO48	1
5647	FBXO5	1
5648	FBXO6	1
5649	FBXO7	1
5650	FBXO8	1
5651	FBXO9	1
5652	FBXW10	1
Done

Running MutSig 2:
Scatter job 63: processing genes 5563 - 5652
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FAT2
Processing conservation and coverage...
76% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.131130e-02	ci left: 9.178069e-01	ci right 9.283451e-01	k: 9232	n:10000
KS ci ratio: 2.315067e-02	ci left: 7.326985e-01	ci right 7.499607e-01	k: 7414	n:10000
FAT2   10000 perm   4 sec   (2357 perm/sec)   p_kst 7.414000e-01   p_cons 9.232000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000063/FAT2.5_13142_10000_0.7414_0.9232_1.png
                gene_name: FAT2
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 17 percent done.
FAT4
Processing conservation and coverage...
66% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.961576e-02	ci left: 1.533552e-01	ci right 1.678431e-01	k: 1605	n:10000
Cons ci ratio: 3.423800e-02	ci left: 5.574207e-01	ci right 5.769402e-01	k: 5672	n:10000
KS ci ratio: 1.324787e-01	ci left: 7.514340e-02	ci right 8.590246e-02	k: 804	n:10000
FAT4   10000 perm   5 sec   (2136 perm/sec)   p_kst 8.040000e-02   p_cons 5.672000e-01   p_joint 1.605000e-01

Joint ci ratio: 7.178468e-02	ci left: 1.250728e-01	ci right 1.344351e-01	k: 2594	n:20000
Cons ci ratio: 2.460577e-02	ci left: 5.523361e-01	ci right 5.661467e-01	k: 11185	n:20000
KS ci ratio: 9.292732e-02	ci left: 7.789098e-02	ci right 8.553115e-02	k: 1633	n:20000
FAT4   20000 perm   10 sec   (1986 perm/sec)   p_kst 8.165000e-02   p_cons 5.592500e-01   p_joint 1.297000e-01

Outputting figure to mutsig2_images.part000000000063/FAT4.4_15014_20000_0.08165_0.55925_0.1297.png
                gene_name: FAT4
               theta_stop: 0.093 
                    nperm: 20000 
                     p_ks: 0.082 
        ci_ks_bounds_left: 0.078 
       ci_ks_bounds_right: 0.086 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.13 

Current progress: 33 percent done.
FBN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.126149e-02	ci left: 3.594324e-01	ci right 3.784440e-01	k: 3689	n:10000
KS ci ratio: 5.850473e-03	ci left: 9.752511e-01	ci right 9.810657e-01	k: 9783	n:10000
FBN1   10000 perm   3 sec   (3004 perm/sec)   p_kst 9.783000e-01   p_cons 3.689000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000063/FBN1.4_8876_10000_0.9783_0.3689_1.png
                gene_name: FBN1
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.98 
       ci_ks_bounds_right: 0.98 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
FBXO42
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.537380e-02	ci left: 4.175767e-01	ci right 4.370657e-01	k: 4273	n:10000
Cons ci ratio: 2.569156e-02	ci left: 6.904069e-01	ci right 7.084768e-01	k: 6995	n:10000
KS ci ratio: 7.735992e-02	ci left: 1.963361e-01	ci right 2.122365e-01	k: 2042	n:10000
FBXO42   10000 perm   2 sec   (5871 perm/sec)   p_kst 2.042000e-01   p_cons 6.995000e-01   p_joint 4.273000e-01

Outputting figure to mutsig2_images.part000000000063/FBXO42.3_2190_10000_0.2042_0.6995_0.4273.png
                gene_name: FBXO42
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 67 percent done.
FAT3
Processing conservation and coverage...
72% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.061000e-01	ci left: 1.136922e-01	ci right 1.265300e-01	k: 1200	n:10000
KS ci ratio: 2.189552e-02	ci left: 7.537301e-01	ci right 7.705170e-01	k: 7622	n:10000
FAT3   10000 perm   4 sec   (2507 perm/sec)   p_kst 7.622000e-01   p_cons 1.200000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 7.491910e-02	ci left: 1.158711e-01	ci right 1.249396e-01	k: 2407	n:20000
KS ci ratio: 1.551667e-02	ci left: 7.554301e-01	ci right 7.672938e-01	k: 15228	n:20000
FAT3   20000 perm   9 sec   (2325 perm/sec)   p_kst 7.614000e-01   p_cons 1.203500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000063/FAT3.2_13774_20000_0.7614_0.12035_1.png
                gene_name: FAT3
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.12 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
FBXO25
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.426589e-02	ci left: 5.570197e-01	ci right 5.765413e-01	k: 5668	n:10000
Cons ci ratio: 2.547181e-02	ci left: 6.940369e-01	ci right 7.120447e-01	k: 7031	n:10000
KS ci ratio: 5.283892e-02	ci left: 3.455153e-01	ci right 3.643693e-01	k: 3549	n:10000
FBXO25   10000 perm   1 sec   (7002 perm/sec)   p_kst 3.549000e-01   p_cons 7.031000e-01   p_joint 5.668000e-01

Outputting figure to mutsig2_images.part000000000063/FBXO25.2_1144_10000_0.3549_0.7031_0.5668.png
                gene_name: FBXO25
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000063
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 63 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4397996: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000064> was used as the working directory.
Started at Wed Oct 24 16:11:52 2012
Results reported at Wed Oct 24 16:13:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000064.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000064.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 64  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000064.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    128.43 sec.
    Max Memory :      1440 MB
    Max Swap   :      3977 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
64
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 64
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 64: processing genes 5653 - 5741
Calculating significance of each gene.
Using projection method.
5653	FBXW11	1
5654	FBXW12	1
5655	FBXW2	2.225982e-01
5656	FBXW4	1
5657	FBXW5	1
5658	FBXW7	7.723541e-03
5659	FBXW8	1.515001e-01
5660	FBXW9	1.324701e-02
5661	FCAMR	1
5662	FCAR	1
5663	FCER1A	1
5664	FCER1G	1
5665	FCER2	1
5666	FCF1	1
5667	FCGBP	1
5668	FCGR1A	1
5669	FCGR1B	1
5670	FCGR2A	1
5671	FCGR2B	1
5672	FCGR2C	1.240143e-01
5673	FCGR3A	1
5674	FCGR3B	1
5675	FCGRT	1
5676	FCHO1	1
5677	FCHO2	1.919134e-01
5678	FCHSD1	1.779774e-01
5679	FCHSD2	1
5680	FCN1	1
5681	FCN2	1
5682	FCN3	1
5683	FCRL1	1.932115e-04
5684	FCRL2	1
5685	FCRL3	1
5686	FCRL4	1
5687	FCRL5	1
5688	FCRL6	2.323361e-01
5689	FCRLA	1
5690	FCRLB	1
5691	FDFT1	1
5692	FDPS	1.470577e-01
5693	FDX1	1
5694	FDX1L	1
5695	FDXACB1	1
5696	FDXR	1.160783e-01
5697	FECH	1
5698	FEM1A	1
5699	FEM1B	1.666219e-01
5700	FEM1C	1.415708e-01
5701	FEN1	1
5702	FER	1
5703	FER1L5	1.865101e-01
5704	FER1L6	1
5705	FERD3L	3.307832e-02
5706	FERMT1	1
5707	FERMT2	1
5708	FERMT3	3.859597e-02
5709	FES	1
5710	FETUB	7.187586e-03
5711	FEV	1
5712	FEZ1	2.397196e-01
5713	FEZ2	1
5714	FEZF1	1
5715	FEZF2	1
5716	FFAR1	1
5717	FFAR2	1
5718	FFAR3	1
5719	FGA	3.917892e-01
5720	FGB	1
5721	FGD1	1
5722	FGD2	1
5723	FGD3	1
5724	FGD4	1.513913e-01
5725	FGD5	1
5726	FGD6	5.421025e-01
5727	FGF1	1
5728	FGF10	1
5729	FGF11	1
5730	FGF12	1
5731	FGF13	1
5732	FGF14	1
5733	FGF16	1
5734	FGF17	9.737106e-02
5735	FGF18	1
5736	FGF19	1
5737	FGF2	7.292977e-02
5738	FGF20	1
5739	FGF21	1
5740	FGF22	1
5741	FGF23	1
Done

Running MutSig 2:
Scatter job 64: processing genes 5653 - 5741
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FCRL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.040429e-01	ci left: 1.177960e-01	ci right 1.308238e-01	k: 1242	n:10000
Cons ci ratio: 2.742813e-02	ci left: 6.619944e-01	ci right 6.805058e-01	k: 6713	n:10000
KS ci ratio: 2.240477e-01	ci left: 2.636581e-02	ci right 3.311184e-02	k: 296	n:10000
FCRL1   10000 perm   2 sec   (6205 perm/sec)   p_kst 2.960000e-02   p_cons 6.713000e-01   p_joint 1.242000e-01

Joint ci ratio: 1.008374e-01	ci left: 6.669691e-02	ci right 7.382864e-02	k: 1404	n:20000
Cons ci ratio: 2.062815e-02	ci left: 6.368667e-01	ci right 6.501915e-01	k: 12871	n:20000
KS ci ratio: 1.598212e-01	ci left: 2.686219e-02	ci right 3.157601e-02	k: 583	n:20000
FCRL1   20000 perm   6 sec   (3625 perm/sec)   p_kst 2.915000e-02   p_cons 6.435500e-01   p_joint 7.020000e-02

Joint ci ratio: 8.534532e-02	ci left: 6.288924e-02	ci right 6.852856e-02	k: 1970	n:30000
Cons ci ratio: 1.684734e-02	ci left: 6.379829e-01	ci right 6.488560e-01	k: 19303	n:30000
KS ci ratio: 1.280313e-01	ci left: 2.835696e-02	ci right 3.226803e-02	k: 908	n:30000
FCRL1   30000 perm   8 sec   (3978 perm/sec)   p_kst 3.026667e-02   p_cons 6.434333e-01   p_joint 6.566667e-02

Joint ci ratio: 7.119465e-02	ci left: 6.793635e-02	ci right 7.297623e-02	k: 2817	n:40000
Cons ci ratio: 1.454849e-02	ci left: 6.400370e-01	ci right 6.494419e-01	k: 25790	n:40000
KS ci ratio: 1.114012e-01	ci left: 2.834996e-02	ci right 3.171872e-02	k: 1200	n:40000
FCRL1   40000 perm   10 sec   (4151 perm/sec)   p_kst 3.000000e-02   p_cons 6.447500e-01   p_joint 7.042500e-02

Joint ci ratio: 6.036438e-02	ci left: 7.542729e-02	ci right 8.014187e-02	k: 3888	n:50000
Cons ci ratio: 1.296125e-02	ci left: 6.423515e-01	ci right 6.507515e-01	k: 32328	n:50000
KS ci ratio: 1.012958e-01	ci left: 2.760505e-02	ci right 3.056996e-02	k: 1453	n:50000
FCRL1   50000 perm   12 sec   (4239 perm/sec)   p_kst 2.906000e-02   p_cons 6.465600e-01   p_joint 7.776000e-02

Joint ci ratio: 5.900608e-02	ci left: 6.649137e-02	ci right 7.055048e-02	k: 4110	n:60000
Cons ci ratio: 1.181284e-02	ci left: 6.434614e-01	ci right 6.511243e-01	k: 38838	n:60000
KS ci ratio: 9.268374e-02	ci left: 2.760661e-02	ci right 3.030587e-02	k: 1736	n:60000
FCRL1   60000 perm   14 sec   (4275 perm/sec)   p_kst 2.893333e-02   p_cons 6.473000e-01   p_joint 6.850000e-02

Outputting figure to mutsig2_images.part000000000064/FCRL1.3_1400_60000_0.028933_0.6473_0.0685.png
                gene_name: FCRL1
               theta_stop: 0.093 
                    nperm: 60000 
                     p_ks: 0.029 
        ci_ks_bounds_left: 0.028 
       ci_ks_bounds_right: 0.030 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.069 
     ci_joint_bounds_left: 0.066 
    ci_joint_bounds_right: 0.071 

Current progress: 25 percent done.
FBXW7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.485738e-02	ci left: 2.070805e-01	ci right 2.232857e-01	k: 2151	n:10000
Cons ci ratio: 2.278862e-02	ci left: 7.387626e-01	ci right 7.558931e-01	k: 7474	n:10000
KS ci ratio: 8.720168e-02	ci left: 1.607198e-01	ci right 1.754741e-01	k: 1680	n:10000
FBXW7   10000 perm   2 sec   (5876 perm/sec)   p_kst 1.680000e-01   p_cons 7.474000e-01   p_joint 2.151000e-01

Outputting figure to mutsig2_images.part000000000064/FBXW7.2_2584_10000_0.168_0.7474_0.2151.png
                gene_name: FBXW7
               theta_stop: 0.087 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 50 percent done.
FBXW9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.272236e-02	ci left: 4.472002e-01	ci right 4.668248e-01	k: 4570	n:10000
Cons ci ratio: 7.714091e-03	ci left: 9.589035e-01	ci right 9.664239e-01	k: 9628	n:10000
KS ci ratio: 5.906185e-02	ci left: 2.966780e-01	ci right 3.148353e-01	k: 3057	n:10000
FBXW9   10000 perm   2 sec   (5925 perm/sec)   p_kst 3.057000e-01   p_cons 9.628000e-01   p_joint 4.570000e-01

Outputting figure to mutsig2_images.part000000000064/FBXW9.2_1417_10000_0.3057_0.9628_0.457.png
                gene_name: FBXW9
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 75 percent done.
FETUB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.338274e-01	ci left: 1.133070e-02	ci right 1.595903e-02	k: 135	n:10000
Cons ci ratio: 2.521293e-01	ci left: 2.062036e-02	ci right 2.666153e-02	k: 235	n:10000
KS ci ratio: 1.318562e-01	ci left: 7.582209e-02	ci right 8.662335e-02	k: 811	n:10000
FETUB   10000 perm   2 sec   (6400 perm/sec)   p_kst 8.110000e-02   p_cons 2.350000e-02   p_joint 1.350000e-02

Joint ci ratio: 2.309462e-01	ci left: 1.255904e-02	ci right 1.588439e-02	k: 283	n:20000
Cons ci ratio: 1.752676e-01	ci left: 2.225822e-02	ci right 2.658156e-02	k: 487	n:20000
KS ci ratio: 9.201059e-02	ci left: 7.935919e-02	ci right 8.706249e-02	k: 1663	n:20000
FETUB   20000 perm   4 sec   (5693 perm/sec)   p_kst 8.315000e-02   p_cons 2.435000e-02   p_joint 1.415000e-02

Joint ci ratio: 2.597662e-01	ci left: 6.554965e-03	ci right 8.542192e-03	k: 225	n:30000
Cons ci ratio: 1.440166e-01	ci left: 2.236198e-02	ci right 2.586435e-02	k: 722	n:30000
KS ci ratio: 7.480044e-02	ci left: 8.072102e-02	ci right 8.702651e-02	k: 2515	n:30000
FETUB   30000 perm   5 sec   (5493 perm/sec)   p_kst 8.383333e-02   p_cons 2.406667e-02   p_joint 7.500000e-03

Joint ci ratio: 2.182537e-01	ci left: 7.126712e-03	ci right 8.895833e-03	k: 319	n:40000
Cons ci ratio: 1.247226e-01	ci left: 2.259499e-02	ci right 2.562464e-02	k: 963	n:40000
KS ci ratio: 6.506198e-02	ci left: 8.048664e-02	ci right 8.592405e-02	k: 3327	n:40000
FETUB   40000 perm   8 sec   (5329 perm/sec)   p_kst 8.317500e-02   p_cons 2.407500e-02   p_joint 7.975000e-03

Joint ci ratio: 2.041484e-01	ci left: 6.572555e-03	ci right 8.085491e-03	k: 365	n:50000
Cons ci ratio: 1.128089e-01	ci left: 2.224826e-02	ci right 2.492744e-02	k: 1178	n:50000
KS ci ratio: 5.798830e-02	ci left: 8.130653e-02	ci right 8.618192e-02	k: 4186	n:50000
FETUB   50000 perm   10 sec   (5175 perm/sec)   p_kst 8.372000e-02   p_cons 2.356000e-02   p_joint 7.300000e-03

Joint ci ratio: 1.853438e-01	ci left: 6.713914e-03	ci right 8.101039e-03	k: 443	n:60000
Cons ci ratio: 1.017279e-01	ci left: 2.292012e-02	ci right 2.539287e-02	k: 1448	n:60000
KS ci ratio: 5.308827e-02	ci left: 8.108429e-02	ci right 8.552278e-02	k: 4997	n:60000
FETUB   60000 perm   12 sec   (5060 perm/sec)   p_kst 8.328333e-02   p_cons 2.413333e-02   p_joint 7.383333e-03

Joint ci ratio: 1.683513e-01	ci left: 7.038413e-03	ci right 8.345749e-03	k: 537	n:70000
Cons ci ratio: 9.368608e-02	ci left: 2.325569e-02	ci right 2.555540e-02	k: 1707	n:70000
KS ci ratio: 4.916404e-02	ci left: 8.120657e-02	ci right 8.531376e-02	k: 5827	n:70000
FETUB   70000 perm   14 sec   (4955 perm/sec)   p_kst 8.324286e-02   p_cons 2.438571e-02   p_joint 7.671429e-03

Joint ci ratio: 1.570743e-01	ci left: 7.117951e-03	ci right 8.343154e-03	k: 617	n:80000
Cons ci ratio: 8.726947e-02	ci left: 2.352538e-02	ci right 2.568428e-02	k: 1967	n:80000
KS ci ratio: 4.603996e-02	ci left: 8.117138e-02	ci right 8.500892e-02	k: 6646	n:80000
FETUB   80000 perm   16 sec   (4851 perm/sec)   p_kst 8.307500e-02   p_cons 2.458750e-02   p_joint 7.712500e-03

Joint ci ratio: 1.487666e-01	ci left: 7.085775e-03	ci right 8.235188e-03	k: 688	n:90000
Cons ci ratio: 8.256569e-02	ci left: 2.342358e-02	ci right 2.545168e-02	k: 2198	n:90000
KS ci ratio: 4.334334e-02	ci left: 8.150254e-02	ci right 8.512437e-02	k: 7497	n:90000
FETUB   90000 perm   19 sec   (4755 perm/sec)   p_kst 8.330000e-02   p_cons 2.442222e-02   p_joint 7.644444e-03

Joint ci ratio: 1.197044e-01	ci left: 9.974499e-03	ci right 1.125413e-02	k: 1060	n:100000
Cons ci ratio: 7.838356e-02	ci left: 2.344274e-02	ci right 2.536498e-02	k: 2439	n:100000
KS ci ratio: 4.120852e-02	ci left: 8.126749e-02	ci right 8.469674e-02	k: 8297	n:100000
FETUB   100000 perm   21 sec   (4664 perm/sec)   p_kst 8.297000e-02   p_cons 2.439000e-02   p_joint 1.060000e-02

Joint ci ratio: 1.333814e-01	ci left: 7.271010e-03	ci right 8.318828e-03	k: 856	n:110000
Cons ci ratio: 7.475010e-02	ci left: 2.347840e-02	ci right 2.531043e-02	k: 2682	n:110000
KS ci ratio: 3.933734e-02	ci left: 8.116892e-02	ci right 8.443494e-02	k: 9107	n:110000
FETUB   110000 perm   24 sec   (4574 perm/sec)   p_kst 8.279091e-02   p_cons 2.438182e-02   p_joint 7.781818e-03

Joint ci ratio: 1.078789e-01	ci left: 1.029587e-02	ci right 1.147795e-02	k: 1305	n:120000
Cons ci ratio: 7.173010e-02	ci left: 2.341158e-02	ci right 2.516151e-02	k: 2913	n:120000
KS ci ratio: 3.762344e-02	ci left: 8.139543e-02	ci right 8.452476e-02	k: 9954	n:120000
FETUB   120000 perm   27 sec   (4487 perm/sec)   p_kst 8.295000e-02   p_cons 2.427500e-02   p_joint 1.087500e-02

Joint ci ratio: 9.979003e-02	ci left: 1.114503e-02	ci right 1.232305e-02	k: 1524	n:130000
Cons ci ratio: 6.894779e-02	ci left: 2.342438e-02	ci right 2.510463e-02	k: 3153	n:130000
KS ci ratio: 3.605017e-02	ci left: 8.186435e-02	ci right 8.487735e-02	k: 10837	n:130000
FETUB   130000 perm   29 sec   (4407 perm/sec)   p_kst 8.336154e-02   p_cons 2.425385e-02   p_joint 1.172308e-02

Outputting figure to mutsig2_images.part000000000064/FETUB.2_1177_130000_0.083362_0.024254_0.011723.png
                gene_name: FETUB
               theta_stop: 0.100 
                    nperm: 130000 
                     p_ks: 0.083 
        ci_ks_bounds_left: 0.082 
       ci_ks_bounds_right: 0.085 
                   p_cons: 0.024 
      ci_cons_bounds_left: 0.023 
     ci_cons_bounds_right: 0.025 
                  p_joint: 0.012 
     ci_joint_bounds_left: 0.011 
    ci_joint_bounds_right: 0.012 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000064
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 64 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4397998: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000065> was used as the working directory.
Started at Wed Oct 24 16:11:52 2012
Results reported at Wed Oct 24 16:14:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000065.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000065.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 65  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000065.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    154.87 sec.
    Max Memory :      1302 MB
    Max Swap   :      4062 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
65
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 65
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 65: processing genes 5742 - 5831
Calculating significance of each gene.
Using projection method.
5742	FGF3	1
5743	FGF4	1
5744	FGF5	1
5745	FGF6	1
5746	FGF7	1
5747	FGF8	1
5748	FGF9	3.795211e-02
5749	FGFBP1	1
5750	FGFBP2	1
5751	FGFBP3	1
5752	FGFR1	1
5753	FGFR1OP	1
5754	FGFR1OP2	6.561786e-02
5755	FGFR2	1
5756	FGFR3	1
5757	FGFR4	1
5758	FGFRL1	1
5759	FGG	1
5760	FGGY	1
5761	FGL1	1
5762	FGL2	1.499629e-01
5763	FGR	1
5764	FH	1
5765	FHDC1	2.989336e-01
5766	FHIT	1
5767	FHL1	1
5768	FHL2	1
5769	FHL3	1
5770	FHL5	1
5771	FHOD1	1
5772	FHOD3	1
5773	FIBCD1	1
5774	FIBIN	1
5775	FIBP	1
5776	FICD	1
5777	FIG4	3.928147e-03
5778	FIGF	1
5779	FIGLA	1
5780	FIGN	1
5781	FIGNL1	1
5782	FILIP1	2.548897e-01
5783	FILIP1L	4.742613e-01
5784	FIP1L1	2.950648e-01
5785	FIS1	1
5786	FITM1	1
5787	FITM2	1
5788	FIZ1	1
5789	FJX1	1
5790	FKBP10	1
5791	FKBP11	1
5792	FKBP14	1
5793	FKBP15	1
5794	FKBP1A	1
5795	FKBP1B	1
5796	FKBP2	1
5797	FKBP3	1
5798	FKBP4	1
5799	FKBP5	2.291656e-01
5800	FKBP6	1
5801	FKBP7	6.590519e-03
5802	FKBP8	1.112456e-01
5803	FKBP9	3.063071e-02
5804	FKBPL	1
5805	FKRP	1
5806	FKSG83	1
5807	FKTN	1
5808	FLAD1	1
5809	FLCN	1.693103e-01
5810	FLG	2.786618e-02
5811	FLG2	7.672986e-01
5812	FLI1	1.431831e-01
5813	FLII	1
5814	FLJ10357	1
5815	FLJ35220	1
5816	FLJ37543	1
5817	FLJ43860	1
5818	FLJ44635	1
5819	FLJ46321	7.581195e-02
5820	FLNA	2.426798e-01
5821	FLNB	1
5822	FLNC	7.483248e-01
5823	FLOT1	1
5824	FLOT2	1
5825	FLRT1	1
5826	FLRT2	1
5827	FLRT3	1
5828	FLT1	2.768969e-01
5829	FLT3	1
5830	FLT3LG	1
5831	FLT4	1.579886e-01
Done

Running MutSig 2:
Scatter job 65: processing genes 5742 - 5831
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FLG
Processing conservation and coverage...
81% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.990594e-02	ci left: 4.811556e-01	ci right 5.008497e-01	k: 4910	n:10000
Cons ci ratio: 4.096618e-02	ci left: 4.680674e-01	ci right 4.877455e-01	k: 4779	n:10000
KS ci ratio: 5.812920e-02	ci left: 3.034210e-01	ci right 3.216883e-01	k: 3125	n:10000
FLG   10000 perm   3 sec   (3195 perm/sec)   p_kst 3.125000e-01   p_cons 4.779000e-01   p_joint 4.910000e-01

Outputting figure to mutsig2_images.part000000000065/FLG.7_12194_10000_0.3125_0.4779_0.491.png
                gene_name: FLG
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 17 percent done.
FIG4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.682149e-02	ci left: 4.023300e-01	ci right 4.217213e-01	k: 4120	n:10000
Cons ci ratio: 4.999771e-02	ci left: 3.710696e-01	ci right 3.902000e-01	k: 3806	n:10000
KS ci ratio: 4.898462e-02	ci left: 3.807221e-01	ci right 3.999419e-01	k: 3903	n:10000
FIG4   10000 perm   2 sec   (5572 perm/sec)   p_kst 3.903000e-01   p_cons 3.806000e-01   p_joint 4.120000e-01

Outputting figure to mutsig2_images.part000000000065/FIG4.3_2816_10000_0.3903_0.3806_0.412.png
                gene_name: FIG4
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 33 percent done.
FLG2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.711799e-02	ci left: 6.670292e-01	ci right 6.854680e-01	k: 6763	n:10000
Cons ci ratio: 4.707361e-02	ci left: 3.997400e-01	ci right 4.191128e-01	k: 4094	n:10000
KS ci ratio: 1.661111e-02	ci left: 8.406084e-01	ci right 8.547884e-01	k: 8478	n:10000
FLG2   10000 perm   2 sec   (4552 perm/sec)   p_kst 8.478000e-01   p_cons 4.094000e-01   p_joint 6.763000e-01

Outputting figure to mutsig2_images.part000000000065/FLG2.3_7184_10000_0.8478_0.4094_0.6763.png
                gene_name: FLG2
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.69 

Current progress: 50 percent done.
FKBP9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.729818e-02	ci left: 3.974490e-01	ci right 4.168051e-01	k: 4071	n:10000
Cons ci ratio: 2.048496e-02	ci left: 7.773223e-01	ci right 7.935111e-01	k: 7855	n:10000
KS ci ratio: 5.569174e-02	ci left: 3.219758e-01	ci right 3.405226e-01	k: 3312	n:10000
FKBP9   10000 perm   2 sec   (6312 perm/sec)   p_kst 3.312000e-01   p_cons 7.855000e-01   p_joint 4.071000e-01

Outputting figure to mutsig2_images.part000000000065/FKBP9.2_1753_10000_0.3312_0.7855_0.4071.png
                gene_name: FKBP9
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 67 percent done.
FLJ46321
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.973370e-02	ci left: 3.735570e-01	ci right 3.927111e-01	k: 3831	n:10000
Cons ci ratio: 4.930512e-02	ci left: 3.776368e-01	ci right 3.968289e-01	k: 3872	n:10000
KS ci ratio: 2.621813e-02	ci left: 6.817379e-01	ci right 6.999508e-01	k: 6909	n:10000
FLJ46321   10000 perm   2 sec   (5243 perm/sec)   p_kst 6.909000e-01   p_cons 3.872000e-01   p_joint 3.831000e-01

Outputting figure to mutsig2_images.part000000000065/FLJ46321.2_4747_10000_0.6909_0.3872_0.3831.png
                gene_name: FLJ46321
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 83 percent done.
FLNA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.994587e-02	ci left: 4.806559e-01	ci right 5.003496e-01	k: 4905	n:10000
Cons ci ratio: 4.462184e-02	ci left: 4.257520e-01	ci right 4.452856e-01	k: 4355	n:10000
KS ci ratio: 5.906185e-02	ci left: 2.966780e-01	ci right 3.148353e-01	k: 3057	n:10000
FLNA   10000 perm   2 sec   (4252 perm/sec)   p_kst 3.057000e-01   p_cons 4.355000e-01   p_joint 4.905000e-01

Outputting figure to mutsig2_images.part000000000065/FLNA.2_8132_10000_0.3057_0.4355_0.4905.png
                gene_name: FLNA
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000065
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 65 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1555>
Subject: Job 4398002: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1555>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000066> was used as the working directory.
Started at Wed Oct 24 16:12:01 2012
Results reported at Wed Oct 24 16:15:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000066.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000066.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 66  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000066.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    284.72 sec.
    Max Memory :      1346 MB
    Max Swap   :      3997 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
66
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 66
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 66: processing genes 5832 - 5921
Calculating significance of each gene.
Using projection method.
5832	FLVCR1	1
5833	FLVCR2	4.539463e-02
5834	FLYWCH1	1
5835	FLYWCH2	1
5836	FMN1	1
5837	FMN2	3.580100e-01
5838	FMNL1	1
5839	FMNL2	1
5840	FMNL3	2.035915e-01
5841	FMO1	1
5842	FMO2	1
5843	FMO3	1
5844	FMO4	1
5845	FMO5	2.620438e-01
5846	FMOD	1
5847	FMR1	1
5848	FMR1NB	1.353150e-01
5849	FN1	3.410166e-01
5850	FN3K	1
5851	FN3KRP	1
5852	FNBP1	1
5853	FNBP1L	1
5854	FNBP4	1
5855	FNDC1	2.533222e-02
5856	FNDC3A	1
5857	FNDC3B	1
5858	FNDC4	1
5859	FNDC5	1
5860	FNDC7	1
5861	FNDC8	1
5862	FNIP1	1
5863	FNIP2	1
5864	FNTA	1.568936e-01
5865	FNTB	1
5866	FOLH1	1
5867	FOLH1B	1
5868	FOLR1	8.923834e-02
5869	FOLR2	1
5870	FOLR3	1
5871	FOLR4	1
5872	FOS	1
5873	FOSB	1
5874	FOSL1	1
5875	FOSL2	7.311493e-02
5876	FOXA1	1
5877	FOXA2	1
5878	FOXA3	1
5879	FOXB1	1
5880	FOXB2	1
5881	FOXC1	1
5882	FOXC2	6.490899e-02
5883	FOXD2	1
5884	FOXD3	7.437114e-02
5885	FOXD4	1.200289e-01
5886	FOXD4L1	1
5887	FOXD4L3	1
5888	FOXE1	1
5889	FOXE3	1
5890	FOXF1	1
5891	FOXF2	1
5892	FOXG1	1
5893	FOXH1	1
5894	FOXI1	1
5895	FOXJ1	1
5896	FOXJ2	1.187531e-01
5897	FOXJ3	1
5898	FOXK1	2.067714e-01
5899	FOXK2	1
5900	FOXL1	1
5901	FOXL2	1
5902	FOXM1	1
5903	FOXN1	1
5904	FOXN2	1
5905	FOXN3	1
5906	FOXN4	1
5907	FOXO1	1.259638e-02
5908	FOXO3	1
5909	FOXO4	3.748698e-02
5910	FOXP1	1
5911	FOXP2	1
5912	FOXP3	1
5913	FOXP4	1
5914	FOXQ1	1
5915	FOXR1	1
5916	FOXR2	1
5917	FOXRED1	1
5918	FOXRED2	2.183685e-01
5919	FOXS1	1
5920	FPGS	1
5921	FPGT	1
Done

Running MutSig 2:
Scatter job 66: processing genes 5832 - 5921
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FNDC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.598151e-02	ci left: 4.110981e-01	ci right 4.305480e-01	k: 4208	n:10000
Cons ci ratio: 4.495000e-02	ci left: 4.221625e-01	ci right 4.416772e-01	k: 4319	n:10000
KS ci ratio: 4.887162e-02	ci left: 3.818169e-01	ci right 4.010464e-01	k: 3914	n:10000
FNDC1   10000 perm   2 sec   (4051 perm/sec)   p_kst 3.914000e-01   p_cons 4.319000e-01   p_joint 4.208000e-01

Outputting figure to mutsig2_images.part000000000066/FNDC1.4_5777_10000_0.3914_0.4319_0.4208.png
                gene_name: FNDC1
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 33 percent done.
FN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.929411e-02	ci left: 7.970962e-01	ci right 8.127257e-01	k: 8050	n:10000
Cons ci ratio: 1.509149e-01	ci left: 5.841227e-02	ci right 6.804410e-02	k: 631	n:10000
KS ci ratio: 3.842359e-01	ci left: 8.324320e-03	ci right 1.236857e-02	k: 102	n:10000
FN1   10000 perm   3 sec   (3718 perm/sec)   p_kst 1.020000e-02   p_cons 6.310000e-02   p_joint 8.050000e-01

Joint ci ratio: 1.362748e-02	ci left: 7.997936e-01	ci right 8.108175e-01	k: 16107	n:20000
Cons ci ratio: 1.059125e-01	ci left: 6.069528e-02	ci right 6.753211e-02	k: 1281	n:20000
KS ci ratio: 2.845415e-01	ci left: 8.062881e-03	ci right 1.078261e-02	k: 187	n:20000
FN1   20000 perm   6 sec   (3406 perm/sec)   p_kst 9.350000e-03   p_cons 6.405000e-02   p_joint 8.053500e-01

Joint ci ratio: 2.132588e-02	ci left: 5.239994e-01	ci right 5.353282e-01	k: 15890	n:30000
Cons ci ratio: 8.635796e-02	ci left: 6.148468e-02	ci right 6.706674e-02	k: 1927	n:30000
KS ci ratio: 2.244287e-01	ci left: 8.936542e-03	ci right 1.122650e-02	k: 301	n:30000
FN1   30000 perm   9 sec   (3288 perm/sec)   p_kst 1.003333e-02   p_cons 6.423333e-02   p_joint 5.296667e-01

Joint ci ratio: 9.609849e-03	ci left: 8.022917e-01	ci right 8.100638e-01	k: 32248	n:40000
Cons ci ratio: 7.452032e-02	ci left: 6.228388e-02	ci right 6.712954e-02	k: 2587	n:40000
KS ci ratio: 1.928357e-01	ci left: 9.238511e-03	ci right 1.123355e-02	k: 408	n:40000
FN1   40000 perm   12 sec   (3214 perm/sec)   p_kst 1.020000e-02   p_cons 6.467500e-02   p_joint 8.062000e-01

Joint ci ratio: 6.971012e-02	ci left: 5.740279e-02	ci right 6.156854e-02	k: 2973	n:50000
Cons ci ratio: 6.602257e-02	ci left: 6.368146e-02	ci right 6.804911e-02	k: 3292	n:50000
KS ci ratio: 1.706741e-01	ci left: 9.548446e-03	ci right 1.134907e-02	k: 521	n:50000
FN1   50000 perm   16 sec   (3138 perm/sec)   p_kst 1.042000e-02   p_cons 6.584000e-02   p_joint 5.946000e-02

Joint ci ratio: 5.916822e-03	ci left: 8.771208e-01	ci right 8.823424e-01	k: 52785	n:60000
Cons ci ratio: 6.015293e-02	ci left: 6.410822e-02	ci right 6.810054e-02	k: 3965	n:60000
KS ci ratio: 1.586964e-01	ci left: 9.267325e-03	ci right 1.088059e-02	k: 603	n:60000
FN1   60000 perm   20 sec   (3060 perm/sec)   p_kst 1.005000e-02   p_cons 6.608333e-02   p_joint 8.797500e-01

Joint ci ratio: 5.488789e-03	ci left: 8.768926e-01	ci right 8.817331e-01	k: 61553	n:70000
Cons ci ratio: 5.556878e-02	ci left: 6.452412e-02	ci right 6.822621e-02	k: 4645	n:70000
KS ci ratio: 1.474184e-01	ci left: 9.262376e-03	ci right 1.075009e-02	k: 699	n:70000
FN1   70000 perm   23 sec   (3001 perm/sec)   p_kst 9.985714e-03   p_cons 6.635714e-02   p_joint 8.793286e-01

Joint ci ratio: 5.537989e-02	ci left: 5.730297e-02	ci right 6.057910e-02	k: 4714	n:80000
Cons ci ratio: 5.208351e-02	ci left: 6.440017e-02	ci right 6.785638e-02	k: 5289	n:80000
KS ci ratio: 1.381593e-01	ci left: 9.273797e-03	ci right 1.066209e-02	k: 796	n:80000
FN1   80000 perm   27 sec   (2953 perm/sec)   p_kst 9.950000e-03   p_cons 6.611250e-02   p_joint 5.892500e-02

Joint ci ratio: 4.846850e-03	ci left: 8.769075e-01	ci right 8.811791e-01	k: 79115	n:90000
Cons ci ratio: 4.916790e-02	ci left: 6.434244e-02	ci right 6.759672e-02	k: 5936	n:90000
KS ci ratio: 1.313442e-01	ci left: 9.155955e-03	ci right 1.045371e-02	k: 881	n:90000
FN1   90000 perm   31 sec   (2914 perm/sec)   p_kst 9.788889e-03   p_cons 6.595556e-02   p_joint 8.790556e-01

Joint ci ratio: 4.592395e-03	ci left: 8.772850e-01	ci right 8.813330e-01	k: 87932	n:100000
Cons ci ratio: 4.675364e-02	ci left: 6.414235e-02	ci right 6.722290e-02	k: 6567	n:100000
KS ci ratio: 1.239669e-01	ci left: 9.285927e-03	ci right 1.052275e-02	k: 989	n:100000
FN1   100000 perm   35 sec   (2874 perm/sec)   p_kst 9.890000e-03   p_cons 6.567000e-02   p_joint 8.793200e-01

Joint ci ratio: 4.385080e-03	ci left: 8.770674e-01	ci right 8.809308e-01	k: 96691	n:110000
Cons ci ratio: 4.450473e-02	ci left: 6.441373e-02	ci right 6.735466e-02	k: 7246	n:110000
KS ci ratio: 1.178704e-01	ci left: 9.367458e-03	ci right 1.054950e-02	k: 1094	n:110000
FN1   110000 perm   39 sec   (2843 perm/sec)   p_kst 9.945455e-03   p_cons 6.587273e-02   p_joint 8.790091e-01

Joint ci ratio: 4.191492e-03	ci left: 8.775021e-01	ci right 8.811962e-01	k: 105523	n:120000
Cons ci ratio: 4.270792e-02	ci left: 6.419729e-02	ci right 6.700708e-02	k: 7871	n:120000
KS ci ratio: 1.126879e-01	ci left: 9.420440e-03	ci right 1.055343e-02	k: 1197	n:120000
FN1   120000 perm   43 sec   (2808 perm/sec)   p_kst 9.975000e-03   p_cons 6.559167e-02   p_joint 8.793583e-01

Joint ci ratio: 4.032827e-03	ci left: 8.772691e-01	ci right 8.808217e-01	k: 114277	n:130000
Cons ci ratio: 4.098618e-02	ci left: 6.438953e-02	ci right 6.709142e-02	k: 8545	n:130000
KS ci ratio: 1.079663e-01	ci left: 9.496179e-03	ci right 1.058738e-02	k: 1304	n:130000
FN1   130000 perm   47 sec   (2773 perm/sec)   p_kst 1.003077e-02   p_cons 6.573077e-02   p_joint 8.790538e-01

Joint ci ratio: 1.036074e-01	ci left: 9.596743e-03	ci right 1.065227e-02	k: 1416	n:140000
Cons ci ratio: 3.953296e-02	ci left: 6.432270e-02	ci right 6.692390e-02	k: 9186	n:140000
KS ci ratio: 1.036074e-01	ci left: 9.596743e-03	ci right 1.065227e-02	k: 1416	n:140000
FN1   140000 perm   51 sec   (2741 perm/sec)   p_kst 1.011429e-02   p_cons 6.561429e-02   p_joint 1.011429e-02

Joint ci ratio: 3.756359e-03	ci left: 8.772786e-01	ci right 8.805868e-01	k: 131841	n:150000
Cons ci ratio: 3.815767e-02	ci left: 6.447770e-02	ci right 6.699245e-02	k: 9859	n:150000
KS ci ratio: 9.983595e-02	ci left: 9.665159e-03	ci right 1.068724e-02	k: 1525	n:150000
FN1   150000 perm   55 sec   (2710 perm/sec)   p_kst 1.016667e-02   p_cons 6.572667e-02   p_joint 8.789400e-01

Outputting figure to mutsig2_images.part000000000066/FN1.2_7651_150000_0.010167_0.065727_0.87894.png
                gene_name: FN1
               theta_stop: 0.100 
                    nperm: 150000 
                     p_ks: 0.010 
        ci_ks_bounds_left: 0.0097 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.066 
      ci_cons_bounds_left: 0.064 
     ci_cons_bounds_right: 0.067 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.88 

Current progress: 67 percent done.
FOXO1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.892304e-02	ci left: 2.976695e-01	ci right 3.158432e-01	k: 3067	n:10000
Cons ci ratio: 2.791418e-02	ci left: 6.541423e-01	ci right 6.727624e-01	k: 6635	n:10000
KS ci ratio: 1.785097e-01	ci left: 4.188120e-02	ci right 5.018585e-02	k: 459	n:10000
FOXO1   10000 perm   2 sec   (6149 perm/sec)   p_kst 4.590000e-02   p_cons 6.635000e-01   p_joint 3.067000e-01

Joint ci ratio: 7.826432e-02	ci left: 1.070713e-01	ci right 1.158420e-01	k: 2228	n:20000
Cons ci ratio: 1.979434e-02	ci left: 6.556472e-01	ci right 6.688056e-01	k: 13245	n:20000
KS ci ratio: 1.253030e-01	ci left: 4.371988e-02	ci right 4.961282e-02	k: 932	n:20000
FOXO1   20000 perm   4 sec   (5424 perm/sec)   p_kst 4.660000e-02   p_cons 6.622500e-01   p_joint 1.114000e-01

Joint ci ratio: 1.012709e-01	ci left: 4.515283e-02	ci right 5.000194e-02	k: 1426	n:30000
Cons ci ratio: 1.613393e-02	ci left: 6.576524e-01	ci right 6.683827e-01	k: 19891	n:30000
KS ci ratio: 1.012709e-01	ci left: 4.515283e-02	ci right 5.000194e-02	k: 1426	n:30000
FOXO1   30000 perm   6 sec   (5149 perm/sec)   p_kst 4.753333e-02   p_cons 6.630333e-01   p_joint 4.753333e-02

Joint ci ratio: 8.716774e-02	ci left: 4.602343e-02	ci right 5.024248e-02	k: 1924	n:40000
Cons ci ratio: 1.390947e-02	ci left: 6.604004e-01	ci right 6.696756e-01	k: 26602	n:40000
KS ci ratio: 8.716774e-02	ci left: 4.602343e-02	ci right 5.024248e-02	k: 1924	n:40000
FOXO1   40000 perm   8 sec   (4952 perm/sec)   p_kst 4.810000e-02   p_cons 6.650500e-01   p_joint 4.810000e-02

Outputting figure to mutsig2_images.part000000000066/FOXO1.2_1976_40000_0.0481_0.66505_0.0481.png
                gene_name: FOXO1
               theta_stop: 0.087 
                    nperm: 40000 
                     p_ks: 0.048 
        ci_ks_bounds_left: 0.046 
       ci_ks_bounds_right: 0.050 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.67 
                  p_joint: 0.048 
     ci_joint_bounds_left: 0.046 
    ci_joint_bounds_right: 0.050 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000066
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 66 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4398004: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000067> was used as the working directory.
Started at Wed Oct 24 16:12:04 2012
Results reported at Wed Oct 24 16:14:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000067.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000067.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 67  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000067.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    157.28 sec.
    Max Memory :      1460 MB
    Max Swap   :      3926 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
67
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 67
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 67: processing genes 5922 - 6011
Calculating significance of each gene.
Using projection method.
5922	FPR1	1
5923	FPR2	1
5924	FPR3	1
5925	FRA10AC1	1
5926	FRAS1	1.121047e-01
5927	FREM1	1.689630e-01
5928	FREM2	5.803964e-01
5929	FRG1	1
5930	FRG2B	7.018428e-02
5931	FRK	1
5932	FRMD1	1
5933	FRMD3	1
5934	FRMD4A	1
5935	FRMD4B	8.954407e-02
5936	FRMD5	1.456887e-01
5937	FRMD6	1
5938	FRMD7	1
5939	FRMD8	1
5940	FRMPD1	1
5941	FRMPD2	4.755676e-02
5942	FRMPD4	3.804377e-01
5943	FRRS1	1
5944	FRS2	1
5945	FRS3	1
5946	FRY	3.311855e-01
5947	FRYL	6.102258e-01
5948	FRZB	1
5949	FSCB	1
5950	FSCN1	1
5951	FSCN3	1
5952	FSD1	2.383233e-01
5953	FSD2	1
5954	FSHB	1
5955	FSHR	1
5956	FSIP1	1
5957	FST	1
5958	FSTL1	9.125527e-02
5959	FSTL3	1
5960	FSTL4	1
5961	FSTL5	3.631854e-01
5962	FTCD	1
5963	FTH1	1
5964	FTHL17	1
5965	FTL	1.037309e-01
5966	FTMT	1
5967	FTO	1
5968	FTSJ1	1
5969	FTSJ2	1
5970	FTSJ3	1
5971	FTSJD1	1
5972	FTSJD2	1
5973	FUBP1	1
5974	FUBP3	1
5975	FUCA1	1
5976	FUCA2	1
5977	FUK	1
5978	FUNDC1	1
5979	FUNDC2	1
5980	FURIN	1
5981	FUS	1
5982	FUT1	1
5983	FUT10	1.121902e-01
5984	FUT11	1
5985	FUT2	1
5986	FUT3	1.751803e-01
5987	FUT4	1
5988	FUT5	1.079711e-01
5989	FUT6	1
5990	FUT7	1
5991	FUT8	1
5992	FUT9	1
5993	FUZ	1
5994	FXC1	1
5995	FXN	1
5996	FXR1	1.055093e-01
5997	FXR2	1
5998	FXYD1	1
5999	FXYD3	1
6000/17942 6000	FXYD4	1
6001	FXYD5	1
6002	FXYD6	1
6003	FXYD7	1
6004	FYB	1
6005	FYCO1	3.897500e-01
6006	FYN	1
6007	FYTTD1	1
6008	FZD1	1.394398e-01
6009	FZD10	1
6010	FZD2	1
6011	FZD3	1
Done

Running MutSig 2:
Scatter job 67: processing genes 5922 - 6011
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FRAS1
Processing conservation and coverage...
80% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.533675e-02	ci left: 4.179754e-01	ci right 4.374667e-01	k: 4277	n:10000
Cons ci ratio: 2.321103e-02	ci left: 7.316880e-01	ci right 7.489718e-01	k: 7404	n:10000
KS ci ratio: 8.438058e-02	ci left: 1.699576e-01	ci right 1.850308e-01	k: 1774	n:10000
FRAS1   10000 perm   3 sec   (3257 perm/sec)   p_kst 1.774000e-01   p_cons 7.404000e-01   p_joint 4.277000e-01

Outputting figure to mutsig2_images.part000000000067/FRAS1.4_12410_10000_0.1774_0.7404_0.4277.png
                gene_name: FRAS1
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 25 percent done.
FREM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.556068e-02	ci left: 5.386835e-01	ci right 5.582883e-01	k: 5485	n:10000
KS ci ratio: 3.621153e-02	ci left: 5.296705e-01	ci right 5.493065e-01	k: 5395	n:10000
FREM1   10000 perm   2 sec   (4728 perm/sec)   p_kst 5.395000e-01   p_cons 5.485000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000067/FREM1.2_6734_10000_0.5395_0.5485_1.png
                gene_name: FREM1
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
FRMPD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.391342e-03	ci left: 9.853418e-01	ci right 9.897674e-01	k: 9877	n:10000
Cons ci ratio: 2.914909e-02	ci left: 6.344240e-01	ci right 6.532922e-01	k: 6439	n:10000
KS ci ratio: 3.116972e-02	ci left: 6.029702e-01	ci right 6.221641e-01	k: 6126	n:10000
FRMPD2   10000 perm   2 sec   (5369 perm/sec)   p_kst 6.126000e-01   p_cons 6.439000e-01   p_joint 9.877000e-01

Outputting figure to mutsig2_images.part000000000067/FRMPD2.2_4046_10000_0.6126_0.6439_0.9877.png
                gene_name: FRMPD2
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 75 percent done.
FRY
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.377591e-03	ci left: 9.522126e-01	ci right 9.603189e-01	k: 9564	n:10000
Cons ci ratio: 3.879644e-02	ci left: 4.952504e-01	ci right 5.149466e-01	k: 5051	n:10000
KS ci ratio: 1.851014e-02	ci left: 8.099906e-01	ci right 8.252239e-01	k: 8177	n:10000
FRY   10000 perm   3 sec   (3765 perm/sec)   p_kst 8.177000e-01   p_cons 5.051000e-01   p_joint 9.564000e-01

Outputting figure to mutsig2_images.part000000000067/FRY.2_9286_10000_0.8177_0.5051_0.9564.png
                gene_name: FRY
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000067
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 67 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4398006: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000068> was used as the working directory.
Started at Wed Oct 24 16:12:04 2012
Results reported at Wed Oct 24 16:13:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000068.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000068.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 68  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000068.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     72.73 sec.
    Max Memory :       986 MB
    Max Swap   :      3792 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
68
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 68
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 68: processing genes 6012 - 6100
Calculating significance of each gene.
Using projection method.
6012	FZD4	1
6013	FZD5	1
6014	FZD6	1
6015	FZD7	1
6016	FZD8	1
6017	FZD9	1
6018	FZR1	1
6019	G0S2	1
6020	G2E3	1
6021	G3BP1	1
6022	G3BP2	1
6023	G6PC	1
6024	G6PC2	1
6025	G6PC3	1
6026	G6PD	1
6027	GAA	1
6028	GAB1	1
6029	GAB2	1
6030	GAB3	1.980079e-01
6031	GAB4	1
6032	GABARAP	1
6033	GABARAPL1	1
6034	GABARAPL2	1
6035	GABBR1	2.565078e-01
6036	GABBR2	1
6037	GABPA	1
6038	GABPB1	1.946539e-01
6039	GABPB2	1
6040	GABRA1	5.962007e-02
6041	GABRA2	2.434304e-02
6042	GABRA3	1
6043	GABRA4	1
6044	GABRA5	1
6045	GABRA6	1
6046	GABRB1	1
6047	GABRB2	1
6048	GABRB3	1
6049	GABRD	1
6050	GABRE	1
6051	GABRG1	2.434149e-02
6052	GABRG2	1.713425e-01
6053	GABRG3	1.513332e-01
6054	GABRP	1.044867e-01
6055	GABRQ	1
6056	GABRR1	1.667951e-01
6057	GABRR2	1
6058	GABRR3	1.766182e-01
6059	GAD1	1
6060	GAD2	1
6061	GADD45A	1
6062	GADD45B	4.511275e-02
6063	GADD45G	1
6064	GADD45GIP1	1
6065	GADL1	1.459910e-01
6066	GAGE1	1
6067	GAGE10	1
6068	GAGE2B	1
6069	GAGE2C	1
6070	GAK	1
6071	GAL	2.089113e-02
6072	GAL3ST1	1
6073	GAL3ST2	1
6074	GAL3ST3	1
6075	GAL3ST4	6.751992e-02
6076	GALC	1
6077	GALE	1
6078	GALK1	1
6079	GALK2	1
6080	GALM	1
6081	GALNS	1
6082	GALNT1	1
6083	GALNT10	1
6084	GALNT11	1
6085	GALNT12	1
6086	GALNT13	1
6087	GALNT14	2.808576e-01
6088	GALNT2	1
6089	GALNT3	1
6090	GALNT4	1
6091	GALNT5	3.707929e-02
6092	GALNT6	1
6093	GALNT7	1
6094	GALNT8	1
6095	GALNT9	1
6096	GALNTL1	1
6097	GALNTL2	1
6098	GALNTL4	1
6099	GALNTL5	2.114441e-01
6100	GALNTL6	2.399013e-02
Done

Running MutSig 2:
Scatter job 68: processing genes 6012 - 6100
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GABRB3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.677346e-02	ci left: 2.476661e-01	ci right 2.648761e-01	k: 2562	n:10000
KS ci ratio: 3.616056e-02	ci left: 5.303714e-01	ci right 5.500052e-01	k: 5402	n:10000
GABRB3   10000 perm   2 sec   (6352 perm/sec)   p_kst 5.402000e-01   p_cons 2.562000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000068/GABRB3.2_1542_10000_0.5402_0.2562_1.png
                gene_name: GABRB3
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
GALNT5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.098128e-02	ci left: 9.220356e-01	ci right 9.323139e-01	k: 9273	n:10000
KS ci ratio: 3.015439e-02	ci left: 6.186415e-01	ci right 6.376837e-01	k: 6282	n:10000
GALNT5   10000 perm   2 sec   (6289 perm/sec)   p_kst 6.282000e-01   p_cons 9.273000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000068/GALNT5.2_2863_10000_0.6282_0.9273_1.png
                gene_name: GALNT5
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
GALNTL6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.321103e-02	ci left: 7.316880e-01	ci right 7.489718e-01	k: 7404	n:10000
KS ci ratio: 1.157215e-02	ci left: 9.144065e-01	ci right 9.251474e-01	k: 9199	n:10000
GALNTL6   10000 perm   1 sec   (6681 perm/sec)   p_kst 9.199000e-01   p_cons 7.404000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000068/GALNTL6.2_1854_10000_0.9199_0.7404_1.png
                gene_name: GALNTL6
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.75 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000068
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 68 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1430>
Subject: Job 4398009: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1430>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000069> was used as the working directory.
Started at Wed Oct 24 16:12:09 2012
Results reported at Wed Oct 24 16:14:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000069.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000069.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 69  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000069.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    209.26 sec.
    Max Memory :      1270 MB
    Max Swap   :      4019 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
69
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 69
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 69: processing genes 6101 - 6190
Calculating significance of each gene.
Using projection method.
6101	GALP	1
6102	GALR1	1
6103	GALR2	1
6104	GALR3	1
6105	GALT	1
6106	GAMT	1
6107	GAN	2.189791e-01
6108	GANAB	6.833835e-02
6109	GANC	1
6110	GAP43	1
6111	GAPDH	1.072864e-01
6112	GAPDHS	1
6113	GAPT	1
6114	GAPVD1	1
6115	GAR1	1
6116	GARNL3	1
6117	GARS	2.671896e-01
6118	GART	1
6119	GAS2	1
6120	GAS2L1	1
6121	GAS2L2	1
6122	GAS2L3	1
6123	GAS6	1
6124	GAS7	1
6125	GAS8	1
6126	GAST	1
6127	GATA1	1.881739e-01
6128	GATA2	2.268688e-02
6129	GATA3	1
6130	GATA4	1
6131	GATA5	1
6132	GATA6	1
6133	GATAD1	1
6134	GATAD2A	1
6135	GATAD2B	1
6136	GATC	1
6137	GATM	1
6138	GATS	1
6139	GATSL3	1
6140	GBA	1
6141	GBA2	1
6142	GBA3	1
6143	GBAS	1
6144	GBE1	1
6145	GBF1	5.582250e-01
6146	GBGT1	1
6147	GBP1	1
6148	GBP2	1
6149	GBP3	1
6150	GBP4	8.586549e-02
6151	GBP5	1
6152	GBP6	2.556663e-01
6153	GBP7	1
6154	GBX1	1
6155	GBX2	1
6156	GC	1
6157	GCA	1
6158	GCAT	1
6159	GCC1	1
6160	GCC2	1
6161	GCDH	9.284687e-02
6162	GCET2	1
6163	GCFC1	1
6164	GCG	5.253925e-02
6165	GCH1	1
6166	GCHFR	1
6167	GCK	1
6168	GCKR	1
6169	GCLC	1
6170	GCLM	1
6171	GCM1	1
6172	GCM2	5.147670e-02
6173	GCN1L1	3.713542e-01
6174	GCNT1	1
6175	GCNT2	1
6176	GCNT3	1.297329e-01
6177	GCNT4	1
6178	GCOM1	1
6179	GCSH	1
6180	GDA	1
6181	GDAP1	1
6182	GDAP1L1	3.311375e-02
6183	GDAP2	1
6184	GDE1	1
6185	GDF10	1
6186	GDF11	1
6187	GDF15	1
6188	GDF2	1
6189	GDF3	1
6190	GDF5	2.319116e-01
Done

Running MutSig 2:
Scatter job 69: processing genes 6101 - 6190
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GCN1L1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.559642e-02	ci left: 2.038267e-01	ci right 2.199415e-01	k: 2118	n:10000
Cons ci ratio: 1.819913e-02	ci left: 8.150708e-01	ci right 8.301408e-01	k: 8227	n:10000
KS ci ratio: 8.162590e-02	ci left: 1.796951e-01	ci right 1.950875e-01	k: 1873	n:10000
GCN1L1   10000 perm   3 sec   (3416 perm/sec)   p_kst 1.873000e-01   p_cons 8.227000e-01   p_joint 2.118000e-01

Outputting figure to mutsig2_images.part000000000069/GCN1L1.3_8248_10000_0.1873_0.8227_0.2118.png
                gene_name: GCN1L1
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 50 percent done.
GANAB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.937393e-02	ci left: 7.957771e-01	ci right 8.114456e-01	k: 8037	n:10000
Cons ci ratio: 2.396016e-02	ci left: 7.191628e-01	ci right 7.367042e-01	k: 7280	n:10000
KS ci ratio: 1.172700e-01	ci left: 9.457666e-02	ci right 1.064572e-01	k: 1004	n:10000
GANAB   10000 perm   2 sec   (5406 perm/sec)   p_kst 1.004000e-01   p_cons 7.280000e-01   p_joint 8.037000e-01

Joint ci ratio: 1.502944e-02	ci left: 7.669283e-01	ci right 7.785923e-01	k: 15456	n:20000
Cons ci ratio: 1.771671e-02	ci left: 7.036058e-01	ci right 7.162331e-01	k: 14199	n:20000
KS ci ratio: 8.301585e-02	ci left: 9.612099e-02	ci right 1.044956e-01	k: 2005	n:20000
GANAB   20000 perm   4 sec   (4831 perm/sec)   p_kst 1.002500e-01   p_cons 7.099500e-01   p_joint 7.728000e-01

Outputting figure to mutsig2_images.part000000000069/GANAB.2_3001_20000_0.10025_0.70995_0.7728.png
                gene_name: GANAB
               theta_stop: 0.083 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.096 
       ci_ks_bounds_right: 0.10 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.78 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000069
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 69 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1428>
Subject: Job 4398014: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000070> was used as the working directory.
Started at Wed Oct 24 16:12:09 2012
Results reported at Wed Oct 24 16:14:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000070.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000070.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 70  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000070.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    203.20 sec.
    Max Memory :      1373 MB
    Max Swap   :      3959 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
70
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 70
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 70: processing genes 6191 - 6280
Calculating significance of each gene.
Using projection method.
6191	GDF6	1
6192	GDF7	1
6193	GDF9	1
6194	GDI1	1.645878e-01
6195	GDI2	1
6196	GDNF	1
6197	GDPD1	1
6198	GDPD2	1
6199	GDPD3	1
6200	GDPD4	1
6201	GDPD5	1
6202	GEFT	1
6203	GEM	1
6204	GEMIN4	2.172575e-01
6205	GEMIN5	1
6206	GEMIN6	1
6207	GEMIN7	1
6208	GEMIN8	1
6209	GEN1	1
6210	GET4	1
6211	GFAP	1
6212	GFER	1
6213	GFI1	1
6214	GFI1B	1
6215	GFM1	1
6216	GFM2	1
6217	GFOD1	1
6218	GFOD2	1
6219	GFPT1	2.474259e-01
6220	GFPT2	1.910786e-01
6221	GFRA1	1
6222	GFRA2	1
6223	GFRA3	1
6224	GFRAL	1
6225	GGA1	1
6226	GGA2	1
6227	GGA3	1
6228	GGCT	1
6229	GGCX	1
6230	GGH	4.152706e-03
6231	GGN	1
6232	GGNBP2	1
6233	GGPS1	1
6234	GGT1	1
6235	GGT5	1
6236	GGT6	1
6237	GGT7	1
6238	GGTLC1	1
6239	GGTLC2	1
6240	GH1	1
6241	GH2	1
6242	GHDC	1.878389e-01
6243	GHITM	1
6244	GHR	1
6245	GHRH	1
6246	GHRHR	1
6247	GHRL	1
6248	GHSR	1
6249	GIF	8.557447e-02
6250	GIGYF1	3.241303e-01
6251	GIGYF2	5.094056e-01
6252	GIMAP1	1
6253	GIMAP2	1
6254	GIMAP4	1
6255	GIMAP5	1
6256	GIMAP6	1
6257	GIMAP7	1
6258	GIMAP8	1.965436e-01
6259	GIN1	1
6260	GINS1	1
6261	GINS2	1
6262	GINS3	6.647988e-02
6263	GINS4	1
6264	GIP	1
6265	GIPC1	1
6266	GIPC2	1
6267	GIPC3	1
6268	GIPR	1
6269	GIT1	1
6270	GIT2	1
6271	GJA1	1.899337e-01
6272	GJA10	1
6273	GJA3	1
6274	GJA4	1
6275	GJA5	1
6276	GJA8	1
6277	GJA9	1
6278	GJB1	1
6279	GJB2	1.317742e-02
6280	GJB3	1
Done

Running MutSig 2:
Scatter job 70: processing genes 6191 - 6280
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GEMIN4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.419274e-02	ci left: 3.340900e-01	ci right 3.528013e-01	k: 3434	n:10000
Cons ci ratio: 7.327604e-02	ci left: 2.142811e-01	ci right 2.306809e-01	k: 2224	n:10000
KS ci ratio: 1.512887e-02	ci left: 8.636592e-01	ci right 8.769242e-01	k: 8704	n:10000
GEMIN4   10000 perm   2 sec   (4866 perm/sec)   p_kst 8.704000e-01   p_cons 2.224000e-01   p_joint 3.434000e-01

Outputting figure to mutsig2_images.part000000000070/GEMIN4.2_3185_10000_0.8704_0.2224_0.3434.png
                gene_name: GEMIN4
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.35 

Current progress: 50 percent done.
GGH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.476979e-01	ci left: 6.092108e-02	ci right 7.073370e-02	k: 657	n:10000
Cons ci ratio: 1.812101e-01	ci left: 4.063733e-02	ci right 4.883054e-02	k: 446	n:10000
KS ci ratio: 7.959375e-02	ci left: 1.873727e-01	ci right 2.030052e-01	k: 1951	n:10000
GGH   10000 perm   2 sec   (6661 perm/sec)   p_kst 1.951000e-01   p_cons 4.460000e-02   p_joint 6.570000e-02

Joint ci ratio: 1.631610e-01	ci left: 2.575746e-02	ci right 3.038111e-02	k: 560	n:20000
Cons ci ratio: 1.327092e-01	ci left: 3.901975e-02	ci right 4.461445e-02	k: 835	n:20000
KS ci ratio: 5.576779e-02	ci left: 1.925459e-01	ci right 2.036420e-01	k: 3961	n:20000
GGH   20000 perm   3 sec   (5744 perm/sec)   p_kst 1.980500e-01   p_cons 4.175000e-02   p_joint 2.800000e-02

Joint ci ratio: 1.434081e-01	ci left: 2.255495e-02	ci right 2.607133e-02	k: 728	n:30000
Cons ci ratio: 1.069412e-01	ci left: 4.056979e-02	ci right 4.518594e-02	k: 1285	n:30000
KS ci ratio: 4.546287e-02	ci left: 1.940652e-01	ci right 2.031266e-01	k: 5957	n:30000
GGH   30000 perm   6 sec   (5378 perm/sec)   p_kst 1.985667e-01   p_cons 4.283333e-02   p_joint 2.426667e-02

Joint ci ratio: 1.564608e-01	ci left: 1.424009e-02	ci right 1.668099e-02	k: 617	n:40000
Cons ci ratio: 9.343317e-02	ci left: 4.017727e-02	ci right 4.413955e-02	k: 1685	n:40000
KS ci ratio: 3.938445e-02	ci left: 1.945758e-01	ci right 2.024180e-01	k: 7939	n:40000
GGH   40000 perm   8 sec   (5142 perm/sec)   p_kst 1.984750e-01   p_cons 4.212500e-02   p_joint 1.542500e-02

Joint ci ratio: 1.418673e-01	ci left: 1.397209e-02	ci right 1.612475e-02	k: 751	n:50000
Cons ci ratio: 8.368342e-02	ci left: 4.027802e-02	ci right 4.381539e-02	k: 2101	n:50000
KS ci ratio: 3.529313e-02	ci left: 1.943955e-01	ci right 2.013996e-01	k: 9894	n:50000
GGH   50000 perm   10 sec   (5026 perm/sec)   p_kst 1.978800e-01   p_cons 4.202000e-02   p_joint 1.502000e-02

Joint ci ratio: 1.241920e-01	ci left: 1.531806e-02	ci right 1.736244e-02	k: 979	n:60000
Cons ci ratio: 7.643024e-02	ci left: 4.039247e-02	ci right 4.361868e-02	k: 2519	n:60000
KS ci ratio: 3.218938e-02	ci left: 1.949834e-01	ci right 2.013791e-01	k: 11890	n:60000
GGH   60000 perm   12 sec   (4913 perm/sec)   p_kst 1.981667e-01   p_cons 4.198333e-02   p_joint 1.631667e-02

Joint ci ratio: 1.150478e-01	ci left: 1.537490e-02	ci right 1.726550e-02	k: 1141	n:70000
Cons ci ratio: 7.079845e-02	ci left: 4.046974e-02	ci right 4.345410e-02	k: 2936	n:70000
KS ci ratio: 2.980941e-02	ci left: 1.951386e-01	ci right 2.010578e-01	k: 13866	n:70000
GGH   70000 perm   15 sec   (4802 perm/sec)   p_kst 1.980857e-01   p_cons 4.194286e-02   p_joint 1.630000e-02

Joint ci ratio: 1.070825e-01	ci left: 1.559207e-02	ci right 1.736825e-02	k: 1317	n:80000
Cons ci ratio: 6.610855e-02	ci left: 4.070651e-02	ci right 4.350182e-02	k: 3367	n:80000
KS ci ratio: 2.786772e-02	ci left: 1.955169e-01	ci right 2.010550e-01	k: 15862	n:80000
GGH   80000 perm   17 sec   (4692 perm/sec)   p_kst 1.982750e-01   p_cons 4.208750e-02   p_joint 1.646250e-02

Joint ci ratio: 1.009498e-01	ci left: 1.564530e-02	ci right 1.731941e-02	k: 1482	n:90000
Cons ci ratio: 6.263907e-02	ci left: 4.039228e-02	ci right 4.301514e-02	k: 3752	n:90000
KS ci ratio: 2.627750e-02	ci left: 1.956329e-01	ci right 2.008532e-01	k: 17841	n:90000
GGH   90000 perm   20 sec   (4595 perm/sec)   p_kst 1.982333e-01   p_cons 4.168889e-02   p_joint 1.646667e-02

Joint ci ratio: 9.585157e-02	ci left: 1.566092e-02	ci right 1.724731e-02	k: 1644	n:100000
Cons ci ratio: 5.949916e-02	ci left: 4.036089e-02	ci right 4.284579e-02	k: 4159	n:100000
KS ci ratio: 2.485123e-02	ci left: 1.967582e-01	ci right 2.017193e-01	k: 19923	n:100000
GGH   100000 perm   22 sec   (4496 perm/sec)   p_kst 1.992300e-01   p_cons 4.159000e-02   p_joint 1.644000e-02

Outputting figure to mutsig2_images.part000000000070/GGH.2_993_100000_0.19923_0.04159_0.01644.png
                gene_name: GGH
               theta_stop: 0.096 
                    nperm: 100000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.042 
      ci_cons_bounds_left: 0.040 
     ci_cons_bounds_right: 0.043 
                  p_joint: 0.016 
     ci_joint_bounds_left: 0.016 
    ci_joint_bounds_right: 0.017 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000070
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 70 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1705>
Subject: Job 4398019: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000071> was used as the working directory.
Started at Wed Oct 24 16:12:09 2012
Results reported at Wed Oct 24 16:14:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000071.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000071.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 71  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000071.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    138.49 sec.
    Max Memory :      1215 MB
    Max Swap   :      4019 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
71
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 71
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 71: processing genes 6281 - 6369
Calculating significance of each gene.
Using projection method.
6281	GJB4	1
6282	GJB5	1
6283	GJB6	1
6284	GJB7	1
6285	GJC1	1.248596e-01
6286	GJC2	1
6287	GJC3	1
6288	GJD2	1
6289	GJD4	1
6290	GK	3.169990e-02
6291	GK2	1
6292	GK5	3.412583e-03
6293	GKAP1	1
6294	GKN1	1
6295	GKN2	1
6296	GLA	1.258759e-01
6297	GLB1	1
6298	GLB1L	1
6299	GLB1L2	1
6300	GLB1L3	1
6301	GLCCI1	1
6302	GLCE	1
6303	GLDC	1.413623e-02
6304	GLDN	1
6305	GLE1	1.020628e-01
6306	GLG1	2.745818e-02
6307	GLI1	3.584686e-01
6308	GLI2	1.936449e-01
6309	GLI3	3.362552e-01
6310	GLI4	1
6311	GLIPR1	1
6312	GLIPR1L1	1
6313	GLIPR1L2	1
6314	GLIPR2	1
6315	GLIS1	1
6316	GLIS2	1
6317	GLIS3	1
6318	GLMN	1
6319	GLO1	1
6320	GLOD4	1
6321	GLOD5	1
6322	GLP1R	1
6323	GLP2R	1
6324	GLRA1	1
6325	GLRA2	1.087161e-01
6326	GLRA3	1.012532e-01
6327	GLRA4	7.611845e-02
6328	GLRB	1
6329	GLRX	1
6330	GLRX2	1
6331	GLRX3	1
6332	GLRX5	1
6333	GLS	1
6334	GLS2	1
6335	GLT1D1	2.647259e-02
6336	GLT25D1	1
6337	GLT25D2	1
6338	GLT6D1	1
6339	GLT8D1	1
6340	GLT8D2	1
6341	GLTP	1
6342	GLTPD1	1
6343	GLTPD2	1
6344	GLTSCR2	1.236268e-01
6345	GLUD1	1
6346	GLUD2	1
6347	GLUL	1
6348	GLYAT	1
6349	GLYATL1	1
6350	GLYATL2	1
6351	GLYCTK	1
6352	GLYR1	1
6353	GM2A	1
6354	GMCL1	1
6355	GMDS	1.783062e-01
6356	GMEB1	1
6357	GMEB2	1
6358	GMFB	1
6359	GMFG	1
6360	GMIP	1
6361	GML	1
6362	GMNN	1
6363	GMPPA	1
6364	GMPPB	1
6365	GMPR	1.639354e-01
6366	GMPR2	1
6367	GMPS	2.770280e-01
6368	GNA11	1.407837e-01
6369	GNA12	1
Done

Running MutSig 2:
Scatter job 71: processing genes 6281 - 6369
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GLG1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.240382e-01	ci left: 8.514113e-02	ci right 9.649855e-02	k: 907	n:10000
Cons ci ratio: 1.284434e-01	ci left: 7.970251e-02	ci right 9.074052e-02	k: 851	n:10000
KS ci ratio: 1.388648e-01	ci left: 6.865367e-02	ci right 7.899624e-02	k: 737	n:10000
GLG1   10000 perm   2 sec   (5185 perm/sec)   p_kst 7.370000e-02   p_cons 8.510000e-02   p_joint 9.070000e-02

Joint ci ratio: 8.887212e-02	ci left: 8.469674e-02	ci right 9.262332e-02	k: 1772	n:20000
Cons ci ratio: 9.126482e-02	ci left: 8.058298e-02	ci right 8.833833e-02	k: 1688	n:20000
KS ci ratio: 9.899308e-02	ci left: 6.909005e-02	ci right 7.633477e-02	k: 1453	n:20000
GLG1   20000 perm   6 sec   (3301 perm/sec)   p_kst 7.265000e-02   p_cons 8.440000e-02   p_joint 8.860000e-02

Outputting figure to mutsig2_images.part000000000071/GLG1.3_3724_20000_0.07265_0.0844_0.0886.png
                gene_name: GLG1
               theta_stop: 0.099 
                    nperm: 20000 
                     p_ks: 0.073 
        ci_ks_bounds_left: 0.069 
       ci_ks_bounds_right: 0.076 
                   p_cons: 0.084 
      ci_cons_bounds_left: 0.081 
     ci_cons_bounds_right: 0.088 
                  p_joint: 0.089 
     ci_joint_bounds_left: 0.085 
    ci_joint_bounds_right: 0.093 

Current progress: 25 percent done.
GK5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.627086e-03	ci left: 9.769554e-01	ci right 9.825602e-01	k: 9799	n:10000
Cons ci ratio: 4.248217e-02	ci left: 4.499948e-01	ci right 4.696286e-01	k: 4598	n:10000
KS ci ratio: 4.046880e-02	ci left: 4.741611e-01	ci right 4.938483e-01	k: 4840	n:10000
GK5   10000 perm   2 sec   (6214 perm/sec)   p_kst 4.840000e-01   p_cons 4.598000e-01   p_joint 9.799000e-01

Outputting figure to mutsig2_images.part000000000071/GK5.2_1654_10000_0.484_0.4598_0.9799.png
                gene_name: GK5
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 50 percent done.
GLDC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.140372e-02	ci left: 4.627741e-01	ci right 4.824419e-01	k: 4726	n:10000
KS ci ratio: 2.452213e-03	ci left: 9.947879e-01	ci right 9.973095e-01	k: 9962	n:10000
GLDC   10000 perm   2 sec   (5603 perm/sec)   p_kst 9.962000e-01   p_cons 4.726000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000071/GLDC.2_3163_10000_0.9962_0.4726_1.png
                gene_name: GLDC
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 1.00 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 1.00 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
GLIS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.038068e-02	ci left: 6.151246e-01	ci right 6.342027e-01	k: 6247	n:10000
Cons ci ratio: 4.810093e-02	ci left: 3.893828e-01	ci right 4.086761e-01	k: 3990	n:10000
KS ci ratio: 1.236641e-01	ci left: 8.562704e-02	ci right 9.701233e-02	k: 912	n:10000
GLIS2   10000 perm   2 sec   (6594 perm/sec)   p_kst 9.120000e-02   p_cons 3.990000e-01   p_joint 6.247000e-01

Joint ci ratio: 2.363212e-02	ci left: 5.721716e-01	ci right 5.859055e-01	k: 11581	n:20000
Cons ci ratio: 3.411881e-02	ci left: 3.907578e-01	ci right 4.043720e-01	k: 7951	n:20000
KS ci ratio: 8.749820e-02	ci left: 8.719570e-02	ci right 9.522361e-02	k: 1823	n:20000
GLIS2   20000 perm   3 sec   (5870 perm/sec)   p_kst 9.115000e-02   p_cons 3.975500e-01   p_joint 5.790500e-01

Outputting figure to mutsig2_images.part000000000071/GLIS2.2_1599_20000_0.09115_0.39755_0.57905.png
                gene_name: GLIS2
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.091 
        ci_ks_bounds_left: 0.087 
       ci_ks_bounds_right: 0.095 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000071
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 71 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4398024: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000072> was used as the working directory.
Started at Wed Oct 24 16:12:19 2012
Results reported at Wed Oct 24 16:14:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000072.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000072.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 72  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000072.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    128.30 sec.
    Max Memory :      1072 MB
    Max Swap   :      3877 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
72
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 72
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 72: processing genes 6370 - 6459
Calculating significance of each gene.
Using projection method.
6370	GNA13	1.596599e-01
6371	GNA14	1
6372	GNA15	1
6373	GNAI1	1
6374	GNAI2	4.509895e-02
6375	GNAI3	1
6376	GNAL	1
6377	GNAO1	1
6378	GNAQ	1
6379	GNAS	1
6380	GNAT1	1.039783e-01
6381	GNAT2	1
6382	GNAT3	1
6383	GNAZ	1
6384	GNB1	1
6385	GNB1L	1
6386	GNB2	1
6387	GNB2L1	1.458089e-02
6388	GNB3	1.656115e-01
6389	GNB4	1
6390	GNB5	1
6391	GNE	1
6392	GNG10	1
6393	GNG11	1
6394	GNG12	1
6395	GNG13	1
6396	GNG2	1
6397	GNG3	1
6398	GNG4	1
6399	GNG5	1
6400	GNG7	1
6401	GNG8	1
6402	GNGT1	1
6403	GNGT2	1
6404	GNL1	2.824293e-01
6405	GNL2	1
6406	GNL3	1
6407	GNL3L	1
6408	GNLY	1
6409	GNMT	1
6410	GNPAT	1.109679e-01
6411	GNPDA1	1
6412	GNPDA2	1
6413	GNPNAT1	1
6414	GNPTAB	2.491362e-01
6415	GNPTG	1
6416	GNRH1	1
6417	GNRH2	1
6418	GNRHR	1
6419	GNS	1.730664e-01
6420	GOLGA1	1
6421	GOLGA2	1
6422	GOLGA2B	1
6423	GOLGA3	1
6424	GOLGA4	1
6425	GOLGA5	1
6426	GOLGA6A	1
6427	GOLGA6B	1
6428	GOLGA7	1
6429	GOLGA7B	1
6430	GOLGB1	9.936748e-02
6431	GOLIM4	1
6432	GOLM1	1
6433	GOLPH3	1
6434	GOLPH3L	1
6435	GOLT1A	1
6436	GOLT1B	1
6437	GON4L	3.134002e-01
6438	GOPC	1
6439	GORAB	1
6440	GORASP1	1
6441	GORASP2	1
6442	GOSR1	1
6443	GOSR2	1
6444	GOT1	1
6445	GOT1L1	1
6446	GOT2	1.268794e-01
6447	GP2	1
6448	GP5	1
6449	GP6	1
6450	GP9	1
6451	GPA33	1
6452	GPAA1	1
6453	GPAM	1
6454	GPAT2	6.480938e-02
6455	GPATCH1	1
6456	GPATCH2	1.884009e-01
6457	GPATCH3	2.787905e-02
6458	GPATCH4	1
6459	GPATCH8	1
Done

Running MutSig 2:
Scatter job 72: processing genes 6370 - 6459
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GOLGB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.393873e-02	ci left: 1.412895e-01	ci right 1.553161e-01	k: 1482	n:10000
Cons ci ratio: 8.285235e-02	ci left: 1.752679e-01	ci right 1.905173e-01	k: 1828	n:10000
KS ci ratio: 9.093456e-02	ci left: 1.495278e-01	ci right 1.638728e-01	k: 1566	n:10000
GOLGB1   10000 perm   3 sec   (3763 perm/sec)   p_kst 1.566000e-01   p_cons 1.828000e-01   p_joint 1.482000e-01

Outputting figure to mutsig2_images.part000000000072/GOLGB1.4_9864_10000_0.1566_0.1828_0.1482.png
                gene_name: GOLGB1
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.16 

Current progress: 33 percent done.
GON4L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.595771e-03	ci left: 9.499184e-01	ci right 9.582145e-01	k: 9542	n:10000
Cons ci ratio: 4.626559e-02	ci left: 4.081086e-01	ci right 4.275393e-01	k: 4178	n:10000
KS ci ratio: 3.463008e-02	ci left: 5.518081e-01	ci right 5.713560e-01	k: 5616	n:10000
GON4L   10000 perm   2 sec   (4473 perm/sec)   p_kst 5.616000e-01   p_cons 4.178000e-01   p_joint 9.542000e-01

Outputting figure to mutsig2_images.part000000000072/GON4L.2_6964_10000_0.5616_0.4178_0.9542.png
                gene_name: GON4L
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 67 percent done.
GPATCH3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.733853e-02	ci left: 8.290021e-01	ci right 8.436014e-01	k: 8364	n:10000
KS ci ratio: 2.911097e-02	ci left: 6.350273e-01	ci right 6.538884e-01	k: 6445	n:10000
GPATCH3   10000 perm   1 sec   (6679 perm/sec)   p_kst 6.445000e-01   p_cons 8.364000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000072/GPATCH3.2_1606_10000_0.6445_0.8364_1.png
                gene_name: GPATCH3
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000072
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 72 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1650>
Subject: Job 4398028: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1650>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000073> was used as the working directory.
Started at Wed Oct 24 16:12:22 2012
Results reported at Wed Oct 24 16:15:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000073.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000073.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 73  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000073.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    219.71 sec.
    Max Memory :      1429 MB
    Max Swap   :      3988 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
73
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 73
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 73: processing genes 6460 - 6549
Calculating significance of each gene.
Using projection method.
6460	GPBP1	1.287776e-02
6461	GPBP1L1	1
6462	GPC1	1
6463	GPC2	1
6464	GPC3	1
6465	GPC4	1
6466	GPC5	1
6467	GPC6	1
6468	GPCPD1	3.099622e-01
6469	GPD1	1
6470	GPD1L	1
6471	GPD2	1
6472	GPER	1
6473	GPHA2	1
6474	GPHB5	1
6475	GPHN	1
6476	GPI	1
6477	GPIHBP1	1
6478	GPKOW	1.035851e-01
6479	GPLD1	1
6480	GPM6A	5.312585e-02
6481	GPM6B	1
6482	GPN1	1
6483	GPN2	1
6484	GPN3	1
6485	GPNMB	1
6486	GPR1	1
6487	GPR101	1
6488	GPR107	1
6489	GPR108	1
6490	GPR109A	1
6491	GPR109B	1
6492	GPR110	1
6493	GPR111	1
6494	GPR112	3.737047e-02
6495	GPR113	1
6496	GPR114	1
6497	GPR115	1.526039e-01
6498	GPR116	3.724532e-01
6499	GPR119	1
6500	GPR12	1
6501	GPR120	1
6502	GPR123	5.179651e-02
6503	GPR124	1
6504	GPR125	1
6505	GPR126	1.694947e-01
6506	GPR128	1.209173e-01
6507	GPR132	1
6508	GPR133	1
6509	GPR135	1
6510	GPR137	6.614415e-02
6511	GPR137B	1.330801e-01
6512	GPR137C	1.377341e-01
6513	GPR139	1
6514	GPR141	1
6515	GPR142	1
6516	GPR143	5.626762e-02
6517	GPR146	1
6518	GPR148	5.036504e-02
6519	GPR149	1
6520	GPR15	9.683394e-02
6521	GPR151	4.989309e-02
6522	GPR152	1
6523	GPR153	1.470346e-03
6524	GPR155	1.990929e-01
6525	GPR156	2.755178e-01
6526	GPR157	1
6527	GPR158	1.552967e-01
6528	GPR160	1
6529	GPR161	1
6530	GPR162	1
6531	GPR17	1
6532	GPR171	1
6533	GPR172A	1.140432e-01
6534	GPR172B	1
6535	GPR173	6.298620e-03
6536	GPR174	1
6537	GPR176	1.500446e-01
6538	GPR179	7.269809e-01
6539	GPR18	1
6540	GPR180	1
6541	GPR182	1
6542	GPR183	2.852064e-02
6543	GPR19	1
6544	GPR20	1
6545	GPR21	1
6546	GPR22	1
6547	GPR25	1
6548	GPR26	1
6549	GPR27	1
Done

Running MutSig 2:
Scatter job 73: processing genes 6460 - 6549
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GPR112
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.991394e-01	ci left: 3.357607e-02	ci right 4.109654e-02	k: 372	n:10000
Cons ci ratio: 6.746352e-02	ci left: 2.438103e-01	ci right 2.609341e-01	k: 2523	n:10000
KS ci ratio: 3.512569e-01	ci left: 1.014137e-02	ci right 1.454954e-02	k: 122	n:10000
GPR112   10000 perm   3 sec   (3987 perm/sec)   p_kst 1.220000e-02   p_cons 2.523000e-01   p_joint 3.720000e-02

Joint ci ratio: 1.050830e-01	ci left: 6.162181e-02	ci right 6.850530e-02	k: 1300	n:20000
Cons ci ratio: 4.563509e-02	ci left: 2.633100e-01	ci right 2.756571e-01	k: 5389	n:20000
KS ci ratio: 2.509773e-01	ci left: 1.053722e-02	ci right 1.360709e-02	k: 240	n:20000
GPR112   20000 perm   7 sec   (2674 perm/sec)   p_kst 1.200000e-02   p_cons 2.694500e-01   p_joint 6.500000e-02

Joint ci ratio: 8.581225e-02	ci left: 6.223591e-02	ci right 6.784869e-02	k: 1950	n:30000
Cons ci ratio: 3.712581e-02	ci left: 2.658767e-01	ci right 2.759677e-01	k: 8127	n:30000
KS ci ratio: 2.107542e-01	ci left: 1.019794e-02	ci right 1.263140e-02	k: 341	n:30000
GPR112   30000 perm   10 sec   (2872 perm/sec)   p_kst 1.136667e-02   p_cons 2.709000e-01   p_joint 6.500000e-02

Joint ci ratio: 8.550099e-02	ci left: 4.778644e-02	ci right 5.207920e-02	k: 1996	n:40000
Cons ci ratio: 3.213431e-02	ci left: 2.667728e-01	ci right 2.755104e-01	k: 10845	n:40000
KS ci ratio: 1.813164e-01	ci left: 1.050210e-02	ci right 1.261970e-02	k: 461	n:40000
GPR112   40000 perm   13 sec   (2968 perm/sec)   p_kst 1.152500e-02   p_cons 2.711250e-01   p_joint 4.990000e-02

Joint ci ratio: 8.662929e-02	ci left: 3.763322e-02	ci right 4.106052e-02	k: 1966	n:50000
Cons ci ratio: 2.875418e-02	ci left: 2.670676e-01	ci right 2.748790e-01	k: 13548	n:50000
KS ci ratio: 1.594727e-01	ci left: 1.098716e-02	ci right 1.291013e-02	k: 596	n:50000
GPR112   50000 perm   17 sec   (3006 perm/sec)   p_kst 1.192000e-02   p_cons 2.709600e-01   p_joint 3.932000e-02

Joint ci ratio: 6.991599e-02	ci left: 4.804011e-02	ci right 5.153693e-02	k: 2986	n:60000
Cons ci ratio: 2.613288e-02	ci left: 2.691559e-01	ci right 2.762995e-01	k: 16363	n:60000
KS ci ratio: 1.470816e-01	ci left: 1.083887e-02	ci right 1.257551e-02	k: 701	n:60000
GPR112   60000 perm   20 sec   (3019 perm/sec)   p_kst 1.168333e-02   p_cons 2.727167e-01   p_joint 4.976667e-02

Joint ci ratio: 7.500244e-02	ci left: 3.614675e-02	ci right 3.897747e-02	k: 2628	n:70000
Cons ci ratio: 2.419813e-02	ci left: 2.693605e-01	ci right 2.759726e-01	k: 19086	n:70000
KS ci ratio: 1.350905e-01	ci left: 1.108223e-02	ci right 1.270147e-02	k: 831	n:70000
GPR112   70000 perm   23 sec   (3018 perm/sec)   p_kst 1.187143e-02   p_cons 2.726571e-01   p_joint 3.754286e-02

Joint ci ratio: 7.628726e-02	ci left: 3.072980e-02	ci right 3.317929e-02	k: 2555	n:80000
Cons ci ratio: 2.262652e-02	ci left: 2.697281e-01	ci right 2.759134e-01	k: 21825	n:80000
KS ci ratio: 1.264908e-01	ci left: 1.111164e-02	ci right 1.262407e-02	k: 948	n:80000
GPR112   80000 perm   27 sec   (3008 perm/sec)   p_kst 1.185000e-02   p_cons 2.728125e-01   p_joint 3.193750e-02

Joint ci ratio: 7.368314e-02	ci left: 2.936433e-02	ci right 3.162162e-02	k: 2743	n:90000
Cons ci ratio: 2.132189e-02	ci left: 2.701023e-01	ci right 2.759345e-01	k: 24571	n:90000
KS ci ratio: 1.188421e-01	ci left: 1.123413e-02	ci right 1.266426e-02	k: 1074	n:90000
GPR112   90000 perm   30 sec   (2993 perm/sec)   p_kst 1.193333e-02   p_cons 2.730111e-01   p_joint 3.047778e-02

Joint ci ratio: 7.481431e-02	ci left: 2.571942e-02	ci right 2.772816e-02	k: 2671	n:100000
Cons ci ratio: 2.020697e-02	ci left: 2.706591e-01	ci right 2.761941e-01	k: 27342	n:100000
KS ci ratio: 1.119608e-01	ci left: 1.143154e-02	ci right 1.279698e-02	k: 1210	n:100000
GPR112   100000 perm   34 sec   (2976 perm/sec)   p_kst 1.210000e-02   p_cons 2.734200e-01   p_joint 2.671000e-02

Joint ci ratio: 7.611326e-02	ci left: 2.264852e-02	ci right 2.444945e-02	k: 2589	n:110000
Cons ci ratio: 1.924031e-02	ci left: 2.713295e-01	ci right 2.766097e-01	k: 30136	n:110000
KS ci ratio: 1.062311e-01	ci left: 1.157731e-02	ci right 1.288496e-02	k: 1344	n:110000
GPR112   110000 perm   37 sec   (2945 perm/sec)   p_kst 1.221818e-02   p_cons 2.739636e-01   p_joint 2.353636e-02

Joint ci ratio: 6.800658e-02	ci left: 2.602466e-02	ci right 2.786497e-02	k: 3232	n:120000
Cons ci ratio: 1.841955e-02	ci left: 2.714778e-01	ci right 2.765331e-01	k: 32880	n:120000
KS ci ratio: 1.020709e-01	ci left: 1.152154e-02	ci right 1.276887e-02	k: 1456	n:120000
GPR112   120000 perm   41 sec   (2923 perm/sec)   p_kst 1.213333e-02   p_cons 2.740000e-01   p_joint 2.693333e-02

Joint ci ratio: 6.172346e-02	ci left: 2.916269e-02	ci right 3.102758e-02	k: 3911	n:130000
Cons ci ratio: 1.768533e-02	ci left: 2.718375e-01	ci right 2.766956e-01	k: 35654	n:130000
KS ci ratio: 9.811114e-02	ci left: 1.153525e-02	ci right 1.273282e-02	k: 1576	n:130000
GPR112   130000 perm   45 sec   (2900 perm/sec)   p_kst 1.212308e-02   p_cons 2.742615e-01   p_joint 3.008462e-02

Outputting figure to mutsig2_images.part000000000073/GPR112.3_9335_130000_0.012123_0.27426_0.030085.png
                gene_name: GPR112
               theta_stop: 0.098 
                    nperm: 130000 
                     p_ks: 0.012 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.030 
     ci_joint_bounds_left: 0.029 
    ci_joint_bounds_right: 0.031 

Current progress: 20 percent done.
GPBP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.879503e-02	ci left: 8.053187e-01	ci right 8.206985e-01	k: 8131	n:10000
Cons ci ratio: 1.153651e-01	ci left: 9.749841e-02	ci right 1.095337e-01	k: 1034	n:10000
KS ci ratio: 2.066714e-02	ci left: 7.742826e-01	ci right 7.905526e-01	k: 7825	n:10000
GPBP1   10000 perm   1 sec   (6803 perm/sec)   p_kst 7.825000e-01   p_cons 1.034000e-01   p_joint 8.131000e-01

Joint ci ratio: 1.214971e-02	ci left: 8.336803e-01	ci right 8.439210e-01	k: 16777	n:20000
Cons ci ratio: 8.107548e-02	ci left: 1.003913e-01	ci right 1.089240e-01	k: 2092	n:20000
KS ci ratio: 1.458800e-02	ci left: 7.773223e-01	ci right 7.887953e-01	k: 15662	n:20000
GPBP1   20000 perm   3 sec   (5936 perm/sec)   p_kst 7.831000e-01   p_cons 1.046000e-01   p_joint 8.388500e-01

Outputting figure to mutsig2_images.part000000000073/GPBP1.2_1487_20000_0.7831_0.1046_0.83885.png
                gene_name: GPBP1
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.84 

Current progress: 40 percent done.
GPR153
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.325900e-01	ci left: 1.142242e-02	ci right 1.606722e-02	k: 136	n:10000
Cons ci ratio: 2.292716e-01	ci left: 2.513779e-02	ci right 3.174074e-02	k: 283	n:10000
KS ci ratio: 1.016747e-01	ci left: 1.227823e-01	ci right 1.360344e-01	k: 1293	n:10000
GPR153   10000 perm   2 sec   (6359 perm/sec)   p_kst 1.293000e-01   p_cons 2.830000e-02   p_joint 1.360000e-02

Joint ci ratio: 2.321934e-01	ci left: 1.241764e-02	ci right 1.572585e-02	k: 280	n:20000
Cons ci ratio: 1.613936e-01	ci left: 2.633371e-02	ci right 3.100466e-02	k: 572	n:20000
KS ci ratio: 7.295216e-02	ci left: 1.215289e-01	ci right 1.307801e-01	k: 2522	n:20000
GPR153   20000 perm   4 sec   (5549 perm/sec)   p_kst 1.261000e-01   p_cons 2.860000e-02   p_joint 1.400000e-02

Joint ci ratio: 1.852866e-01	ci left: 1.333682e-02	ci right 1.609167e-02	k: 440	n:30000
Cons ci ratio: 1.312683e-01	ci left: 2.696883e-02	ci right 3.078980e-02	k: 865	n:30000
KS ci ratio: 5.966029e-02	ci left: 1.220342e-01	ci right 1.295718e-01	k: 3773	n:30000
GPR153   30000 perm   6 sec   (5266 perm/sec)   p_kst 1.257667e-01   p_cons 2.883333e-02   p_joint 1.466667e-02

Joint ci ratio: 1.581589e-01	ci left: 1.392770e-02	ci right 1.634343e-02	k: 604	n:40000
Cons ci ratio: 1.135135e-01	ci left: 2.730436e-02	ci right 3.061450e-02	k: 1157	n:40000
KS ci ratio: 5.134698e-02	ci left: 1.238999e-01	ci right 1.304543e-01	k: 5086	n:40000
GPR153   40000 perm   8 sec   (5103 perm/sec)   p_kst 1.271500e-01   p_cons 2.892500e-02   p_joint 1.510000e-02

Joint ci ratio: 1.414857e-01	ci left: 1.404930e-02	ci right 1.620753e-02	k: 755	n:50000
Cons ci ratio: 1.000621e-01	ci left: 2.828792e-02	ci right 3.128700e-02	k: 1488	n:50000
KS ci ratio: 4.609559e-02	ci left: 1.234397e-01	ci right 1.292838e-01	k: 6317	n:50000
GPR153   50000 perm   10 sec   (4960 perm/sec)   p_kst 1.263400e-01   p_cons 2.976000e-02   p_joint 1.510000e-02

Joint ci ratio: 1.305685e-01	ci left: 1.383286e-02	ci right 1.578115e-02	k: 887	n:60000
Cons ci ratio: 9.200413e-02	ci left: 2.801393e-02	ci right 3.073185e-02	k: 1761	n:60000
KS ci ratio: 4.210036e-02	ci left: 1.235857e-01	ci right 1.289172e-01	k: 7574	n:60000
GPR153   60000 perm   12 sec   (4817 perm/sec)   p_kst 1.262333e-01   p_cons 2.935000e-02   p_joint 1.478333e-02

Joint ci ratio: 1.208239e-01	ci left: 1.391849e-02	ci right 1.572206e-02	k: 1036	n:70000
Cons ci ratio: 8.527914e-02	ci left: 2.804908e-02	ci right 3.056156e-02	k: 2050	n:70000
KS ci ratio: 3.897613e-02	ci left: 1.237909e-01	ci right 1.287259e-01	k: 8837	n:70000
GPR153   70000 perm   15 sec   (4723 perm/sec)   p_kst 1.262429e-01   p_cons 2.928571e-02   p_joint 1.480000e-02

Joint ci ratio: 1.126900e-01	ci left: 1.405969e-02	ci right 1.575075e-02	k: 1191	n:80000
Cons ci ratio: 7.963152e-02	ci left: 2.822801e-02	ci right 3.058128e-02	k: 2351	n:80000
KS ci ratio: 3.640025e-02	ci left: 1.243031e-01	ci right 1.289240e-01	k: 10128	n:80000
GPR153   80000 perm   17 sec   (4624 perm/sec)   p_kst 1.266000e-01   p_cons 2.938750e-02   p_joint 1.488750e-02

Joint ci ratio: 1.066090e-01	ci left: 1.401040e-02	ci right 1.559888e-02	k: 1331	n:90000
Cons ci ratio: 7.484454e-02	ci left: 2.846964e-02	ci right 3.069415e-02	k: 2661	n:90000
KS ci ratio: 3.437054e-02	ci left: 1.241032e-01	ci right 1.284543e-01	k: 11364	n:90000
GPR153   90000 perm   20 sec   (4532 perm/sec)   p_kst 1.262667e-01   p_cons 2.956667e-02   p_joint 1.478889e-02

Joint ci ratio: 1.010689e-01	ci left: 1.407044e-02	ci right 1.557790e-02	k: 1481	n:100000
Cons ci ratio: 7.111261e-02	ci left: 2.844030e-02	ci right 3.054711e-02	k: 2948	n:100000
KS ci ratio: 3.265084e-02	ci left: 1.239193e-01	ci right 1.280424e-01	k: 12597	n:100000
GPR153   100000 perm   23 sec   (4442 perm/sec)   p_kst 1.259700e-01   p_cons 2.948000e-02   p_joint 1.481000e-02

Joint ci ratio: 9.670323e-02	ci left: 1.400594e-02	ci right 1.543799e-02	k: 1618	n:110000
Cons ci ratio: 6.776989e-02	ci left: 2.851691e-02	ci right 3.052618e-02	k: 3246	n:110000
KS ci ratio: 3.122398e-02	ci left: 1.233670e-01	ci right 1.272891e-01	k: 13785	n:110000
GPR153   110000 perm   25 sec   (4364 perm/sec)   p_kst 1.253182e-01   p_cons 2.950909e-02   p_joint 1.470909e-02

Outputting figure to mutsig2_images.part000000000073/GPR153.2_1850_110000_0.12532_0.029509_0.014709.png
                gene_name: GPR153
               theta_stop: 0.097 
                    nperm: 110000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.030 
      ci_cons_bounds_left: 0.029 
     ci_cons_bounds_right: 0.031 
                  p_joint: 0.015 
     ci_joint_bounds_left: 0.014 
    ci_joint_bounds_right: 0.015 

Current progress: 60 percent done.
GPR173
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.901550e-02	ci left: 3.804235e-01	ci right 3.996406e-01	k: 3900	n:10000
KS ci ratio: 2.834030e-02	ci left: 6.472993e-01	ci right 6.660094e-01	k: 6567	n:10000
GPR173   10000 perm   2 sec   (6462 perm/sec)   p_kst 6.567000e-01   p_cons 3.900000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000073/GPR173.2_1126_10000_0.6567_0.39_1.png
                gene_name: GPR173
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
GPR179
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.665324e-02	ci left: 1.992924e-01	ci right 2.152785e-01	k: 2072	n:10000
Cons ci ratio: 1.232190e-01	ci left: 8.621021e-02	ci right 9.762881e-02	k: 918	n:10000
KS ci ratio: 2.838430e-02	ci left: 6.465950e-01	ci right 6.653141e-01	k: 6560	n:10000
GPR179   10000 perm   2 sec   (4494 perm/sec)   p_kst 6.560000e-01   p_cons 9.180000e-02   p_joint 2.072000e-01

Joint ci ratio: 8.643344e-02	ci left: 8.920534e-02	ci right 9.731335e-02	k: 1864	n:20000
Cons ci ratio: 8.645901e-02	ci left: 8.915632e-02	ci right 9.726239e-02	k: 1863	n:20000
KS ci ratio: 2.021626e-02	ci left: 6.461049e-01	ci right 6.593506e-01	k: 13055	n:20000
GPR179   20000 perm   5 sec   (4098 perm/sec)   p_kst 6.527500e-01   p_cons 9.315000e-02   p_joint 9.320000e-02

Outputting figure to mutsig2_images.part000000000073/GPR179.2_7148_20000_0.65275_0.09315_0.0932.png
                gene_name: GPR179
               theta_stop: 0.086 
                    nperm: 20000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.093 
      ci_cons_bounds_left: 0.089 
     ci_cons_bounds_right: 0.097 
                  p_joint: 0.093 
     ci_joint_bounds_left: 0.089 
    ci_joint_bounds_right: 0.097 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000073
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 73 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1547>
Subject: Job 4398032: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000074> was used as the working directory.
Started at Wed Oct 24 16:12:27 2012
Results reported at Wed Oct 24 16:15:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000074.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000074.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 74  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000074.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    194.23 sec.
    Max Memory :      1269 MB
    Max Swap   :      3896 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
74
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 74
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 74: processing genes 6550 - 6639
Calculating significance of each gene.
Using projection method.
6550	GPR3	1
6551	GPR31	1
6552	GPR32	1
6553	GPR34	6.736976e-02
6554	GPR35	1.419147e-01
6555	GPR37	1
6556	GPR37L1	1
6557	GPR39	1
6558	GPR4	1
6559	GPR45	1
6560	GPR50	1
6561	GPR52	1
6562	GPR55	1
6563	GPR56	1
6564	GPR6	1
6565	GPR61	3.533975e-02
6566	GPR62	1
6567	GPR63	1
6568	GPR64	4.254554e-01
6569	GPR65	1
6570	GPR68	1
6571	GPR75	1
6572	GPR77	1.147774e-01
6573	GPR78	1
6574	GPR81	1
6575	GPR82	1
6576	GPR83	1
6577	GPR84	1
6578	GPR85	1.193493e-01
6579	GPR87	1
6580	GPR89A	1
6581	GPR89B	1
6582	GPR97	1
6583	GPR98	4.714394e-01
6584	GPRASP1	4.092140e-01
6585	GPRASP2	1
6586	GPRC5A	1
6587	GPRC5B	1
6588	GPRC5C	1
6589	GPRC5D	1
6590	GPRC6A	3.855109e-01
6591	GPRIN1	3.989674e-01
6592	GPRIN2	1
6593	GPRIN3	3.033772e-01
6594	GPS1	1
6595	GPS2	1
6596	GPSM1	1
6597	GPSM2	1
6598	GPSM3	1
6599	GPT	1
6600	GPT2	6.766618e-02
6601	GPX1	1
6602	GPX2	1
6603	GPX3	1
6604	GPX4	1
6605	GPX5	1
6606	GPX6	1
6607	GPX7	1
6608	GPX8	8.697401e-02
6609	GRAMD1A	1
6610	GRAMD1B	1
6611	GRAMD1C	1
6612	GRAMD2	1.870420e-01
6613	GRAMD3	1
6614	GRAMD4	1.765940e-01
6615	GRAP2	1
6616	GRASP	1
6617	GRB10	1
6618	GRB14	1
6619	GRB2	1
6620	GRB7	1
6621	GREB1	1
6622	GREM1	1
6623	GREM2	1
6624	GRHL1	1
6625	GRHL2	1
6626	GRHL3	1
6627	GRHPR	1
6628	GRIA1	1
6629	GRIA2	1
6630	GRIA3	1
6631	GRIA4	1
6632	GRID1	4.273375e-01
6633	GRID2	1
6634	GRIK1	8.134495e-03
6635	GRIK2	1
6636	GRIK3	3.171093e-02
6637	GRIK4	1
6638	GRIK5	1
6639	GRIN1	3.229229e-02
Done

Running MutSig 2:
Scatter job 74: processing genes 6550 - 6639
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GPR98
Processing conservation and coverage...
51% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.549620e-02	ci left: 6.936335e-01	ci right 7.116483e-01	k: 7027	n:10000
KS ci ratio: 3.538158e-02	ci left: 5.411876e-01	ci right 5.607827e-01	k: 5510	n:10000
GPR98   10000 perm   6 sec   (1690 perm/sec)   p_kst 5.510000e-01   p_cons 7.027000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000074/GPR98.3_19281_10000_0.551_0.7027_1.png
                gene_name: GPR98
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
GRIK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.618673e-02	ci left: 1.639619e-01	ci right 1.788300e-01	k: 1713	n:10000
KS ci ratio: 1.512887e-02	ci left: 8.636592e-01	ci right 8.769242e-01	k: 8704	n:10000
GRIK1   10000 perm   2 sec   (5384 perm/sec)   p_kst 8.704000e-01   p_cons 1.713000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000074/GRIK1.3_2985_10000_0.8704_0.1713_1.png
                gene_name: GRIK1
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.18 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
GRIK3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.194188e-03	ci left: 9.638355e-01	ci right 9.708888e-01	k: 9675	n:10000
Cons ci ratio: 6.123146e-02	ci left: 2.817130e-01	ci right 2.996091e-01	k: 2906	n:10000
KS ci ratio: 1.316462e-02	ci left: 8.926197e-01	ci right 9.045470e-01	k: 8987	n:10000
GRIK3   10000 perm   2 sec   (5573 perm/sec)   p_kst 8.987000e-01   p_cons 2.906000e-01   p_joint 9.675000e-01

Outputting figure to mutsig2_images.part000000000074/GRIK3.2_2824_10000_0.8987_0.2906_0.9675.png
                gene_name: GRIK3
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 75 percent done.
GRIN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.827391e-02	ci left: 8.138514e-01	ci right 8.289609e-01	k: 8215	n:10000
KS ci ratio: 6.651539e-03	ci left: 9.686815e-01	ci right 9.752397e-01	k: 9721	n:10000
GRIN1   10000 perm   2 sec   (5463 perm/sec)   p_kst 9.721000e-01   p_cons 8.215000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000074/GRIN1.2_3037_10000_0.9721_0.8215_1.png
                gene_name: GRIN1
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.98 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000074
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 74 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4398035: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000075> was used as the working directory.
Started at Wed Oct 24 16:12:30 2012
Results reported at Wed Oct 24 16:14:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000075.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000075.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 75  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000075.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    135.34 sec.
    Max Memory :      1197 MB
    Max Swap   :      3930 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
75
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 75
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 75: processing genes 6640 - 6728
Calculating significance of each gene.
Using projection method.
6640	GRIN2A	1
6641	GRIN2B	1.606512e-01
6642	GRIN2C	1
6643	GRIN2D	1
6644	GRIN3A	3.664883e-01
6645	GRIN3B	1
6646	GRINA	1
6647	GRINL1A	1
6648	GRIP1	1.578372e-01
6649	GRIP2	1
6650	GRIPAP1	1
6651	GRK1	1
6652	GRK4	1
6653	GRK5	1
6654	GRK6	1
6655	GRK7	1
6656	GRLF1	3.871939e-01
6657	GRM1	1
6658	GRM2	1
6659	GRM3	1
6660	GRM4	1
6661	GRM5	1
6662	GRM6	1
6663	GRM7	1
6664	GRM8	1.012726e-01
6665	GRN	1.290342e-01
6666	GRP	1
6667	GRPEL1	1
6668	GRPEL2	1
6669	GRPR	1
6670	GRSF1	1
6671	GRTP1	1
6672	GRWD1	1
6673	GRXCR1	1
6674	GRXCR2	1
6675	GSC	1
6676	GSDMA	1
6677	GSDMB	1
6678	GSDMC	1
6679	GSDMD	1
6680	GSG1	1
6681	GSG1L	1
6682	GSG2	1
6683	GSK3A	1
6684	GSK3B	1
6685	GSN	1
6686	GSPT1	1
6687	GSPT2	2.864604e-01
6688	GSR	1
6689	GSS	1
6690	GSTA1	1
6691	GSTA2	1
6692	GSTA3	1
6693	GSTA4	1
6694	GSTA5	1
6695	GSTCD	1
6696	GSTK1	1
6697	GSTM1	1
6698	GSTM2	1
6699	GSTM3	1
6700	GSTM4	1
6701	GSTM5	1
6702	GSTO1	1
6703	GSTO2	1
6704	GSTP1	1
6705	GSTT1	9.594878e-02
6706	GSTZ1	1
6707	GSX1	2.315046e-02
6708	GSX2	1
6709	GTDC1	1
6710	GTF2A1	1
6711	GTF2A1L	1
6712	GTF2A2	1
6713	GTF2B	1
6714	GTF2E1	1
6715	GTF2E2	1
6716	GTF2F1	1
6717	GTF2F2	1
6718	GTF2H1	1
6719	GTF2H2C	1
6720	GTF2H2D	1
6721	GTF2H3	1
6722	GTF2H4	1
6723	GTF2H5	1
6724	GTF2I	1.167504e-01
6725	GTF2IRD1	3.160749e-01
6726	GTF2IRD2	1
6727	GTF2IRD2B	1
6728	GTF3A	1
Done

Running MutSig 2:
Scatter job 75: processing genes 6640 - 6728
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GRIN2B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.454018e-02	ci left: 8.725497e-01	ci right 8.854286e-01	k: 8791	n:10000
KS ci ratio: 6.100950e-02	ci left: 2.831991e-01	ci right 3.011221e-01	k: 2921	n:10000
GRIN2B   10000 perm   2 sec   (4463 perm/sec)   p_kst 2.921000e-01   p_cons 8.791000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000075/GRIN2B.2_4503_10000_0.2921_0.8791_1.png
                gene_name: GRIN2B
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.89 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
GRIP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.699905e-02	ci left: 3.118529e-01	ci right 3.302514e-01	k: 3210	n:10000
KS ci ratio: 1.869758e-01	ci left: 3.815245e-02	ci right 4.611708e-02	k: 420	n:10000
GRIP1   10000 perm   2 sec   (5786 perm/sec)   p_kst 4.200000e-02   p_cons 3.210000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 4.067717e-02	ci left: 3.106030e-01	ci right 3.235502e-01	k: 6341	n:20000
KS ci ratio: 1.342244e-01	ci left: 3.814864e-02	ci right 4.368584e-02	k: 817	n:20000
GRIP1   20000 perm   4 sec   (5119 perm/sec)   p_kst 4.085000e-02   p_cons 3.170500e-01   p_joint 1

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 3.336162e-02	ci left: 3.098778e-01	ci right 3.204247e-01	k: 9454	n:30000
KS ci ratio: 1.089940e-01	ci left: 3.907619e-02	ci right 4.361318e-02	k: 1239	n:30000
GRIP1   30000 perm   6 sec   (4789 perm/sec)   p_kst 4.130000e-02   p_cons 3.151333e-01   p_joint 1

Joint ci ratio: 9.799510e-05	ci left: 9.999078e-01	ci right 1	k: 40000	n:40000
Cons ci ratio: 2.870512e-02	ci left: 3.133873e-01	ci right 3.225392e-01	k: 12718	n:40000
KS ci ratio: 9.437205e-02	ci left: 3.939530e-02	ci right 4.332164e-02	k: 1653	n:40000
GRIP1   40000 perm   10 sec   (4089 perm/sec)   p_kst 4.132500e-02   p_cons 3.179500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000075/GRIP1.2_3327_40000_0.041325_0.31795_1.png
                gene_name: GRIP1
               theta_stop: 0.094 
                    nperm: 40000 
                     p_ks: 0.041 
        ci_ks_bounds_left: 0.039 
       ci_ks_bounds_right: 0.043 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.32 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000075
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 75 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4398038: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000076> was used as the working directory.
Started at Wed Oct 24 16:12:30 2012
Results reported at Wed Oct 24 16:14:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000076.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000076.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 76  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000076.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     93.46 sec.
    Max Memory :      1222 MB
    Max Swap   :      3936 MB

    Max Processes  :         7
    Max Threads    :        71

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
76
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 76
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 76: processing genes 6729 - 6818
Calculating significance of each gene.
Using projection method.
6729	GTF3C1	1
6730	GTF3C2	1.567600e-01
6731	GTF3C3	1
6732	GTF3C4	1
6733	GTF3C5	5.293280e-02
6734	GTF3C6	1
6735	GTPBP1	1
6736	GTPBP10	1
6737	GTPBP2	2.770677e-01
6738	GTPBP3	1
6739	GTPBP4	1
6740	GTPBP5	1
6741	GTPBP8	1
6742	GTSE1	3.846791e-02
6743	GTSF1	1
6744	GTSF1L	1
6745	GUCA1A	1
6746	GUCA1B	1
6747	GUCA1C	1
6748	GUCA2A	1
6749	GUCA2B	1
6750	GUCY1A2	1
6751	GUCY1A3	1
6752	GUCY1B3	1
6753	GUCY2C	2.152168e-01
6754	GUCY2D	1
6755	GUCY2F	1
6756	GUF1	1
6757	GUK1	1
6758	GULP1	1
6759	GUSB	2.876093e-01
6760	GXYLT1	5.099878e-02
6761	GXYLT2	1
6762	GYG1	1
6763	GYG2	1
6764	GYLTL1B	1
6765	GYPA	1
6766	GYPB	1
6767	GYPC	1
6768	GYPE	1
6769	GYS1	1
6770	GYS2	1
6771	GZF1	1
6772	GZMA	1
6773	GZMB	1
6774	GZMH	1
6775	GZMK	1
6776	GZMM	1
6777	H1F0	3.492574e-02
6778	H1FNT	1
6779	H1FOO	1
6780	H1FX	1
6781	H2AFJ	1
6782	H2AFV	1
6783	H2AFX	2.172822e-02
6784	H2AFY	1
6785	H2AFY2	1
6786	H2AFZ	1
6787	H2BFWT	2.236633e-02
6788	H3F3A	3.729100e-02
6789	H3F3B	1
6790	H3F3C	1
6791	H6PD	1
6792	HAAO	1.176250e-01
6793	HABP2	1
6794	HABP4	1.774157e-01
6795	HACE1	1
6796	HACL1	1.604724e-01
6797	HADH	7.378747e-03
6798	HADHA	1.475435e-01
6799	HADHB	1
6800	HAGH	1
6801	HAGHL	1
6802	HAL	1
6803	HAMP	1
6804	HAND1	1
6805	HAND2	1
6806	HAO1	1.541929e-01
6807	HAO2	1
6808	HAP1	2.325832e-01
6809	HAPLN1	1
6810	HAPLN2	1
6811	HAPLN3	1
6812	HAPLN4	1
6813	HARBI1	1
6814	HARS	1
6815	HARS2	1
6816	HAS1	1
6817	HAS2	1
6818	HAS3	2.686803e-01
Done

Running MutSig 2:
Scatter job 76: processing genes 6729 - 6818
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GTSE1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.008330e-02	ci left: 7.840118e-01	ci right 8.000177e-01	k: 7921	n:10000
Cons ci ratio: 4.991301e-02	ci left: 3.718655e-01	ci right 3.910036e-01	k: 3814	n:10000
KS ci ratio: 7.031466e-02	ci left: 2.286929e-01	ci right 2.454605e-01	k: 2370	n:10000
GTSE1   10000 perm   1 sec   (6755 perm/sec)   p_kst 2.370000e-01   p_cons 3.814000e-01   p_joint 7.921000e-01

Outputting figure to mutsig2_images.part000000000076/GTSE1.2_2264_10000_0.237_0.3814_0.7921.png
                gene_name: GTSE1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 33 percent done.
GUSB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.551513e-01	ci left: 5.532768e-02	ci right 6.473065e-02	k: 599	n:10000
Cons ci ratio: 9.892388e-03	ci left: 9.353730e-01	ci right 9.447687e-01	k: 9402	n:10000
KS ci ratio: 3.484002e-01	ci left: 1.032396e-02	ci right 1.476677e-02	k: 124	n:10000
GUSB   10000 perm   1 sec   (7197 perm/sec)   p_kst 1.240000e-02   p_cons 9.402000e-01   p_joint 5.990000e-02

Joint ci ratio: 1.140188e-01	ci left: 5.260997e-02	ci right 5.901994e-02	k: 1115	n:20000
Cons ci ratio: 6.992765e-03	ci left: 9.368243e-01	ci right 9.434470e-01	k: 18804	n:20000
KS ci ratio: 2.415168e-01	ci left: 1.142923e-02	ci right 1.461469e-02	k: 259	n:20000
GUSB   20000 perm   3 sec   (6404 perm/sec)   p_kst 1.295000e-02   p_cons 9.402000e-01   p_joint 5.575000e-02

Joint ci ratio: 1.170570e-01	ci left: 3.392034e-02	ci right 3.817013e-02	k: 1080	n:30000
Cons ci ratio: 5.692033e-03	ci left: 9.377976e-01	ci right 9.431834e-01	k: 28216	n:30000
KS ci ratio: 1.929815e-01	ci left: 1.225647e-02	ci right 1.490563e-02	k: 406	n:30000
GUSB   30000 perm   5 sec   (6122 perm/sec)   p_kst 1.353333e-02   p_cons 9.405333e-01   p_joint 3.600000e-02

Joint ci ratio: 1.039588e-01	ci left: 3.253782e-02	ci right 3.613020e-02	k: 1372	n:40000
Cons ci ratio: 4.973447e-03	ci left: 9.371445e-01	ci right 9.418415e-01	k: 37581	n:40000
KS ci ratio: 1.667645e-01	ci left: 1.248787e-02	ci right 1.478354e-02	k: 544	n:40000
GUSB   40000 perm   7 sec   (5910 perm/sec)   p_kst 1.360000e-02   p_cons 9.395250e-01   p_joint 3.430000e-02

Joint ci ratio: 9.276711e-02	ci left: 3.287823e-02	ci right 3.609611e-02	k: 1723	n:50000
Cons ci ratio: 4.447661e-03	ci left: 9.374153e-01	ci right 9.416135e-01	k: 46977	n:50000
KS ci ratio: 1.479798e-01	ci left: 1.281502e-02	ci right 1.488199e-02	k: 691	n:50000
GUSB   50000 perm   9 sec   (5757 perm/sec)   p_kst 1.382000e-02   p_cons 9.395400e-01   p_joint 3.446000e-02

Joint ci ratio: 8.468029e-02	ci left: 3.302121e-02	ci right 3.595737e-02	k: 2068	n:60000
Cons ci ratio: 4.036423e-03	ci left: 9.382730e-01	ci right 9.420843e-01	k: 56412	n:60000
KS ci ratio: 1.357848e-01	ci left: 1.276902e-02	ci right 1.464512e-02	k: 821	n:60000
GUSB   60000 perm   11 sec   (5619 perm/sec)   p_kst 1.368333e-02   p_cons 9.402000e-01   p_joint 3.446667e-02

Joint ci ratio: 7.684344e-02	ci left: 3.446383e-02	ci right 3.723196e-02	k: 2508	n:70000
Cons ci ratio: 3.741216e-03	ci left: 9.382877e-01	ci right 9.418186e-01	k: 65805	n:70000
KS ci ratio: 1.254475e-01	ci left: 1.289347e-02	ci right 1.463290e-02	k: 962	n:70000
GUSB   70000 perm   13 sec   (5497 perm/sec)   p_kst 1.374286e-02   p_cons 9.400714e-01   p_joint 3.582857e-02

Joint ci ratio: 7.275919e-02	ci left: 3.373713e-02	ci right 3.629673e-02	k: 2800	n:80000
Cons ci ratio: 3.491666e-03	ci left: 9.386612e-01	ci right 9.419568e-01	k: 75226	n:80000
KS ci ratio: 1.164143e-01	ci left: 1.316084e-02	ci right 1.479969e-02	k: 1117	n:80000
GUSB   80000 perm   15 sec   (5382 perm/sec)   p_kst 1.396250e-02   p_cons 9.403250e-01   p_joint 3.500000e-02

Joint ci ratio: 6.847571e-02	ci left: 3.392898e-02	ci right 3.634555e-02	k: 3161	n:90000
Cons ci ratio: 3.287789e-03	ci left: 9.389010e-01	ci right 9.420039e-01	k: 84642	n:90000
KS ci ratio: 1.091748e-01	ci left: 1.335066e-02	ci right 1.490311e-02	k: 1270	n:90000
GUSB   90000 perm   17 sec   (5280 perm/sec)   p_kst 1.411111e-02   p_cons 9.404667e-01   p_joint 3.512222e-02

Joint ci ratio: 6.367981e-02	ci left: 3.534615e-02	ci right 3.768083e-02	k: 3650	n:100000
Cons ci ratio: 3.117284e-03	ci left: 9.390463e-01	ci right 9.419880e-01	k: 94053	n:100000
KS ci ratio: 1.027352e-01	ci left: 1.361225e-02	ci right 1.509612e-02	k: 1434	n:100000
GUSB   100000 perm   19 sec   (5175 perm/sec)   p_kst 1.434000e-02   p_cons 9.405300e-01   p_joint 3.650000e-02

Joint ci ratio: 8.156916e-02	ci left: 1.972417e-02	ci right 2.141033e-02	k: 2261	n:110000
Cons ci ratio: 2.964049e-03	ci left: 9.394259e-01	ci right 9.422235e-01	k: 103492	n:110000
KS ci ratio: 9.812782e-02	ci left: 1.359781e-02	ci right 1.500979e-02	k: 1572	n:110000
GUSB   110000 perm   22 sec   (5082 perm/sec)   p_kst 1.429091e-02   p_cons 9.408364e-01   p_joint 2.055455e-02

Outputting figure to mutsig2_images.part000000000076/GUSB.2_2004_110000_0.014291_0.94084_0.020555.png
                gene_name: GUSB
               theta_stop: 0.098 
                    nperm: 110000 
                     p_ks: 0.014 
        ci_ks_bounds_left: 0.014 
       ci_ks_bounds_right: 0.015 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.021 
     ci_joint_bounds_left: 0.020 
    ci_joint_bounds_right: 0.021 

Current progress: 67 percent done.
HADH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.199590e-02	ci left: 3.528704e-01	ci right 3.718099e-01	k: 3623	n:10000
KS ci ratio: 2.399040e-02	ci left: 7.186579e-01	ci right 7.362094e-01	k: 7275	n:10000
HADH   10000 perm   1 sec   (7924 perm/sec)   p_kst 7.275000e-01   p_cons 3.623000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000076/HADH.2_1032_10000_0.7275_0.3623_1.png
                gene_name: HADH
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000076
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 76 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4398041: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000077> was used as the working directory.
Started at Wed Oct 24 16:12:33 2012
Results reported at Wed Oct 24 16:14:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000077.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000077.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 77  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000077.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     85.31 sec.
    Max Memory :      1195 MB
    Max Swap   :      3942 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
77
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 77
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 77: processing genes 6819 - 6908
Calculating significance of each gene.
Using projection method.
6819	HAT1	1
6820	HAUS1	1
6821	HAUS2	1
6822	HAUS3	1
6823	HAUS4	1.950675e-01
6824	HAUS5	1
6825	HAUS6	1
6826	HAUS7	1
6827	HAUS8	1
6828	HAVCR1	1
6829	HAVCR2	1.512505e-01
6830	HAX1	8.407792e-02
6831	HBA1	1
6832	HBA2	1
6833	HBB	1
6834	HBD	1
6835	HBE1	1
6836	HBEGF	1
6837	HBG1	1
6838	HBG2	1
6839	HBM	1
6840	HBP1	1
6841	HBQ1	1
6842	HBS1L	1
6843	HBXIP	1
6844	HCCS	1
6845	HCFC1	1
6846	HCFC1R1	1
6847	HCFC2	1
6848	HCK	1.891144e-01
6849	HCLS1	1
6850	HCN1	2.871000e-01
6851	HCN2	1
6852	HCN3	1
6853	HCN4	1
6854	HCRTR1	1
6855	HCRTR2	1
6856	HCST	1
6857	HDAC1	1
6858	HDAC10	1
6859	HDAC11	1
6860	HDAC2	1
6861	HDAC3	1
6862	HDAC4	1
6863	HDAC5	1
6864	HDAC6	1
6865	HDAC7	1.240092e-01
6866	HDAC8	9.600939e-02
6867	HDAC9	8.395194e-02
6868	HDC	1.539606e-01
6869	HDDC2	1
6870	HDDC3	1
6871	HDGF	1
6872	HDGFL1	1
6873	HDGFRP2	1
6874	HDGFRP3	1
6875	HDHD1A	1
6876	HDHD2	1
6877	HDHD3	1
6878	HDLBP	5.263468e-01
6879	HDX	1
6880	HEATR1	7.575071e-02
6881	HEATR2	1
6882	HEATR3	1.527475e-01
6883	HEATR4	1
6884	HEATR5A	1
6885	HEATR5B	7.272630e-02
6886	HEATR6	1
6887	HEATR7B2	1
6888	HEBP1	1
6889	HEBP2	1
6890	HECA	1
6891	HECTD1	6.784481e-01
6892	HECTD2	1
6893	HECTD3	1
6894	HECW1	4.099337e-01
6895	HECW2	3.402955e-01
6896	HEG1	4.997461e-01
6897	HELB	3.422878e-01
6898	HELLS	1
6899	HELQ	2.699752e-01
6900	HELT	1
6901	HELZ	4.888114e-01
6902	HEMGN	1
6903	HEMK1	1
6904	HEPACAM	1
6905	HEPACAM2	1
6906	HEPH	1
6907	HEPHL1	1
6908	HEPN1	1
Done

Running MutSig 2:
Scatter job 77: processing genes 6819 - 6908
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HEATR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.248048e-02	ci left: 2.180307e-01	ci right 2.345290e-01	k: 2262	n:10000
Cons ci ratio: 1.147477e-01	ci left: 9.847268e-02	ci right 1.105588e-01	k: 1044	n:10000
KS ci ratio: 3.377316e-02	ci left: 5.641375e-01	ci right 5.836195e-01	k: 5739	n:10000
HEATR1   10000 perm   3 sec   (3992 perm/sec)   p_kst 5.739000e-01   p_cons 1.044000e-01   p_joint 2.262000e-01

Joint ci ratio: 2.939693e-02	ci left: 4.636622e-01	ci right 4.775464e-01	k: 9412	n:20000
Cons ci ratio: 8.081697e-02	ci left: 1.009805e-01	ci right 1.095346e-01	k: 2104	n:20000
KS ci ratio: 2.407117e-02	ci left: 5.631541e-01	ci right 5.769256e-01	k: 11401	n:20000
HEATR1   20000 perm   8 sec   (2635 perm/sec)   p_kst 5.700500e-01   p_cons 1.052000e-01   p_joint 4.706000e-01

Outputting figure to mutsig2_images.part000000000077/HEATR1.3_6611_20000_0.57005_0.1052_0.4706.png
                gene_name: HEATR1
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 33 percent done.
HEATR5B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.323371e-02	ci left: 2.144784e-01	ci right 2.308835e-01	k: 2226	n:10000
Cons ci ratio: 1.304623e-01	ci left: 7.737381e-02	ci right 8.827067e-02	k: 827	n:10000
KS ci ratio: 3.287702e-02	ci left: 5.772755e-01	ci right 5.966738e-01	k: 5870	n:10000
HEATR5B   10000 perm   2 sec   (5239 perm/sec)   p_kst 5.870000e-01   p_cons 8.270000e-02   p_joint 2.226000e-01

Joint ci ratio: 2.664527e-02	ci left: 5.127484e-01	ci right 5.266459e-01	k: 10394	n:20000
Cons ci ratio: 9.314475e-02	ci left: 7.754845e-02	ci right 8.517378e-02	k: 1626	n:20000
KS ci ratio: 2.322493e-02	ci left: 5.806401e-01	ci right 5.943345e-01	k: 11750	n:20000
HEATR5B   20000 perm   4 sec   (4742 perm/sec)   p_kst 5.875000e-01   p_cons 8.130000e-02   p_joint 5.197000e-01

Outputting figure to mutsig2_images.part000000000077/HEATR5B.3_6356_20000_0.5875_0.0813_0.5197.png
                gene_name: HEATR5B
               theta_stop: 0.093 
                    nperm: 20000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.081 
      ci_cons_bounds_left: 0.078 
     ci_cons_bounds_right: 0.085 
                  p_joint: 0.52 
     ci_joint_bounds_left: 0.51 
    ci_joint_bounds_right: 0.53 

Current progress: 67 percent done.
HDAC9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.671727e-02	ci left: 5.227627e-01	ci right 5.424183e-01	k: 5326	n:10000
Cons ci ratio: 3.776400e-03	ci left: 9.888388e-01	ci right 9.926671e-01	k: 9909	n:10000
KS ci ratio: 3.854894e-02	ci left: 4.984503e-01	ci right 5.181449e-01	k: 5083	n:10000
HDAC9   10000 perm   2 sec   (6526 perm/sec)   p_kst 5.083000e-01   p_cons 9.909000e-01   p_joint 5.326000e-01

Outputting figure to mutsig2_images.part000000000077/HDAC9.2_3446_10000_0.5083_0.9909_0.5326.png
                gene_name: HDAC9
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.54 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000077
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 77 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4398045: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000078> was used as the working directory.
Started at Wed Oct 24 16:12:36 2012
Results reported at Wed Oct 24 16:14:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000078.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000078.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 78  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000078.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    157.01 sec.
    Max Memory :      1371 MB
    Max Swap   :      4003 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
78
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 78
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 78: processing genes 6909 - 6997
Calculating significance of each gene.
Using projection method.
6909	HERC1	1
6910	HERC2	2.207372e-01
6911	HERC3	1
6912	HERC4	1
6913	HERC5	1
6914	HERC6	1
6915	HERPUD1	1
6916	HERPUD2	1
6917	HES1	1
6918	HES3	1
6919	HES4	1
6920	HES6	1
6921	HESX1	8.486362e-02
6922	HEXA	1
6923	HEXB	1
6924	HEXDC	1
6925	HEXIM1	1
6926	HEXIM2	1
6927	HEY1	7.451400e-02
6928	HEY2	1
6929	HEYL	1
6930	HFE	1
6931	HFE2	1
6932	HFM1	9.323754e-02
6933	HGD	3.815593e-02
6934	HGF	2.643803e-01
6935	HGFAC	8.555835e-02
6936	HGS	1
6937	HGSNAT	7.348868e-02
6938	HHAT	1
6939	HHATL	1
6940	HHEX	1
6941	HHIP	1
6942	HHIPL1	1
6943	HHIPL2	1
6944	HHLA2	1
6945	HHLA3	1
6946	HIAT1	1
6947	HIATL1	1
6948	HIBADH	1
6949	HIBCH	1
6950	HIC1	1
6951	HIC2	1
6952	HIF1A	1
6953	HIF1AN	1
6954	HIF3A	1
6955	HIGD1A	1
6956	HIGD1B	1
6957	HIGD1C	1
6958	HIGD2A	1
6959	HINFP	1
6960	HINT1	1
6961	HINT2	1
6962	HINT3	1
6963	HIP1	1
6964	HIP1R	1
6965	HIPK1	2.137910e-01
6966	HIPK2	1
6967	HIPK3	1
6968	HIPK4	1
6969	HIRA	4.503379e-01
6970	HIRIP3	1
6971	HIST1H1A	9.241530e-02
6972	HIST1H1B	8.527271e-02
6973	HIST1H1C	1
6974	HIST1H1D	1
6975	HIST1H1E	6.398169e-02
6976	HIST1H1T	1
6977	HIST1H2AA	1
6978	HIST1H2AB	1
6979	HIST1H2AC	1
6980	HIST1H2AD	1
6981	HIST1H2AE	3.931853e-02
6982	HIST1H2AG	1
6983	HIST1H2AH	1
6984	HIST1H2AI	1
6985	HIST1H2AJ	1
6986	HIST1H2AK	1
6987	HIST1H2AL	1
6988	HIST1H2AM	1
6989	HIST1H2BA	1
6990	HIST1H2BB	1
6991	HIST1H2BC	4.386431e-02
6992	HIST1H2BD	7.003241e-02
6993	HIST1H2BE	1
6994	HIST1H2BF	1
6995	HIST1H2BG	1
6996	HIST1H2BH	1
6997	HIST1H2BI	4.274253e-02
Done

Running MutSig 2:
Scatter job 78: processing genes 6909 - 6997
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HERC2
Processing conservation and coverage...
67% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.499582e-02	ci left: 4.216640e-01	ci right 4.411760e-01	k: 4314	n:10000
Cons ci ratio: 5.814273e-02	ci left: 3.033218e-01	ci right 3.215876e-01	k: 3124	n:10000
KS ci ratio: 4.594381e-02	ci left: 4.114968e-01	ci right 4.309491e-01	k: 4212	n:10000
HERC2   10000 perm   3 sec   (3008 perm/sec)   p_kst 4.212000e-01   p_cons 3.124000e-01   p_joint 4.314000e-01

Outputting figure to mutsig2_images.part000000000078/HERC2.3_14873_10000_0.4212_0.3124_0.4314.png
                gene_name: HERC2
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 25 percent done.
HFM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.992472e-02	ci left: 7.866480e-01	ci right 8.025800e-01	k: 7947	n:10000
Cons ci ratio: 2.890169e-02	ci left: 6.383461e-01	ci right 6.571677e-01	k: 6478	n:10000
KS ci ratio: 4.157017e-02	ci left: 4.607769e-01	ci right 4.804402e-01	k: 4706	n:10000
HFM1   10000 perm   3 sec   (3673 perm/sec)   p_kst 4.706000e-01   p_cons 6.478000e-01   p_joint 7.947000e-01

Outputting figure to mutsig2_images.part000000000078/HFM1.3_4460_10000_0.4706_0.6478_0.7947.png
                gene_name: HFM1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.80 

Current progress: 50 percent done.
HIPK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.232947e-02	ci left: 1.771369e-01	ci right 1.924471e-01	k: 1847	n:10000
KS ci ratio: 5.211988e-02	ci left: 3.517769e-01	ci right 3.707040e-01	k: 3612	n:10000
HIPK1   10000 perm   2 sec   (5592 perm/sec)   p_kst 3.612000e-01   p_cons 1.847000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000078/HIPK1.2_3795_10000_0.3612_0.1847_1.png
                gene_name: HIPK1
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.19 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
HIST1H2BI
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.200305e-02	ci left: 1.783175e-01	ci right 1.936658e-01	k: 1859	n:10000
Cons ci ratio: 4.211635e-02	ci left: 4.542871e-01	ci right 4.739338e-01	k: 4641	n:10000
KS ci ratio: 1.516850e-01	ci left: 5.783363e-02	ci right 6.742310e-02	k: 625	n:10000
HIST1H2BI   10000 perm   1 sec   (6842 perm/sec)   p_kst 6.250000e-02   p_cons 4.641000e-01   p_joint 1.859000e-01

Joint ci ratio: 4.928460e-02	ci left: 2.343420e-01	ci right 2.462336e-01	k: 4805	n:20000
Cons ci ratio: 2.990924e-02	ci left: 4.550715e-01	ci right 4.689396e-01	k: 9240	n:20000
KS ci ratio: 1.088451e-01	ci left: 5.757595e-02	ci right 6.425241e-02	k: 1217	n:20000
HIST1H2BI   20000 perm   3 sec   (6166 perm/sec)   p_kst 6.085000e-02   p_cons 4.620000e-01   p_joint 2.402500e-01

Joint ci ratio: 4.359843e-02	ci left: 2.076178e-01	ci right 2.169047e-01	k: 6367	n:30000
Cons ci ratio: 2.432507e-02	ci left: 4.583105e-01	ci right 4.696298e-01	k: 13919	n:30000
KS ci ratio: 8.902807e-02	ci left: 5.799134e-02	ci right 6.342745e-02	k: 1820	n:30000
HIST1H2BI   30000 perm   5 sec   (5876 perm/sec)   p_kst 6.066667e-02   p_cons 4.639667e-01   p_joint 2.122333e-01

Outputting figure to mutsig2_images.part000000000078/HIST1H2BI.2_385_30000_0.060667_0.46397_0.21223.png
                gene_name: HIST1H2BI
               theta_stop: 0.089 
                    nperm: 30000 
                     p_ks: 0.061 
        ci_ks_bounds_left: 0.058 
       ci_ks_bounds_right: 0.063 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000078
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 78 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1728>
Subject: Job 4398047: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000079> was used as the working directory.
Started at Wed Oct 24 16:12:42 2012
Results reported at Wed Oct 24 16:15:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000079.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000079.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 79  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000079.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    152.32 sec.
    Max Memory :      1393 MB
    Max Swap   :      4144 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
79
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 79
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 79: processing genes 6998 - 7087
Calculating significance of each gene.
Using projection method.
6998	HIST1H2BJ	1
6999	HIST1H2BK	4.611411e-02
7000/17942 7000	HIST1H2BL	1
7001	HIST1H2BM	1
7002	HIST1H2BN	1
7003	HIST1H2BO	1
7004	HIST1H3A	1
7005	HIST1H3B	5.232075e-02
7006	HIST1H3C	1
7007	HIST1H3D	1
7008	HIST1H3E	8.870348e-03
7009	HIST1H3F	1
7010	HIST1H3G	1
7011	HIST1H3H	1
7012	HIST1H3I	1
7013	HIST1H3J	1
7014	HIST1H4A	1
7015	HIST1H4B	1
7016	HIST1H4C	6.993269e-03
7017	HIST1H4D	1
7018	HIST1H4E	1.320457e-02
7019	HIST1H4F	3.425197e-02
7020	HIST1H4G	1
7021	HIST1H4H	1
7022	HIST1H4I	1
7023	HIST1H4J	1
7024	HIST1H4K	4.226337e-03
7025	HIST1H4L	1
7026	HIST2H2AB	6.669482e-02
7027	HIST2H2AC	1
7028	HIST2H2BE	4.585464e-02
7029	HIST2H2BF	2.028007e-02
7030	HIST2H3D	1
7031	HIST3H2A	1
7032	HIST3H2BB	1
7033	HIST3H3	1
7034	HIST4H4	1
7035	HIVEP1	4.501960e-01
7036	HIVEP2	1
7037	HIVEP3	1
7038	HJURP	3.296588e-01
7039	HK1	1
7040	HK2	1.064594e-01
7041	HK3	1.275607e-01
7042	HKDC1	1
7043	HKR1	5.211599e-02
7044	HLA-A	1.311600e-01
7045	HLA-B	1
7046	HLA-C	1
7047	HLA-DMA	1
7048	HLA-DMB	6.714230e-03
7049	HLA-DOA	1
7050	HLA-DOB	1
7051	HLA-DPA1	1
7052	HLA-DPB1	1.393615e-01
7053	HLA-DQA1	1
7054	HLA-DQA2	1
7055	HLA-DQB1	1
7056	HLA-DRA	1
7057	HLA-DRB1	1
7058	HLA-DRB5	1
7059	HLA-E	4.492026e-02
7060	HLA-F	1.550126e-01
7061	HLA-G	1
7062	HLCS	1.926925e-01
7063	HLF	1
7064	HLTF	1
7065	HLX	1
7066	HM13	1
7067	HMBOX1	2.195787e-01
7068	HMBS	1
7069	HMCN1	8.482043e-01
7070	HMG20A	1
7071	HMG20B	4.549149e-02
7072	HMGA1	1
7073	HMGA2	1
7074	HMGB1	1
7075	HMGB2	1
7076	HMGB3	1
7077	HMGB4	1
7078	HMGCL	1
7079	HMGCLL1	1
7080	HMGCR	1
7081	HMGCS1	2.443638e-01
7082	HMGCS2	1
7083	HMGN1	1
7084	HMGN2	1
7085	HMGN3	1
7086	HMGN4	1
7087	HMGN5	1
Done

Running MutSig 2:
Scatter job 79: processing genes 6998 - 7087
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HIVEP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.541967e-01	ci left: 5.600212e-02	ci right 6.545578e-02	k: 606	n:10000
Cons ci ratio: 4.491338e-02	ci left: 4.225613e-01	ci right 4.420781e-01	k: 4323	n:10000
KS ci ratio: 3.602602e-01	ci left: 9.594514e-03	ci right 1.389697e-02	k: 116	n:10000
HIVEP1   10000 perm   2 sec   (4860 perm/sec)   p_kst 1.160000e-02   p_cons 4.323000e-01   p_joint 6.060000e-02

Joint ci ratio: 2.553012e-01	ci left: 1.016235e-02	ci right 1.318213e-02	k: 232	n:20000
Cons ci ratio: 3.161300e-02	ci left: 4.277149e-01	ci right 4.415041e-01	k: 8692	n:20000
KS ci ratio: 2.553012e-01	ci left: 1.016235e-02	ci right 1.318213e-02	k: 232	n:20000
HIVEP1   20000 perm   6 sec   (3200 perm/sec)   p_kst 1.160000e-02   p_cons 4.346000e-01   p_joint 1.160000e-02

Joint ci ratio: 2.139407e-01	ci left: 9.882165e-03	ci right 1.228060e-02	k: 331	n:30000
Cons ci ratio: 2.565919e-02	ci left: 4.319093e-01	ci right 4.431694e-01	k: 13126	n:30000
KS ci ratio: 2.139407e-01	ci left: 9.882165e-03	ci right 1.228060e-02	k: 331	n:30000
HIVEP1   30000 perm   9 sec   (3437 perm/sec)   p_kst 1.103333e-02   p_cons 4.375333e-01   p_joint 1.103333e-02

Joint ci ratio: 1.833343e-01	ci left: 1.026340e-02	ci right 1.235845e-02	k: 451	n:40000
Cons ci ratio: 2.305060e-02	ci left: 4.147573e-01	ci right 4.244543e-01	k: 16784	n:40000
KS ci ratio: 1.833343e-01	ci left: 1.026340e-02	ci right 1.235845e-02	k: 451	n:40000
HIVEP1   40000 perm   11 sec   (3558 perm/sec)   p_kst 1.127500e-02   p_cons 4.196000e-01   p_joint 1.127500e-02

Joint ci ratio: 1.641266e-01	ci left: 1.035361e-02	ci right 1.222378e-02	k: 563	n:50000
Cons ci ratio: 2.066560e-02	ci left: 4.141309e-01	ci right 4.227986e-01	k: 20923	n:50000
KS ci ratio: 1.641266e-01	ci left: 1.035361e-02	ci right 1.222378e-02	k: 563	n:50000
HIVEP1   50000 perm   14 sec   (3619 perm/sec)   p_kst 1.126000e-02   p_cons 4.184600e-01   p_joint 1.126000e-02

Joint ci ratio: 6.533116e-05	ci left: 9.999385e-01	ci right 1	k: 60000	n:60000
Cons ci ratio: 1.886617e-02	ci left: 4.144819e-01	ci right 4.223927e-01	k: 25106	n:60000
KS ci ratio: 1.495809e-01	ci left: 1.046961e-02	ci right 1.217815e-02	k: 678	n:60000
HIVEP1   60000 perm   16 sec   (3643 perm/sec)   p_kst 1.130000e-02   p_cons 4.184333e-01   p_joint 1

Joint ci ratio: 5.599840e-05	ci left: 9.999473e-01	ci right 1	k: 70000	n:70000
Cons ci ratio: 1.744951e-02	ci left: 4.152556e-01	ci right 4.225797e-01	k: 29324	n:70000
KS ci ratio: 1.400279e-01	ci left: 1.029567e-02	ci right 1.185954e-02	k: 774	n:70000
HIVEP1   70000 perm   19 sec   (3645 perm/sec)   p_kst 1.105714e-02   p_cons 4.189143e-01   p_joint 1

Joint ci ratio: 4.899878e-05	ci left: 9.999539e-01	ci right 1	k: 80000	n:80000
Cons ci ratio: 1.630923e-02	ci left: 4.158899e-01	ci right 4.227410e-01	k: 33545	n:80000
KS ci ratio: 1.305908e-01	ci left: 1.040971e-02	ci right 1.187607e-02	k: 890	n:80000
HIVEP1   80000 perm   22 sec   (3634 perm/sec)   p_kst 1.112500e-02   p_cons 4.193125e-01   p_joint 1

Joint ci ratio: 4.355459e-05	ci left: 9.999590e-01	ci right 1	k: 90000	n:90000
Cons ci ratio: 1.537447e-02	ci left: 4.161510e-01	ci right 4.226098e-01	k: 37744	n:90000
KS ci ratio: 1.238980e-01	ci left: 1.031804e-02	ci right 1.169153e-02	k: 989	n:90000
HIVEP1   90000 perm   25 sec   (3617 perm/sec)   p_kst 1.098889e-02   p_cons 4.193778e-01   p_joint 1

Joint ci ratio: 1.169502e-01	ci left: 1.045985e-02	ci right 1.176874e-02	k: 1110	n:100000
Cons ci ratio: 1.457768e-02	ci left: 4.165787e-01	ci right 4.227060e-01	k: 41964	n:100000
KS ci ratio: 1.169502e-01	ci left: 1.045985e-02	ci right 1.176874e-02	k: 1110	n:100000
HIVEP1   100000 perm   28 sec   (3595 perm/sec)   p_kst 1.110000e-02   p_cons 4.196400e-01   p_joint 1.110000e-02

Joint ci ratio: 3.563572e-05	ci left: 9.999665e-01	ci right 1	k: 110000	n:110000
Cons ci ratio: 1.342559e-02	ci left: 4.336844e-01	ci right 4.395553e-01	k: 48028	n:110000
KS ci ratio: 1.123049e-01	ci left: 1.033897e-02	ci right 1.157793e-02	k: 1204	n:110000
HIVEP1   110000 perm   31 sec   (3568 perm/sec)   p_kst 1.094545e-02   p_cons 4.366182e-01   p_joint 1

Joint ci ratio: 3.266612e-05	ci left: 9.999693e-01	ci right 1	k: 120000	n:120000
Cons ci ratio: 1.285364e-02	ci left: 4.338246e-01	ci right 4.394452e-01	k: 52396	n:120000
KS ci ratio: 1.082145e-01	ci left: 1.023098e-02	ci right 1.140950e-02	k: 1297	n:120000
HIVEP1   120000 perm   34 sec   (3542 perm/sec)   p_kst 1.080833e-02   p_cons 4.366333e-01   p_joint 1

Joint ci ratio: 3.015338e-05	ci left: 9.999716e-01	ci right 1	k: 130000	n:130000
Cons ci ratio: 1.232786e-02	ci left: 4.347932e-01	ci right 4.401942e-01	k: 56874	n:130000
KS ci ratio: 1.036405e-01	ci left: 1.032017e-02	ci right 1.145565e-02	k: 1414	n:130000
HIVEP1   130000 perm   37 sec   (3514 perm/sec)   p_kst 1.087692e-02   p_cons 4.374923e-01   p_joint 1

Joint ci ratio: 2.799960e-05	ci left: 9.999737e-01	ci right 1	k: 140000	n:140000
Cons ci ratio: 1.187425e-02	ci left: 4.351062e-01	ci right 4.403107e-01	k: 61279	n:140000
KS ci ratio: 1.000981e-01	ci left: 1.029302e-02	ci right 1.138453e-02	k: 1516	n:140000
HIVEP1   140000 perm   40 sec   (3481 perm/sec)   p_kst 1.082857e-02   p_cons 4.377071e-01   p_joint 1

Joint ci ratio: 2.613298e-05	ci left: 9.999754e-01	ci right 1	k: 150000	n:150000
Cons ci ratio: 1.146915e-02	ci left: 4.353006e-01	ci right 4.403285e-01	k: 65672	n:150000
KS ci ratio: 9.710820e-02	ci left: 1.022451e-02	ci right 1.127453e-02	k: 1611	n:150000
HIVEP1   150000 perm   43 sec   (3451 perm/sec)   p_kst 1.074000e-02   p_cons 4.378133e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000079/HIVEP1.2_8189_150000_0.01074_0.43781_1.png
                gene_name: HIVEP1
               theta_stop: 0.097 
                    nperm: 150000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.44 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
HLA-DMB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.428697e-02	ci left: 7.137110e-01	ci right 7.313592e-01	k: 7226	n:10000
Cons ci ratio: 1.578567e-02	ci left: 8.535544e-01	ci right 8.672349e-01	k: 8605	n:10000
KS ci ratio: 3.376227e-01	ci left: 1.105573e-02	ci right 1.563427e-02	k: 132	n:10000
HLA-DMB   10000 perm   1 sec   (7805 perm/sec)   p_kst 1.320000e-02   p_cons 8.605000e-01   p_joint 7.226000e-01

Joint ci ratio: 4.396825e-02	ci left: 2.781048e-01	ci right 2.906579e-01	k: 5687	n:20000
Cons ci ratio: 1.177696e-02	ci left: 8.420369e-01	ci right 8.520620e-01	k: 16942	n:20000
KS ci ratio: 2.494107e-01	ci left: 1.067791e-02	ci right 1.376634e-02	k: 243	n:20000
HLA-DMB   20000 perm   3 sec   (6861 perm/sec)   p_kst 1.215000e-02   p_cons 8.471000e-01   p_joint 2.843500e-01

Joint ci ratio: 7.859634e-02	ci left: 7.354946e-02	ci right 7.959951e-02	k: 2296	n:30000
Cons ci ratio: 9.623077e-03	ci left: 8.427751e-01	ci right 8.509576e-01	k: 25407	n:30000
KS ci ratio: 2.080031e-01	ci left: 1.048237e-02	ci right 1.294689e-02	k: 350	n:30000
HLA-DMB   30000 perm   5 sec   (6539 perm/sec)   p_kst 1.166667e-02   p_cons 8.469000e-01   p_joint 7.653333e-02

Joint ci ratio: 7.055036e-02	ci left: 6.911662e-02	ci right 7.419577e-02	k: 2865	n:40000
Cons ci ratio: 8.305614e-03	ci left: 8.442168e-01	ci right 8.512826e-01	k: 33911	n:40000
KS ci ratio: 1.852084e-01	ci left: 1.004868e-02	ci right 1.212322e-02	k: 442	n:40000
HLA-DMB   40000 perm   6 sec   (6315 perm/sec)   p_kst 1.105000e-02   p_cons 8.477750e-01   p_joint 7.162500e-02

Joint ci ratio: 5.942503e-02	ci left: 7.767594e-02	ci right 8.245295e-02	k: 4002	n:50000
Cons ci ratio: 7.446413e-03	ci left: 8.439758e-01	ci right 8.503038e-01	k: 42358	n:50000
KS ci ratio: 1.662259e-01	ci left: 1.008506e-02	ci right 1.193237e-02	k: 549	n:50000
HLA-DMB   50000 perm   8 sec   (6128 perm/sec)   p_kst 1.098000e-02   p_cons 8.471600e-01   p_joint 8.004000e-02

Joint ci ratio: 6.117501e-02	ci left: 6.208725e-02	ci right 6.602171e-02	k: 3842	n:60000
Cons ci ratio: 6.818397e-03	ci left: 8.434563e-01	ci right 8.492435e-01	k: 50782	n:60000
KS ci ratio: 1.516269e-01	ci left: 1.018081e-02	ci right 1.186699e-02	k: 660	n:60000
HLA-DMB   60000 perm   10 sec   (5968 perm/sec)   p_kst 1.100000e-02   p_cons 8.463667e-01   p_joint 6.403333e-02

Joint ci ratio: 5.018548e-02	ci left: 7.815590e-02	ci right 8.219327e-02	k: 5611	n:70000
Cons ci ratio: 6.304846e-03	ci left: 8.439952e-01	ci right 8.493475e-01	k: 59268	n:70000
KS ci ratio: 1.408573e-01	ci left: 1.017157e-02	ci right 1.172651e-02	k: 765	n:70000
HLA-DMB   70000 perm   12 sec   (5820 perm/sec)   p_kst 1.092857e-02   p_cons 8.466857e-01   p_joint 8.015714e-02

Joint ci ratio: 3.889986e-02	ci left: 1.104422e-01	ci right 1.148360e-01	k: 9010	n:80000
Cons ci ratio: 5.891343e-03	ci left: 8.444489e-01	ci right 8.494509e-01	k: 67757	n:80000
KS ci ratio: 1.310377e-01	ci left: 1.033714e-02	ci right 1.179865e-02	k: 884	n:80000
HLA-DMB   80000 perm   14 sec   (5694 perm/sec)   p_kst 1.105000e-02   p_cons 8.469625e-01   p_joint 1.126250e-01

Joint ci ratio: 4.001760e-02	ci left: 9.441320e-02	ci right 9.827953e-02	k: 8670	n:90000
Cons ci ratio: 5.549789e-03	ci left: 8.448103e-01	ci right 8.495229e-01	k: 76246	n:90000
KS ci ratio: 1.238980e-01	ci left: 1.031804e-02	ci right 1.169153e-02	k: 989	n:90000
HLA-DMB   90000 perm   16 sec   (5588 perm/sec)   p_kst 1.098889e-02   p_cons 8.471778e-01   p_joint 9.633333e-02

Joint ci ratio: 4.386324e-02	ci left: 7.233543e-02	ci right 7.558933e-02	k: 7395	n:100000
Cons ci ratio: 5.272258e-03	ci left: 8.445727e-01	ci right 8.490472e-01	k: 84682	n:100000
KS ci ratio: 1.181936e-01	ci left: 1.023655e-02	ci right 1.153206e-02	k: 1087	n:100000
HLA-DMB   100000 perm   18 sec   (5479 perm/sec)   p_kst 1.087000e-02   p_cons 8.468200e-01   p_joint 7.395000e-02

Joint ci ratio: 4.542419e-02	ci left: 6.196694e-02	ci right 6.485613e-02	k: 6974	n:110000
Cons ci ratio: 5.027459e-03	ci left: 8.446487e-01	ci right 8.489148e-01	k: 93147	n:110000
KS ci ratio: 1.138432e-01	ci left: 1.005620e-02	ci right 1.127890e-02	k: 1172	n:110000
HLA-DMB   110000 perm   20 sec   (5377 perm/sec)   p_kst 1.065455e-02   p_cons 8.467909e-01   p_joint 6.340000e-02

Joint ci ratio: 3.258168e-02	ci left: 1.058852e-01	ci right 1.094005e-01	k: 12916	n:120000
Cons ci ratio: 4.813871e-03	ci left: 8.447161e-01	ci right 8.488005e-01	k: 101612	n:120000
KS ci ratio: 1.091535e-01	ci left: 1.005258e-02	ci right 1.122125e-02	k: 1275	n:120000
HLA-DMB   120000 perm   23 sec   (5281 perm/sec)   p_kst 1.062500e-02   p_cons 8.467667e-01   p_joint 1.076333e-01

Joint ci ratio: 3.842061e-02	ci left: 7.271230e-02	ci right 7.556827e-02	k: 9637	n:130000
Cons ci ratio: 4.618798e-03	ci left: 8.451475e-01	ci right 8.490677e-01	k: 110125	n:130000
KS ci ratio: 1.045026e-01	ci left: 1.014780e-02	ci right 1.127418e-02	k: 1391	n:130000
HLA-DMB   130000 perm   25 sec   (5186 perm/sec)   p_kst 1.070000e-02   p_cons 8.471154e-01   p_joint 7.413077e-02

Joint ci ratio: 3.003411e-02	ci left: 1.068470e-01	ci right 1.101121e-01	k: 15186	n:140000
Cons ci ratio: 4.446504e-03	ci left: 8.454697e-01	ci right 8.492445e-01	k: 118631	n:140000
KS ci ratio: 1.005345e-01	ci left: 1.020247e-02	ci right 1.128937e-02	k: 1503	n:140000
HLA-DMB   140000 perm   27 sec   (5094 perm/sec)   p_kst 1.073571e-02   p_cons 8.473643e-01   p_joint 1.084714e-01

Joint ci ratio: 2.904755e-02	ci left: 1.066919e-01	ci right 1.098433e-01	k: 16239	n:150000
Cons ci ratio: 4.295025e-03	ci left: 8.455769e-01	ci right 8.492230e-01	k: 127111	n:150000
KS ci ratio: 9.750642e-02	ci left: 1.013993e-02	ci right 1.118578e-02	k: 1598	n:150000
HLA-DMB   150000 perm   30 sec   (5007 perm/sec)   p_kst 1.065333e-02   p_cons 8.474067e-01   p_joint 1.082600e-01

Outputting figure to mutsig2_images.part000000000079/HLA-DMB.2_816_150000_0.010653_0.84741_0.10826.png
                gene_name: HLA-DMB
               theta_stop: 0.098 
                    nperm: 150000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.11 

Current progress: 67 percent done.
HMCN1
Processing conservation and coverage...
57% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.307472e-03	ci left: 9.627847e-01	ci right 9.699403e-01	k: 9665	n:10000
Cons ci ratio: 1.543566e-02	ci left: 8.589625e-01	ci right 8.724236e-01	k: 8658	n:10000
KS ci ratio: 3.576213e-02	ci left: 5.358791e-01	ci right 5.554943e-01	k: 5457	n:10000
HMCN1   10000 perm   3 sec   (3444 perm/sec)   p_kst 5.457000e-01   p_cons 8.658000e-01   p_joint 9.665000e-01

Outputting figure to mutsig2_images.part000000000079/HMCN1.2_17336_10000_0.5457_0.8658_0.9665.png
                gene_name: HMCN1
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000079
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 79 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 4398051: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000080> was used as the working directory.
Started at Wed Oct 24 16:12:44 2012
Results reported at Wed Oct 24 16:14:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000080.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000080.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 80  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000080.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    127.65 sec.
    Max Memory :      1338 MB
    Max Swap   :      4015 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
80
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 80
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 80: processing genes 7088 - 7177
Calculating significance of each gene.
Using projection method.
7088	HMGXB4	1
7089	HMHA1	1
7090	HMHB1	1
7091	HMMR	1
7092	HMOX1	1.420635e-01
7093	HMOX2	1
7094	HMP19	3.164768e-02
7095	HMSD	1
7096	HMX2	1
7097	HMX3	1
7098	HN1	1
7099	HN1L	1
7100	HNF1A	1
7101	HNF1B	8.105244e-02
7102	HNF4A	1
7103	HNF4G	1
7104	HNMT	1
7105	HNRNPA0	1
7106	HNRNPA1	1
7107	HNRNPA1L2	1.534785e-01
7108	HNRNPA2B1	1
7109	HNRNPA3	1
7110	HNRNPAB	1
7111	HNRNPC	1
7112	HNRNPCL1	1
7113	HNRNPD	1
7114	HNRNPF	1
7115	HNRNPH1	1.579693e-01
7116	HNRNPH2	1
7117	HNRNPH3	1
7118	HNRNPK	1
7119	HNRNPL	5.466810e-02
7120	HNRNPM	1
7121	HNRNPR	1
7122	HNRNPU	1
7123	HNRNPUL1	1
7124	HNRNPUL2	6.383904e-02
7125	HNRPDL	1
7126	HNRPLL	4.229701e-02
7127	HOMER1	1
7128	HOMER2	9.021065e-02
7129	HOMER3	1
7130	HOMEZ	1
7131	HOOK1	2.505482e-01
7132	HOOK2	1
7133	HOOK3	1
7134	HOPX	1
7135	HORMAD1	1.271646e-01
7136	HORMAD2	1
7137	HOXA1	1
7138	HOXA10	1
7139	HOXA11	1
7140	HOXA13	1
7141	HOXA2	1.700150e-01
7142	HOXA3	1.014851e-01
7143	HOXA4	1.113988e-03
7144	HOXA5	1
7145	HOXA6	1
7146	HOXA7	1
7147	HOXA9	1
7148	HOXB1	1
7149	HOXB13	1
7150	HOXB2	1
7151	HOXB3	1
7152	HOXB4	1
7153	HOXB5	1
7154	HOXB6	1
7155	HOXB7	1
7156	HOXB8	1
7157	HOXB9	1
7158	HOXC10	1
7159	HOXC11	1
7160	HOXC12	1
7161	HOXC13	1
7162	HOXC4	9.804723e-02
7163	HOXC5	4.705660e-03
7164	HOXC6	1
7165	HOXC8	1
7166	HOXC9	1
7167	HOXD1	1
7168	HOXD10	1
7169	HOXD11	1
7170	HOXD12	1
7171	HOXD13	1
7172	HOXD3	1
7173	HOXD4	1
7174	HOXD8	1
7175	HOXD9	3.723976e-02
7176	HP	1
7177	HP1BP3	1
Done

Running MutSig 2:
Scatter job 80: processing genes 7088 - 7177
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HOXA4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.407264e-01	ci left: 6.691220e-02	ci right 7.713880e-02	k: 719	n:10000
Cons ci ratio: 1.290236e-01	ci left: 7.902317e-02	ci right 9.002028e-02	k: 844	n:10000
KS ci ratio: 1.407264e-01	ci left: 6.691220e-02	ci right 7.713880e-02	k: 719	n:10000
HOXA4   10000 perm   1 sec   (6685 perm/sec)   p_kst 7.190000e-02   p_cons 8.440000e-02   p_joint 7.190000e-02

Joint ci ratio: 9.992253e-02	ci left: 6.786890e-02	ci right 7.505629e-02	k: 1428	n:20000
Cons ci ratio: 9.240486e-02	ci left: 7.872292e-02	ci right 8.639896e-02	k: 1650	n:20000
KS ci ratio: 9.992253e-02	ci left: 6.786890e-02	ci right 7.505629e-02	k: 1428	n:20000
HOXA4   20000 perm   5 sec   (3840 perm/sec)   p_kst 7.140000e-02   p_cons 8.250000e-02   p_joint 7.140000e-02

Outputting figure to mutsig2_images.part000000000080/HOXA4.2_971_20000_0.0714_0.0825_0.0714.png
                gene_name: HOXA4
               theta_stop: 0.100 
                    nperm: 20000 
                     p_ks: 0.071 
        ci_ks_bounds_left: 0.068 
       ci_ks_bounds_right: 0.075 
                   p_cons: 0.083 
      ci_cons_bounds_left: 0.079 
     ci_cons_bounds_right: 0.086 
                  p_joint: 0.071 
     ci_joint_bounds_left: 0.068 
    ci_joint_bounds_right: 0.075 

Current progress: 50 percent done.
HOXC5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.519581e-02	ci left: 8.626380e-01	ci right 8.759461e-01	k: 8694	n:10000
KS ci ratio: 1.890957e-01	ci left: 3.729324e-02	ci right 4.517686e-02	k: 411	n:10000
HOXC5   10000 perm   1 sec   (7254 perm/sec)   p_kst 4.110000e-02   p_cons 8.694000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 1.084794e-02	ci left: 8.624184e-01	ci right 8.718746e-01	k: 17344	n:20000
KS ci ratio: 1.362337e-01	ci left: 3.703607e-02	ci right 4.249877e-02	k: 794	n:20000
HOXC5   20000 perm   3 sec   (5937 perm/sec)   p_kst 3.970000e-02   p_cons 8.672000e-01   p_joint 1

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 8.840387e-03	ci left: 8.637462e-01	ci right 8.714491e-01	k: 26029	n:30000
KS ci ratio: 1.113569e-01	ci left: 3.745367e-02	ci right 4.190271e-02	k: 1189	n:30000
HOXC5   30000 perm   5 sec   (5608 perm/sec)   p_kst 3.963333e-02   p_cons 8.676333e-01   p_joint 1

Joint ci ratio: 9.799510e-05	ci left: 9.999078e-01	ci right 1	k: 40000	n:40000
Cons ci ratio: 7.648669e-03	ci left: 8.644920e-01	ci right 8.711545e-01	k: 34714	n:40000
KS ci ratio: 9.661803e-02	ci left: 3.761217e-02	ci right 4.145504e-02	k: 1580	n:40000
HOXC5   40000 perm   7 sec   (5511 perm/sec)   p_kst 3.950000e-02   p_cons 8.678500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000080/HOXC5.2_677_40000_0.0395_0.86785_1.png
                gene_name: HOXC5
               theta_stop: 0.097 
                    nperm: 40000 
                     p_ks: 0.040 
        ci_ks_bounds_left: 0.038 
       ci_ks_bounds_right: 0.041 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000080
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 80 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4398054: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000081> was used as the working directory.
Started at Wed Oct 24 16:12:44 2012
Results reported at Wed Oct 24 16:14:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000081.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000081.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 81  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000081.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    123.51 sec.
    Max Memory :      1217 MB
    Max Swap   :      3956 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
81
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 81
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 81: processing genes 7178 - 7267
Calculating significance of each gene.
Using projection method.
7178	HPCA	1
7179	HPCAL1	1.086969e-02
7180	HPCAL4	1
7181	HPD	1
7182	HPDL	1
7183	HPGD	1
7184	HPGDS	1
7185	HPN	1
7186	HPR	5.343785e-02
7187	HPRT1	1
7188	HPS1	1
7189	HPS3	1
7190	HPS4	1
7191	HPS5	1
7192	HPS6	1
7193	HPSE	1
7194	HPSE2	1
7195	HPX	1
7196	HR	1
7197	HRAS	1
7198	HRASLS	1
7199	HRASLS2	1
7200	HRASLS5	1
7201	HRC	1
7202	HRCT1	1.409175e-03
7203	HRG	1
7204	HRH1	1
7205	HRH2	1.803429e-01
7206	HRH3	1
7207	HRH4	1
7208	HRNR	2.071806e-01
7209	HRSP12	1
7210	HS1BP3	1
7211	HS2ST1	1
7212	HS3ST1	1
7213	HS3ST2	1
7214	HS3ST3A1	1
7215	HS3ST3B1	1
7216	HS3ST4	1
7217	HS3ST5	1
7218	HS3ST6	1
7219	HS6ST1	1
7220	HS6ST2	2.028108e-01
7221	HS6ST3	1
7222	HSBP1	1
7223	HSCB	1
7224	HSD11B1	1
7225	HSD11B2	1
7226	HSD17B1	1
7227	HSD17B10	1
7228	HSD17B11	1.447257e-01
7229	HSD17B12	1
7230	HSD17B13	1
7231	HSD17B14	1
7232	HSD17B2	1
7233	HSD17B3	1
7234	HSD17B4	8.816885e-02
7235	HSD17B6	1
7236	HSD17B7	1
7237	HSD17B8	1
7238	HSD3B1	1
7239	HSD3B2	1
7240	HSD3B7	1
7241	HSDL1	1
7242	HSDL2	9.821038e-02
7243	HSF1	1
7244	HSF2	1
7245	HSF2BP	1
7246	HSF4	1.976904e-01
7247	HSF5	1
7248	HSH2D	1
7249	HSP90AA1	1
7250	HSP90AB1	1
7251	HSP90B1	1
7252	HSPA12A	1
7253	HSPA12B	1
7254	HSPA13	1
7255	HSPA14	1
7256	HSPA1A	1
7257	HSPA1B	1
7258	HSPA1L	1
7259	HSPA2	1
7260	HSPA4	1
7261	HSPA4L	1
7262	HSPA5	1
7263	HSPA6	1
7264	HSPA8	1
7265	HSPA9	1
7266	HSPB1	1
7267	HSPB11	1
Done

Running MutSig 2:
Scatter job 81: processing genes 7178 - 7267
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HSD17B4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.176015e-02	ci left: 1.792031e-01	ci right 1.945798e-01	k: 1868	n:10000
Cons ci ratio: 1.714031e-01	ci left: 4.542628e-02	ci right 5.403844e-02	k: 496	n:10000
KS ci ratio: 3.571168e-02	ci left: 5.365801e-01	ci right 5.561928e-01	k: 5464	n:10000
HSD17B4   10000 perm   2 sec   (5482 perm/sec)   p_kst 5.464000e-01   p_cons 4.960000e-02   p_joint 1.868000e-01

Joint ci ratio: 6.409544e-02	ci left: 1.524766e-01	ci right 1.626232e-01	k: 3150	n:20000
Cons ci ratio: 1.205030e-01	ci left: 4.721434e-02	ci right 5.331725e-02	k: 1004	n:20000
KS ci ratio: 2.591010e-02	ci left: 5.267067e-01	ci right 5.405835e-01	k: 10673	n:20000
HSD17B4   20000 perm   6 sec   (3439 perm/sec)   p_kst 5.336500e-01   p_cons 5.020000e-02   p_joint 1.575000e-01

Joint ci ratio: 4.976090e-02	ci left: 1.671178e-01	ci right 1.756792e-01	k: 5141	n:30000
Cons ci ratio: 9.182534e-02	ci left: 5.463110e-02	ci right 5.992171e-02	k: 1717	n:30000
KS ci ratio: 2.125892e-02	ci left: 5.255670e-01	ci right 5.368936e-01	k: 15937	n:30000
HSD17B4   30000 perm   8 sec   (3711 perm/sec)   p_kst 5.312333e-01   p_cons 5.723333e-02   p_joint 1.713667e-01

Outputting figure to mutsig2_images.part000000000081/HSD17B4.4_2307_30000_0.53123_0.057233_0.17137.png
                gene_name: HSD17B4
               theta_stop: 0.092 
                    nperm: 30000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.057 
      ci_cons_bounds_left: 0.055 
     ci_cons_bounds_right: 0.060 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 50 percent done.
HRNR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 9.813094e-03	ci left: 9.363056e-01	ci right 9.456355e-01	k: 9411	n:10000
KS ci ratio: 2.817083e-02	ci left: 6.500161e-01	ci right 6.686910e-01	k: 6594	n:10000
HRNR   10000 perm   2 sec   (4078 perm/sec)   p_kst 6.594000e-01   p_cons 9.411000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000081/HRNR.3_8561_10000_0.6594_0.9411_1.png
                gene_name: HRNR
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000081
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 81 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 4398059: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000082> was used as the working directory.
Started at Wed Oct 24 16:12:44 2012
Results reported at Wed Oct 24 16:16:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000082.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000082.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 82  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000082.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    252.50 sec.
    Max Memory :      1587 MB
    Max Swap   :      4036 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
82
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 82
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 82: processing genes 7268 - 7356
Calculating significance of each gene.
Using projection method.
7268	HSPB2	1
7269	HSPB3	1
7270	HSPB7	1
7271	HSPB8	4.749125e-02
7272	HSPB9	1
7273	HSPBAP1	1
7274	HSPBP1	1
7275	HSPC159	1
7276	HSPD1	1
7277	HSPE1	1
7278	HSPG2	1
7279	HSPH1	1.548693e-01
7280	HTATIP2	1
7281	HTATSF1	5.039894e-02
7282	HTN1	1
7283	HTN3	1
7284	HTR1A	1
7285	HTR1B	1
7286	HTR1D	1
7287	HTR1E	1
7288	HTR1F	1.207604e-01
7289	HTR2A	1
7290	HTR2B	1
7291	HTR2C	1
7292	HTR3A	1
7293	HTR3B	7.823233e-02
7294	HTR3C	1
7295	HTR3D	1
7296	HTR3E	1
7297	HTR4	1
7298	HTR5A	1
7299	HTR6	1
7300	HTR7	1
7301	HTRA1	1
7302	HTRA2	1
7303	HTRA3	1
7304	HTRA4	1
7305	HTT	5.698125e-01
7306	HUNK	1
7307	HUS1	1
7308	HUS1B	1
7309	HUWE1	3.412731e-01
7310	HVCN1	1
7311	HYAL1	1.909679e-01
7312	HYAL2	1
7313	HYAL3	1
7314	HYAL4	1
7315	HYDIN	1
7316	HYI	1
7317	HYLS1	1
7318	HYOU1	1
7319	IAH1	1
7320	IAPP	1
7321	IARS	1
7322	IARS2	1.207049e-01
7323	IBSP	1
7324	IBTK	1
7325	ICA1	2.452819e-01
7326	ICA1L	1
7327	ICAM1	1
7328	ICAM2	2.416831e-02
7329	ICAM3	1
7330	ICAM4	1
7331	ICAM5	1
7332	ICK	1
7333	ICMT	1
7334	ICOS	1
7335	ICOSLG	1
7336	ICT1	1
7337	ID1	1
7338	ID2	1
7339	ID3	1
7340	IDE	1
7341	IDH1	1
7342	IDH2	1
7343	IDH3A	1
7344	IDH3B	1
7345	IDH3G	1
7346	IDI1	1
7347	IDI2	1
7348	IDO1	1
7349	IDO2	1
7350	IDS	1
7351	IDUA	1
7352	IER2	1
7353	IER3	1
7354	IER3IP1	1
7355	IER5	1
7356	IER5L	1
Done

Running MutSig 2:
Scatter job 82: processing genes 7268 - 7356
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HTT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.226904e-02	ci left: 4.524903e-01	ci right 4.721317e-01	k: 4623	n:10000
Cons ci ratio: 4.642761e-02	ci left: 4.064147e-01	ci right 4.258341e-01	k: 4161	n:10000
KS ci ratio: 4.567166e-02	ci left: 4.143870e-01	ci right 4.338572e-01	k: 4241	n:10000
HTT   10000 perm   3 sec   (2929 perm/sec)   p_kst 4.241000e-01   p_cons 4.161000e-01   p_joint 4.623000e-01

Outputting figure to mutsig2_images.part000000000082/HTT.3_9697_10000_0.4241_0.4161_0.4623.png
                gene_name: HTT
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 25 percent done.
HUWE1
Processing conservation and coverage...
74% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.409181e-02	ci left: 5.595257e-01	ci right 5.790339e-01	k: 5693	n:10000
KS ci ratio: 2.111569e-02	ci left: 7.667873e-01	ci right 7.832521e-01	k: 7751	n:10000
HUWE1   10000 perm   5 sec   (2160 perm/sec)   p_kst 7.751000e-01   p_cons 5.693000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000082/HUWE1.3_13449_10000_0.7751_0.5693_1.png
                gene_name: HUWE1
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
HTATSF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.824899e-02	ci left: 8.142578e-01	ci right 8.293542e-01	k: 8219	n:10000
Cons ci ratio: 1.997354e-02	ci left: 7.858368e-01	ci right 8.017917e-01	k: 7939	n:10000
KS ci ratio: 3.268756e-02	ci left: 5.800845e-01	ci right 5.994631e-01	k: 5898	n:10000
HTATSF1   10000 perm   2 sec   (6108 perm/sec)   p_kst 5.898000e-01   p_cons 7.939000e-01   p_joint 8.219000e-01

Outputting figure to mutsig2_images.part000000000082/HTATSF1.2_2304_10000_0.5898_0.7939_0.8219.png
                gene_name: HTATSF1
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.83 

Current progress: 75 percent done.
IARS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.545381e-02	ci left: 3.238620e-01	ci right 3.424353e-01	k: 3331	n:10000
Cons ci ratio: 1.803680e-02	ci left: 8.177134e-01	ci right 8.326966e-01	k: 8253	n:10000
KS ci ratio: 3.842359e-01	ci left: 8.324320e-03	ci right 1.236857e-02	k: 102	n:10000
IARS2   10000 perm   2 sec   (5384 perm/sec)   p_kst 1.020000e-02   p_cons 8.253000e-01   p_joint 3.331000e-01

Joint ci ratio: 1.945223e-01	ci left: 1.796192e-02	ci right 2.187941e-02	k: 397	n:20000
Cons ci ratio: 1.285063e-02	ci left: 8.177398e-01	ci right 8.283661e-01	k: 16462	n:20000
KS ci ratio: 2.807961e-01	ci left: 8.295294e-03	ci right 1.105008e-02	k: 192	n:20000
IARS2   20000 perm   4 sec   (4791 perm/sec)   p_kst 9.600000e-03   p_cons 8.231000e-01   p_joint 1.985000e-02

Joint ci ratio: 2.345460e-02	ci left: 4.764643e-01	ci right 4.878058e-01	k: 14464	n:30000
Cons ci ratio: 1.050077e-02	ci left: 8.184986e-01	ci right 8.271721e-01	k: 24686	n:30000
KS ci ratio: 2.172740e-01	ci left: 9.566664e-03	ci right 1.192952e-02	k: 321	n:30000
IARS2   30000 perm   7 sec   (4559 perm/sec)   p_kst 1.070000e-02   p_cons 8.228667e-01   p_joint 4.821333e-01

Joint ci ratio: 7.027343e-02	ci left: 6.963306e-02	ci right 7.472926e-02	k: 2886	n:40000
Cons ci ratio: 9.097519e-03	ci left: 8.189718e-01	ci right 8.264813e-01	k: 32910	n:40000
KS ci ratio: 1.862743e-01	ci left: 9.929432e-03	ci right 1.199249e-02	k: 437	n:40000
IARS2   40000 perm   9 sec   (4413 perm/sec)   p_kst 1.092500e-02   p_cons 8.227500e-01   p_joint 7.215000e-02

Joint ci ratio: 6.288982e-02	ci left: 6.982802e-02	ci right 7.438181e-02	k: 3604	n:50000
Cons ci ratio: 8.118343e-03	ci left: 8.200490e-01	ci right 8.267534e-01	k: 41171	n:50000
KS ci ratio: 1.629616e-01	ci left: 1.050712e-02	ci right 1.239024e-02	k: 571	n:50000
IARS2   50000 perm   12 sec   (4304 perm/sec)   p_kst 1.142000e-02   p_cons 8.234200e-01   p_joint 7.208000e-02

Joint ci ratio: 5.739607e-02	ci left: 7.005922e-02	ci right 7.421561e-02	k: 4327	n:60000
Cons ci ratio: 7.432293e-03	ci left: 8.195027e-01	ci right 8.256328e-01	k: 49355	n:60000
KS ci ratio: 1.510503e-01	ci left: 1.026102e-02	ci right 1.195344e-02	k: 665	n:60000
IARS2   60000 perm   14 sec   (4215 perm/sec)   p_kst 1.108333e-02   p_cons 8.225833e-01   p_joint 7.211667e-02

Joint ci ratio: 5.319149e-02	ci left: 7.008165e-02	ci right 7.392535e-02	k: 5039	n:70000
Cons ci ratio: 6.881235e-03	ci left: 8.197209e-01	ci right 8.253952e-01	k: 57580	n:70000
KS ci ratio: 1.399367e-01	ci left: 1.030946e-02	ci right 1.187432e-02	k: 775	n:70000
IARS2   70000 perm   17 sec   (4126 perm/sec)   p_kst 1.107143e-02   p_cons 8.225714e-01   p_joint 7.198571e-02

Joint ci ratio: 4.970964e-02	ci left: 7.032930e-02	ci right 7.392680e-02	k: 5769	n:80000
Cons ci ratio: 6.427622e-03	ci left: 8.203247e-01	ci right 8.256269e-01	k: 65839	n:80000
KS ci ratio: 1.311126e-01	ci left: 1.032504e-02	ci right 1.178574e-02	k: 883	n:80000
IARS2   80000 perm   20 sec   (4044 perm/sec)   p_kst 1.103750e-02   p_cons 8.229875e-01   p_joint 7.211250e-02

Joint ci ratio: 4.688327e-02	ci left: 7.038544e-02	ci right 7.377553e-02	k: 6486	n:90000
Cons ci ratio: 6.050971e-03	ci left: 8.209151e-01	ci right 8.259085e-01	k: 74108	n:90000
KS ci ratio: 1.236457e-01	ci left: 1.036112e-02	ci right 1.173733e-02	k: 993	n:90000
IARS2   90000 perm   23 sec   (3966 perm/sec)   p_kst 1.103333e-02   p_cons 8.234222e-01   p_joint 7.206667e-02

Joint ci ratio: 4.433430e-02	ci left: 7.090020e-02	ci right 7.412465e-02	k: 7250	n:100000
Cons ci ratio: 5.738322e-03	ci left: 8.211528e-01	ci right 8.258884e-01	k: 82353	n:100000
KS ci ratio: 1.161077e-01	ci left: 1.061523e-02	ci right 1.193334e-02	k: 1126	n:100000
IARS2   100000 perm   26 sec   (3896 perm/sec)   p_kst 1.126000e-02   p_cons 8.235300e-01   p_joint 7.250000e-02

Joint ci ratio: 5.273080e-03	ci left: 8.317878e-01	ci right 8.361945e-01	k: 91740	n:110000
Cons ci ratio: 5.466018e-03	ci left: 8.215446e-01	ci right 8.260565e-01	k: 90619	n:110000
KS ci ratio: 1.101975e-01	ci left: 1.074563e-02	ci right 1.200760e-02	k: 1250	n:110000
IARS2   110000 perm   29 sec   (3827 perm/sec)   p_kst 1.136364e-02   p_cons 8.238091e-01   p_joint 8.340000e-01

Joint ci ratio: 4.046451e-02	ci left: 7.106376e-02	ci right 7.400694e-02	k: 8703	n:120000
Cons ci ratio: 5.232724e-03	ci left: 8.216743e-01	ci right 8.259934e-01	k: 98861	n:120000
KS ci ratio: 1.058490e-01	ci left: 1.070151e-02	ci right 1.190561e-02	k: 1355	n:120000
IARS2   120000 perm   32 sec   (3763 perm/sec)   p_kst 1.129167e-02   p_cons 8.238417e-01   p_joint 7.252500e-02

Joint ci ratio: 3.888669e-02	ci left: 7.108846e-02	ci right 7.391526e-02	k: 9424	n:130000
Cons ci ratio: 5.018829e-03	ci left: 8.222588e-01	ci right 8.264036e-01	k: 107164	n:130000
KS ci ratio: 1.022612e-01	ci left: 1.060503e-02	ci right 1.175539e-02	k: 1452	n:130000
IARS2   130000 perm   35 sec   (3696 perm/sec)   p_kst 1.116923e-02   p_cons 8.243385e-01   p_joint 7.249231e-02

Joint ci ratio: 3.749407e-02	ci left: 7.106198e-02	ci right 7.378434e-02	k: 10138	n:140000
Cons ci ratio: 4.843583e-03	ci left: 8.218945e-01	ci right 8.258921e-01	k: 115346	n:140000
KS ci ratio: 9.888610e-02	ci left: 1.055079e-02	ci right 1.165531e-02	k: 1553	n:140000
IARS2   140000 perm   39 sec   (3628 perm/sec)   p_kst 1.109286e-02   p_cons 8.239000e-01   p_joint 7.241429e-02

Outputting figure to mutsig2_images.part000000000082/IARS2.2_3131_140000_0.011093_0.8239_0.072414.png
                gene_name: IARS2
               theta_stop: 0.099 
                    nperm: 140000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.011 
       ci_ks_bounds_right: 0.012 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.072 
     ci_joint_bounds_left: 0.071 
    ci_joint_bounds_right: 0.074 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000082
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 82 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 4398062: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000083> was used as the working directory.
Started at Wed Oct 24 16:12:47 2012
Results reported at Wed Oct 24 16:14:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000083.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000083.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 83  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000083.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    141.27 sec.
    Max Memory :      1280 MB
    Max Swap   :      4003 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
83
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 83
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 83: processing genes 7357 - 7446
Calculating significance of each gene.
Using projection method.
7357	IFFO1	1
7358	IFI16	1.601259e-01
7359	IFI27	1
7360	IFI27L1	1
7361	IFI27L2	1
7362	IFI30	1
7363	IFI35	1
7364	IFI44	2.210115e-01
7365	IFI44L	1
7366	IFI6	1
7367	IFIH1	1
7368	IFIT1	1
7369	IFIT1B	1
7370	IFIT2	1
7371	IFIT3	1
7372	IFIT5	1
7373	IFITM1	1
7374	IFITM2	1
7375	IFITM3	1
7376	IFITM5	1
7377	IFLTD1	1
7378	IFNA1	4.308622e-02
7379	IFNA10	1
7380	IFNA13	1
7381	IFNA14	1
7382	IFNA16	1
7383	IFNA17	1
7384	IFNA2	1
7385	IFNA21	1
7386	IFNA4	1
7387	IFNA5	1
7388	IFNA6	1
7389	IFNA7	1
7390	IFNA8	1
7391	IFNAR1	1.083894e-02
7392	IFNAR2	2.650049e-01
7393	IFNB1	1
7394	IFNE	1
7395	IFNG	1
7396	IFNGR1	1.568195e-02
7397	IFNGR2	2.815888e-02
7398	IFNK	1
7399	IFNW1	1
7400	IFRD1	1
7401	IFRD2	1
7402	IFT122	1
7403	IFT140	1
7404	IFT172	2.226875e-01
7405	IFT20	1
7406	IFT27	1
7407	IFT46	1
7408	IFT52	1
7409	IFT57	1
7410	IFT74	1
7411	IFT80	1
7412	IFT81	1
7413	IFT88	1
7414	IGBP1	1
7415	IGDCC3	2.255037e-02
7416	IGDCC4	1
7417	IGF1	1
7418	IGF1R	1
7419	IGF2	1
7420	IGF2BP1	1
7421	IGF2BP2	1
7422	IGF2BP3	2.325114e-01
7423	IGF2R	1
7424	IGFALS	1
7425	IGFBP1	1
7426	IGFBP2	1
7427	IGFBP3	1
7428	IGFBP4	1
7429	IGFBP5	1
7430	IGFBP6	1
7431	IGFBP7	1
7432	IGFBPL1	1
7433	IGFL1	1
7434	IGFL2	1
7435	IGFL3	1
7436	IGFL4	6.106493e-03
7437	IGHMBP2	1.671047e-01
7438	IGJ	1
7439	IGLL1	1
7440	IGLL5	1
7441	IGLON5	1
7442	IGSF1	3.570835e-01
7443	IGSF10	5.230334e-01
7444	IGSF11	5.933451e-02
7445	IGSF21	1
7446	IGSF22	8.011547e-02
Done

Running MutSig 2:
Scatter job 83: processing genes 7357 - 7446
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
IFNAR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.354312e-02	ci left: 7.261314e-01	ci right 7.435316e-01	k: 7349	n:10000
Cons ci ratio: 3.920980e-02	ci left: 4.899514e-01	ci right 5.096487e-01	k: 4998	n:10000
KS ci ratio: 3.062734e-02	ci left: 6.113069e-01	ci right 6.304227e-01	k: 6209	n:10000
IFNAR1   10000 perm   2 sec   (6155 perm/sec)   p_kst 6.209000e-01   p_cons 4.998000e-01   p_joint 7.349000e-01

Outputting figure to mutsig2_images.part000000000083/IFNAR1.2_1718_10000_0.6209_0.4998_0.7349.png
                gene_name: IFNAR1
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.73 
     ci_joint_bounds_left: 0.73 
    ci_joint_bounds_right: 0.74 

Current progress: 20 percent done.
IFNGR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.205181e-02	ci left: 9.080250e-01	ci right 9.191326e-01	k: 9137	n:10000
Cons ci ratio: 8.101469e-02	ci left: 1.819585e-01	ci right 1.974227e-01	k: 1896	n:10000
KS ci ratio: 3.158488e-02	ci left: 5.966444e-01	ci right 6.158937e-01	k: 6063	n:10000
IFNGR1   10000 perm   2 sec   (6467 perm/sec)   p_kst 6.063000e-01   p_cons 1.896000e-01   p_joint 9.137000e-01

Outputting figure to mutsig2_images.part000000000083/IFNGR1.2_1498_10000_0.6063_0.1896_0.9137.png
                gene_name: IFNGR1
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 40 percent done.
IGDCC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.888152e-02	ci left: 8.038971e-01	ci right 8.193209e-01	k: 8117	n:10000
KS ci ratio: 9.536123e-03	ci left: 9.395202e-01	ci right 9.486189e-01	k: 9442	n:10000
IGDCC3   10000 perm   2 sec   (6185 perm/sec)   p_kst 9.442000e-01   p_cons 8.117000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000083/IGDCC3.2_2501_10000_0.9442_0.8117_1.png
                gene_name: IGDCC3
               theta_stop: 0.019 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.94 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.82 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
IGSF10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.630117e-02	ci left: 8.454992e-01	ci right 8.594947e-01	k: 8526	n:10000
Cons ci ratio: 2.095822e-02	ci left: 7.694204e-01	ci right 7.858176e-01	k: 7777	n:10000
KS ci ratio: 5.521756e-02	ci left: 3.257483e-01	ci right 3.443479e-01	k: 3350	n:10000
IGSF10   10000 perm   2 sec   (4258 perm/sec)   p_kst 3.350000e-01   p_cons 7.777000e-01   p_joint 8.526000e-01

Outputting figure to mutsig2_images.part000000000083/IGSF10.2_7944_10000_0.335_0.7777_0.8526.png
                gene_name: IGSF10
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.85 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.86 

Current progress: 80 percent done.
IGSF22
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.019629e-02	ci left: 9.317489e-01	ci right 9.413948e-01	k: 9367	n:10000
KS ci ratio: 3.102546e-02	ci left: 6.051797e-01	ci right 6.243534e-01	k: 6148	n:10000
IGSF22   10000 perm   2 sec   (5600 perm/sec)   p_kst 6.148000e-01   p_cons 9.367000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000083/IGSF22.2_4069_10000_0.6148_0.9367_1.png
                gene_name: IGSF22
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000083
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 83 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4398066: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000084> was used as the working directory.
Started at Wed Oct 24 16:12:53 2012
Results reported at Wed Oct 24 16:15:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000084.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000084.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 84  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000084.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    173.66 sec.
    Max Memory :      1214 MB
    Max Swap   :      3901 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
84
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 84
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 84: processing genes 7447 - 7536
Calculating significance of each gene.
Using projection method.
7447	IGSF3	1
7448	IGSF5	1
7449	IGSF6	1
7450	IGSF8	1
7451	IGSF9	1
7452	IGSF9B	1.146215e-02
7453	IHH	1
7454	IK	1
7455	IKBIP	1
7456	IKBKAP	3.467190e-01
7457	IKBKB	1
7458	IKBKE	1
7459	IKZF1	1.938015e-02
7460	IKZF2	2.810808e-02
7461	IKZF3	1
7462	IKZF4	1
7463	IKZF5	1
7464	IL10	1
7465	IL10RA	1
7466	IL10RB	7.031156e-02
7467	IL11RA	1.691391e-01
7468	IL12A	1
7469	IL12B	9.368630e-02
7470	IL12RB1	1
7471	IL12RB2	1
7472	IL13	1
7473	IL13RA1	1
7474	IL13RA2	6.404945e-02
7475	IL15	1
7476	IL15RA	1.199899e-01
7477	IL16	1
7478	IL17A	1
7479	IL17B	1
7480	IL17C	5.453952e-02
7481	IL17D	1
7482	IL17F	1
7483	IL17RA	1
7484	IL17RB	1
7485	IL17RC	1
7486	IL17RD	1
7487	IL17RE	1
7488	IL17REL	1
7489	IL18	1
7490	IL18BP	1
7491	IL18R1	1
7492	IL18RAP	6.294386e-02
7493	IL19	1
7494	IL1A	4.045873e-02
7495	IL1B	1
7496	IL1F10	1
7497	IL1F5	1
7498	IL1F6	1
7499	IL1F7	1.334547e-01
7500	IL1F8	6.751971e-02
7501	IL1F9	1
7502	IL1R1	9.460173e-02
7503	IL1R2	1
7504	IL1RAP	1
7505	IL1RAPL1	1
7506	IL1RAPL2	1
7507	IL1RL1	1
7508	IL1RL2	1
7509	IL1RN	1
7510	IL2	1
7511	IL20	1
7512	IL20RA	1.081032e-01
7513	IL20RB	1
7514	IL21	1
7515	IL21R	1
7516	IL22	1
7517	IL22RA1	1
7518	IL22RA2	1
7519	IL23A	1
7520	IL23R	1
7521	IL24	1
7522	IL25	1
7523	IL26	1
7524	IL27	1
7525	IL27RA	1
7526	IL28A	9.748894e-02
7527	IL28B	5.833422e-03
7528	IL28RA	7.544162e-02
7529	IL29	1
7530	IL2RA	1
7531	IL2RB	1
7532	IL2RG	1
7533	IL3	1
7534	IL31	1
7535	IL31RA	1
7536	IL32	1
Done

Running MutSig 2:
Scatter job 84: processing genes 7447 - 7536
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
IGSF9B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.265993e-01	ci left: 1.188149e-02	ci right 1.660771e-02	k: 141	n:10000
Cons ci ratio: 1.125355e-01	ci left: 1.020789e-01	ci right 1.143503e-01	k: 1081	n:10000
KS ci ratio: 3.683071e-01	ci left: 9.139894e-03	ci right 1.335208e-02	k: 111	n:10000
IGSF9B   10000 perm   2 sec   (5293 perm/sec)   p_kst 1.110000e-02   p_cons 1.081000e-01   p_joint 1.410000e-02

Joint ci ratio: 4.033559e-01	ci left: 3.754742e-03	ci right 5.693581e-03	k: 93	n:20000
Cons ci ratio: 7.992864e-02	ci left: 1.030430e-01	ci right 1.116715e-01	k: 2146	n:20000
KS ci ratio: 2.710386e-01	ci left: 8.947269e-03	ci right 1.179778e-02	k: 206	n:20000
IGSF9B   20000 perm   6 sec   (3370 perm/sec)   p_kst 1.030000e-02   p_cons 1.073000e-01   p_joint 4.650000e-03

Joint ci ratio: 1.052425e-01	ci left: 4.186922e-02	ci right 4.655289e-02	k: 1325	n:30000
Cons ci ratio: 5.998802e-02	ci left: 1.208497e-01	ci right 1.283565e-01	k: 3737	n:30000
KS ci ratio: 2.255632e-01	ci left: 8.842131e-03	ci right 1.112094e-02	k: 298	n:30000
IGSF9B   30000 perm   8 sec   (3626 perm/sec)   p_kst 9.933333e-03   p_cons 1.245667e-01   p_joint 4.416667e-02

Joint ci ratio: 1.801367e-01	ci left: 1.064539e-02	ci right 1.277639e-02	k: 467	n:40000
Cons ci ratio: 5.201092e-02	ci left: 1.211064e-01	ci right 1.275983e-01	k: 4973	n:40000
KS ci ratio: 1.945245e-01	ci left: 9.071922e-03	ci right 1.105018e-02	k: 401	n:40000
IGSF9B   40000 perm   11 sec   (3676 perm/sec)   p_kst 1.002500e-02   p_cons 1.243250e-01   p_joint 1.167500e-02

Joint ci ratio: 2.160643e-01	ci left: 5.833321e-03	ci right 7.264875e-03	k: 326	n:50000
Cons ci ratio: 4.659069e-02	ci left: 1.211230e-01	ci right 1.269207e-01	k: 6200	n:50000
KS ci ratio: 1.735529e-01	ci left: 9.222959e-03	ci right 1.099461e-02	k: 504	n:50000
IGSF9B   50000 perm   13 sec   (3740 perm/sec)   p_kst 1.008000e-02   p_cons 1.240000e-01   p_joint 6.520000e-03

Joint ci ratio: 1.996607e-01	ci left: 5.745887e-03	ci right 7.035891e-03	k: 382	n:60000
Cons ci ratio: 4.260065e-02	ci left: 1.210260e-01	ci right 1.263105e-01	k: 7419	n:60000
KS ci ratio: 1.622619e-01	ci left: 8.851240e-03	ci right 1.043007e-02	k: 577	n:60000
IGSF9B   60000 perm   16 sec   (3764 perm/sec)   p_kst 9.616667e-03   p_cons 1.236500e-01   p_joint 6.366667e-03

Joint ci ratio: 1.886772e-01	ci left: 5.550207e-03	ci right 6.719871e-03	k: 428	n:70000
Cons ci ratio: 3.939817e-02	ci left: 1.214536e-01	ci right 1.263490e-01	k: 8672	n:70000
KS ci ratio: 1.506018e-01	ci left: 8.863399e-03	ci right 1.032054e-02	k: 670	n:70000
IGSF9B   70000 perm   19 sec   (3723 perm/sec)   p_kst 9.571429e-03   p_cons 1.238857e-01   p_joint 6.114286e-03

Joint ci ratio: 8.284394e-02	ci left: 2.609597e-02	ci right 2.836349e-02	k: 2177	n:80000
Cons ci ratio: 3.682819e-02	ci left: 1.217608e-01	ci right 1.263415e-01	k: 9923	n:80000
KS ci ratio: 1.401260e-01	ci left: 9.008284e-03	ci right 1.037763e-02	k: 774	n:80000
IGSF9B   80000 perm   22 sec   (3719 perm/sec)   p_kst 9.675000e-03   p_cons 1.240375e-01   p_joint 2.721250e-02

Joint ci ratio: 7.919679e-02	ci left: 2.544949e-02	ci right 2.755896e-02	k: 2384	n:90000
Cons ci ratio: 3.470512e-02	ci left: 1.219967e-01	ci right 1.263164e-01	k: 11173	n:90000
KS ci ratio: 1.317977e-01	ci left: 9.091463e-03	ci right 1.038488e-02	k: 875	n:90000
IGSF9B   90000 perm   24 sec   (3706 perm/sec)   p_kst 9.722222e-03   p_cons 1.241444e-01   p_joint 2.648889e-02

Joint ci ratio: 7.526410e-02	ci left: 2.541509e-02	ci right 2.741251e-02	k: 2640	n:100000
Cons ci ratio: 3.288119e-02	ci left: 1.223901e-01	ci right 1.264917e-01	k: 12443	n:100000
KS ci ratio: 1.246684e-01	ci left: 9.179316e-03	ci right 1.040937e-02	k: 978	n:100000
IGSF9B   100000 perm   27 sec   (3684 perm/sec)   p_kst 9.780000e-03   p_cons 1.244300e-01   p_joint 2.640000e-02

Joint ci ratio: 7.352342e-02	ci left: 2.426392e-02	ci right 2.612486e-02	k: 2770	n:110000
Cons ci ratio: 3.141840e-02	ci left: 1.220216e-01	ci right 1.259255e-01	k: 13636	n:110000
KS ci ratio: 1.179248e-01	ci left: 9.358633e-03	ci right 1.054015e-02	k: 1093	n:110000
IGSF9B   110000 perm   30 sec   (3653 perm/sec)   p_kst 9.936364e-03   p_cons 1.239636e-01   p_joint 2.518182e-02

Joint ci ratio: 6.245688e-02	ci left: 3.078976e-02	ci right 3.278295e-02	k: 3813	n:120000
Cons ci ratio: 3.012330e-02	ci left: 1.218007e-01	ci right 1.255341e-01	k: 14839	n:120000
KS ci ratio: 1.120285e-01	ci left: 9.533859e-03	ci right 1.067334e-02	k: 1211	n:120000
IGSF9B   120000 perm   33 sec   (3622 perm/sec)   p_kst 1.009167e-02   p_cons 1.236583e-01   p_joint 3.177500e-02

Joint ci ratio: 5.999790e-02	ci left: 3.083761e-02	ci right 3.275258e-02	k: 4132	n:130000
Cons ci ratio: 2.891554e-02	ci left: 1.220677e-01	ci right 1.256568e-01	k: 16101	n:130000
KS ci ratio: 1.083444e-01	ci left: 9.428804e-03	ci right 1.051630e-02	k: 1295	n:130000
IGSF9B   130000 perm   36 sec   (3586 perm/sec)   p_kst 9.961538e-03   p_cons 1.238538e-01   p_joint 3.178462e-02

Joint ci ratio: 5.788885e-02	ci left: 3.079544e-02	ci right 3.263831e-02	k: 4439	n:140000
Cons ci ratio: 2.786337e-02	ci left: 1.221358e-01	ci right 1.255941e-01	k: 17340	n:140000
KS ci ratio: 1.045430e-01	ci left: 9.422776e-03	ci right 1.046910e-02	k: 1391	n:140000
IGSF9B   140000 perm   39 sec   (3551 perm/sec)   p_kst 9.935714e-03   p_cons 1.238571e-01   p_joint 3.170714e-02

Joint ci ratio: 5.598762e-02	ci left: 3.075992e-02	ci right 3.253824e-02	k: 4746	n:150000
Cons ci ratio: 2.694477e-02	ci left: 1.219848e-01	ci right 1.253231e-01	k: 18547	n:150000
KS ci ratio: 1.013222e-01	ci left: 9.379135e-03	ci right 1.038661e-02	k: 1481	n:150000
IGSF9B   150000 perm   43 sec   (3513 perm/sec)   p_kst 9.873333e-03   p_cons 1.236467e-01   p_joint 3.164000e-02

Joint ci ratio: 5.417923e-02	ci left: 3.082223e-02	ci right 3.254479e-02	k: 5068	n:160000
Cons ci ratio: 2.607378e-02	ci left: 1.221650e-01	ci right 1.253986e-01	k: 19804	n:160000
KS ci ratio: 9.838173e-02	ci left: 9.341383e-03	ci right 1.031400e-02	k: 1571	n:160000
IGSF9B   160000 perm   46 sec   (3476 perm/sec)   p_kst 9.818750e-03   p_cons 1.237750e-01   p_joint 3.167500e-02

Outputting figure to mutsig2_images.part000000000084/IGSF9B.2_4126_160000_0.0098187_0.12377_0.031675.png
                gene_name: IGSF9B
               theta_stop: 0.098 
                    nperm: 160000 
                     p_ks: 0.0098 
        ci_ks_bounds_left: 0.0093 
       ci_ks_bounds_right: 0.010 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.032 
     ci_joint_bounds_left: 0.031 
    ci_joint_bounds_right: 0.033 

Current progress: 25 percent done.
IKBKAP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.946119e-02	ci left: 6.294971e-01	ci right 6.484219e-01	k: 6390	n:10000
Cons ci ratio: 4.788103e-02	ci left: 3.915733e-01	ci right 4.108842e-01	k: 4012	n:10000
KS ci ratio: 2.201022e-02	ci left: 7.518078e-01	ci right 7.686403e-01	k: 7603	n:10000
IKBKAP   10000 perm   2 sec   (5280 perm/sec)   p_kst 7.603000e-01   p_cons 4.012000e-01   p_joint 6.390000e-01

Outputting figure to mutsig2_images.part000000000084/IKBKAP.2_4143_10000_0.7603_0.4012_0.639.png
                gene_name: IKBKAP
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 50 percent done.
IKZF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.810253e-03	ci left: 9.579609e-01	ci right 9.655670e-01	k: 9619	n:10000
Cons ci ratio: 6.070122e-02	ci left: 2.852798e-01	ci right 3.032402e-01	k: 2942	n:10000
KS ci ratio: 6.920559e-02	ci left: 2.344220e-01	ci right 2.513280e-01	k: 2428	n:10000
IKZF1   10000 perm   2 sec   (6205 perm/sec)   p_kst 2.428000e-01   p_cons 2.942000e-01   p_joint 9.619000e-01

Outputting figure to mutsig2_images.part000000000084/IKZF1.2_1588_10000_0.2428_0.2942_0.9619.png
                gene_name: IKZF1
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.29 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 75 percent done.
IKZF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.417902e-01	ci left: 6.594512e-02	ci right 7.610649e-02	k: 709	n:10000
Cons ci ratio: 1.316798e-01	ci left: 7.601602e-02	ci right 8.682930e-02	k: 813	n:10000
KS ci ratio: 7.712279e-02	ci left: 1.973215e-01	ci right 2.132506e-01	k: 2052	n:10000
IKZF2   10000 perm   2 sec   (6360 perm/sec)   p_kst 2.052000e-01   p_cons 8.130000e-02   p_joint 7.090000e-02

Joint ci ratio: 5.825519e-02	ci left: 1.791948e-01	ci right 1.899971e-01	k: 3691	n:20000
Cons ci ratio: 9.289637e-02	ci left: 7.793991e-02	ci right 8.558220e-02	k: 1634	n:20000
KS ci ratio: 5.421917e-02	ci left: 2.015513e-01	ci right 2.128339e-01	k: 4143	n:20000
IKZF2   20000 perm   4 sec   (5676 perm/sec)   p_kst 2.071500e-01   p_cons 8.170000e-02   p_joint 1.845500e-01

Outputting figure to mutsig2_images.part000000000084/IKZF2.2_1609_20000_0.20715_0.0817_0.18455.png
                gene_name: IKZF2
               theta_stop: 0.093 
                    nperm: 20000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.082 
      ci_cons_bounds_left: 0.078 
     ci_cons_bounds_right: 0.086 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000084
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 84 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4398069: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000085> was used as the working directory.
Started at Wed Oct 24 16:12:53 2012
Results reported at Wed Oct 24 16:14:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000085.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000085.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 85  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000085.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     94.58 sec.
    Max Memory :      1164 MB
    Max Swap   :      3911 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
85
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 85
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 85: processing genes 7537 - 7625
Calculating significance of each gene.
Using projection method.
7537	IL33	1
7538	IL34	1
7539	IL3RA	2.007324e-01
7540	IL4	1
7541	IL4I1	1
7542	IL4R	1
7543	IL5	1
7544	IL5RA	1.116296e-01
7545	IL6	1
7546	IL6R	1
7547	IL6ST	1
7548	IL7	1
7549	IL7R	1
7550	IL8	7.865776e-03
7551	IL9	1
7552	IL9R	1.021018e-01
7553	ILDR1	1
7554	ILDR2	2.023558e-01
7555	ILF2	1.502743e-01
7556	ILF3	1
7557	ILK	1
7558	ILKAP	1
7559	ILVBL	1
7560	IMMP1L	1.674342e-02
7561	IMMP2L	1
7562	IMMT	1
7563	IMP3	1
7564	IMP4	1
7565	IMP5	1
7566	IMPA1	1
7567	IMPA2	1
7568	IMPACT	1
7569	IMPAD1	1
7570	IMPDH1	1
7571	IMPDH2	1
7572	IMPG1	2.704360e-01
7573	IMPG2	1
7574	INA	1
7575	INADL	1
7576	INCA1	1
7577	INCENP	1
7578	INF2	1
7579	ING1	1
7580	ING2	1
7581	ING3	1
7582	ING4	1
7583	ING5	1
7584	INHA	1
7585	INHBA	1
7586	INHBB	1
7587	INHBC	1
7588	INHBE	1
7589	INMT	1
7590	INO80	1
7591	INO80B	1
7592	INO80C	1
7593	INO80D	1.356110e-02
7594	INO80E	5.256714e-02
7595	INPP1	1.953221e-01
7596	INPP4A	1
7597	INPP4B	1
7598	INPP5A	1
7599	INPP5B	1
7600	INPP5D	1
7601	INPP5E	1
7602	INPP5F	1
7603	INPP5J	1
7604	INPP5K	1
7605	INPPL1	1
7606	INS	1
7607	INS-IGF2	1
7608	INSC	1
7609	INSIG1	1
7610	INSIG2	1
7611	INSL3	1
7612	INSL4	1
7613	INSL5	1
7614	INSL6	1
7615	INSM2	1
7616	INSR	1
7617	INSRR	1
7618	INTS1	5.451599e-02
7619	INTS10	1
7620	INTS12	1
7621	INTS2	7.386533e-02
7622	INTS3	1
7623	INTS4	5.839479e-02
7624	INTS5	1
7625	INTS6	1
Done

Running MutSig 2:
Scatter job 85: processing genes 7537 - 7625
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
INO80D
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.606034e-03	ci left: 9.599514e-01	ci right 9.673753e-01	k: 9638	n:10000
Cons ci ratio: 3.292450e-02	ci left: 5.765733e-01	ci right 5.959764e-01	k: 5863	n:10000
KS ci ratio: 6.042473e-02	ci left: 2.871625e-01	ci right 3.051564e-01	k: 2961	n:10000
INO80D   10000 perm   2 sec   (5661 perm/sec)   p_kst 2.961000e-01   p_cons 5.863000e-01   p_joint 9.638000e-01

Outputting figure to mutsig2_images.part000000000085/INO80D.2_3120_10000_0.2961_0.5863_0.9638.png
                gene_name: INO80D
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 25 percent done.
INTS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.720472e-02	ci left: 6.656194e-01	ci right 6.840787e-01	k: 6749	n:10000
KS ci ratio: 4.180446e-02	ci left: 4.579811e-01	ci right 4.776377e-01	k: 4678	n:10000
INTS1   10000 perm   2 sec   (4702 perm/sec)   p_kst 4.678000e-01   p_cons 6.749000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000085/INTS1.2_6761_10000_0.4678_0.6749_1.png
                gene_name: INTS1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.68 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
INTS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.522196e-02	ci left: 6.981718e-01	ci right 7.161074e-01	k: 7072	n:10000
Cons ci ratio: 1.043307e-01	ci left: 1.172096e-01	ci right 1.302105e-01	k: 1236	n:10000
KS ci ratio: 8.971858e-03	ci left: 9.458575e-01	ci right 9.544778e-01	k: 9503	n:10000
INTS2   10000 perm   2 sec   (5647 perm/sec)   p_kst 9.503000e-01   p_cons 1.236000e-01   p_joint 7.072000e-01

Joint ci ratio: 4.148935e-02	ci left: 3.021518e-01	ci right 3.150039e-01	k: 6171	n:20000
Cons ci ratio: 7.404775e-02	ci left: 1.183306e-01	ci right 1.274793e-01	k: 2457	n:20000
KS ci ratio: 6.546794e-03	ci left: 9.440100e-01	ci right 9.502592e-01	k: 18944	n:20000
INTS2   20000 perm   4 sec   (5065 perm/sec)   p_kst 9.472000e-01   p_cons 1.228500e-01   p_joint 3.085500e-01

Outputting figure to mutsig2_images.part000000000085/INTS2.2_3715_20000_0.9472_0.12285_0.30855.png
                gene_name: INTS2
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.94 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.32 

Current progress: 75 percent done.
INTS4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.783125e-02	ci left: 3.920712e-01	ci right 4.113861e-01	k: 4017	n:10000
Cons ci ratio: 3.743116e-02	ci left: 5.131551e-01	ci right 5.328315e-01	k: 5230	n:10000
KS ci ratio: 6.601149e-02	ci left: 2.520172e-01	ci right 2.693224e-01	k: 2606	n:10000
INTS4   10000 perm   2 sec   (6193 perm/sec)   p_kst 2.606000e-01   p_cons 5.230000e-01   p_joint 4.017000e-01

Outputting figure to mutsig2_images.part000000000085/INTS4.2_2984_10000_0.2606_0.523_0.4017.png
                gene_name: INTS4
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.40 
     ci_joint_bounds_left: 0.39 
    ci_joint_bounds_right: 0.41 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000085
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 85 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1429>
Subject: Job 4398071: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1429>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000086> was used as the working directory.
Started at Wed Oct 24 16:12:55 2012
Results reported at Wed Oct 24 16:15:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000086.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000086.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 86  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000086.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    220.20 sec.
    Max Memory :      1284 MB
    Max Swap   :      3964 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
86
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 86
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 86: processing genes 7626 - 7715
Calculating significance of each gene.
Using projection method.
7626	INTS7	1
7627	INTS8	1
7628	INTS9	1
7629	INTU	9.719366e-02
7630	INVS	2.164079e-01
7631	IP6K1	1
7632	IP6K2	1
7633	IP6K3	1
7634	IPCEF1	1
7635	IPMK	1.491340e-01
7636	IPO11	1
7637	IPO13	1.165209e-01
7638	IPO4	1
7639	IPO5	3.563113e-02
7640	IPO7	1.647045e-01
7641	IPO8	1
7642	IPO9	4.286596e-01
7643	IPP	1
7644	IPPK	1
7645	IQCA1	1.735631e-01
7646	IQCB1	1.583669e-01
7647	IQCC	1
7648	IQCD	1
7649	IQCE	1
7650	IQCF1	1
7651	IQCF2	1
7652	IQCF3	1
7653	IQCG	4.437892e-03
7654	IQCH	1.089573e-02
7655	IQCJ	1
7656	IQCK	1
7657	IQGAP1	1
7658	IQGAP2	1
7659	IQGAP3	1
7660	IQSEC1	2.543035e-01
7661	IQSEC2	4.487555e-02
7662	IQSEC3	1.766566e-01
7663	IQUB	1
7664	IRAK1	8.663818e-02
7665	IRAK1BP1	8.400601e-03
7666	IRAK2	1
7667	IRAK3	1
7668	IRAK4	1
7669	IREB2	1
7670	IRF1	1
7671	IRF2	1.212348e-02
7672	IRF2BP1	7.129210e-02
7673	IRF2BP2	1
7674	IRF3	1
7675	IRF4	1
7676	IRF5	1
7677	IRF6	2.330716e-01
7678	IRF7	1
7679	IRF8	8.904818e-02
7680	IRF9	1
7681	IRGC	2.834430e-02
7682	IRGQ	1
7683	IRS1	1
7684	IRS4	4.012936e-01
7685	IRX1	1
7686	IRX2	1
7687	IRX3	1
7688	IRX4	1
7689	IRX5	1
7690	IRX6	1
7691	ISCA1	1
7692	ISCA1P1	1
7693	ISCA2	1
7694	ISCU	1
7695	ISG15	2.866290e-02
7696	ISG20	1
7697	ISG20L2	1.146322e-01
7698	ISL1	8.985150e-02
7699	ISL2	1
7700	ISLR	1
7701	ISLR2	1
7702	ISM1	1
7703	ISM2	1
7704	ISOC1	1
7705	ISOC2	1
7706	ISPD	1
7707	ISX	1
7708	ISY1	1
7709	ISYNA1	1
7710	ITCH	1
7711	ITFG1	1
7712	ITFG2	1
7713	ITFG3	1
7714	ITGA1	1
7715	ITGA10	1
Done

Running MutSig 2:
Scatter job 86: processing genes 7626 - 7715
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
IPO5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.646737e-02	ci left: 3.159213e-01	ci right 3.343806e-01	k: 3251	n:10000
Cons ci ratio: 5.482342e-02	ci left: 3.289257e-01	ci right 3.475686e-01	k: 3382	n:10000
KS ci ratio: 5.646737e-02	ci left: 3.159213e-01	ci right 3.343806e-01	k: 3251	n:10000
IPO5   10000 perm   2 sec   (4883 perm/sec)   p_kst 3.251000e-01   p_cons 3.382000e-01   p_joint 3.251000e-01

Outputting figure to mutsig2_images.part000000000086/IPO5.3_3456_10000_0.3251_0.3382_0.3251.png
                gene_name: IPO5
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.33 

Current progress: 20 percent done.
IQCH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.729419e-02	ci left: 8.297144e-01	ci right 8.442887e-01	k: 8371	n:10000
Cons ci ratio: 1.707186e-02	ci left: 8.332766e-01	ci right 8.477245e-01	k: 8406	n:10000
KS ci ratio: 2.393597e-02	ci left: 7.195667e-01	ci right 7.371001e-01	k: 7284	n:10000
IQCH   10000 perm   2 sec   (5070 perm/sec)   p_kst 7.284000e-01   p_cons 8.406000e-01   p_joint 8.371000e-01

Outputting figure to mutsig2_images.part000000000086/IQCH.3_3296_10000_0.7284_0.8406_0.8371.png
                gene_name: IQCH
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.84 

Current progress: 40 percent done.
IQCG
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.994913e-02	ci left: 7.862424e-01	ci right 8.021858e-01	k: 7943	n:10000
KS ci ratio: 1.512887e-02	ci left: 8.636592e-01	ci right 8.769242e-01	k: 8704	n:10000
IQCG   10000 perm   2 sec   (6515 perm/sec)   p_kst 8.704000e-01   p_cons 7.943000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000086/IQCG.2_1372_10000_0.8704_0.7943_1.png
                gene_name: IQCG
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
IQSEC2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.023188e-02	ci left: 6.174357e-01	ci right 6.364903e-01	k: 6270	n:10000
Cons ci ratio: 1.107083e-01	ci left: 1.051997e-01	ci right 1.176277e-01	k: 1113	n:10000
KS ci ratio: 5.410874e-02	ci left: 3.347852e-01	ci right 3.535056e-01	k: 3441	n:10000
IQSEC2   10000 perm   2 sec   (5017 perm/sec)   p_kst 3.441000e-01   p_cons 1.113000e-01   p_joint 6.270000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 7.791074e-02	ci left: 1.079558e-01	ci right 1.167573e-01	k: 2246	n:20000
KS ci ratio: 3.792404e-02	ci left: 3.415452e-01	ci right 3.547989e-01	k: 6963	n:20000
IQSEC2   20000 perm   4 sec   (4470 perm/sec)   p_kst 3.481500e-01   p_cons 1.123000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000086/IQSEC2.2_4657_20000_0.34815_0.1123_1.png
                gene_name: IQSEC2
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
IRF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.255266e-02	ci left: 5.820912e-01	ci right 6.014553e-01	k: 5918	n:10000
Cons ci ratio: 8.219310e-02	ci left: 1.776288e-01	ci right 1.929550e-01	k: 1852	n:10000
KS ci ratio: 1.394590e-02	ci left: 8.813485e-01	ci right 8.938247e-01	k: 8877	n:10000
IRF2   10000 perm   1 sec   (6729 perm/sec)   p_kst 8.877000e-01   p_cons 1.852000e-01   p_joint 5.918000e-01

Outputting figure to mutsig2_images.part000000000086/IRF2.2_1082_10000_0.8877_0.1852_0.5918.png
                gene_name: IRF2
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000086
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 86 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 4398078: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000087> was used as the working directory.
Started at Wed Oct 24 16:12:58 2012
Results reported at Wed Oct 24 16:16:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000087.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000087.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 87  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000087.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    264.44 sec.
    Max Memory :      1583 MB
    Max Swap   :      4104 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
87
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 87
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 87: processing genes 7716 - 7805
Calculating significance of each gene.
Using projection method.
7716	ITGA11	1
7717	ITGA2	1
7718	ITGA2B	1
7719	ITGA3	1
7720	ITGA4	2.285720e-02
7721	ITGA5	1
7722	ITGA6	1
7723	ITGA7	2.926536e-02
7724	ITGA8	7.506234e-02
7725	ITGA9	1
7726	ITGAD	1
7727	ITGAE	2.937906e-01
7728	ITGAL	1
7729	ITGAM	6.493630e-02
7730	ITGAV	4.404394e-01
7731	ITGAX	1.510197e-01
7732	ITGB1	1
7733	ITGB1BP1	1
7734	ITGB1BP2	1
7735	ITGB1BP3	1
7736	ITGB2	1
7737	ITGB3	3.486468e-01
7738	ITGB3BP	1
7739	ITGB4	4.927570e-01
7740	ITGB5	1
7741	ITGB6	1
7742	ITGB7	1
7743	ITGB8	1
7744	ITGBL1	1.234456e-01
7745	ITIH1	1
7746	ITIH2	1
7747	ITIH3	1
7748	ITIH4	1
7749	ITIH5	1.513895e-01
7750	ITIH5L	1
7751	ITK	2.303408e-01
7752	ITLN1	1
7753	ITLN2	1
7754	ITM2A	1
7755	ITM2B	1
7756	ITM2C	1
7757	ITPA	1
7758	ITPK1	1
7759	ITPKA	1
7760	ITPKB	1
7761	ITPKC	1
7762	ITPR1	1
7763	ITPR2	3.124641e-01
7764	ITPR3	1
7765	ITPRIP	1
7766	ITPRIPL1	1
7767	ITPRIPL2	1
7768	ITSN1	1.555270e-01
7769	ITSN2	6.226801e-01
7770	IVD	1
7771	IVL	1
7772	IVNS1ABP	1
7773	IWS1	2.924829e-02
7774	IYD	1
7775	IZUMO1	1.000520e-01
7776	JAG1	1
7777	JAG2	1
7778	JAGN1	1
7779	JAK1	1
7780	JAK2	2.785312e-01
7781	JAK3	1
7782	JAKMIP1	1
7783	JAKMIP2	2.459185e-01
7784	JAKMIP3	1.498795e-01
7785	JAM2	1
7786	JAM3	1
7787	JARID2	1
7788	JAZF1	1
7789	JDP2	1
7790	JHDM1D	1.299859e-01
7791	JKAMP	1
7792	JMJD1C	4.249637e-01
7793	JMJD4	1
7794	JMJD5	1
7795	JMJD6	1
7796	JMJD7	1
7797	JMJD7-PLA2G4B	1
7798	JMJD8	1
7799	JMY	1
7800	JOSD1	1
7801	JOSD2	1
7802	JPH1	2.425664e-01
7803	JPH2	4.033440e-02
7804	JPH3	1
7805	JPH4	1
Done

Running MutSig 2:
Scatter job 87: processing genes 7716 - 7805
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ITGA7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.044595e-02	ci left: 3.668915e-01	ci right 3.859806e-01	k: 3764	n:10000
Cons ci ratio: 5.337388e-02	ci left: 3.409444e-01	ci right 3.597428e-01	k: 3503	n:10000
KS ci ratio: 5.585553e-02	ci left: 3.206853e-01	ci right 3.392138e-01	k: 3299	n:10000
ITGA7   10000 perm   2 sec   (5103 perm/sec)   p_kst 3.299000e-01   p_cons 3.503000e-01   p_joint 3.764000e-01

Outputting figure to mutsig2_images.part000000000087/ITGA7.3_3785_10000_0.3299_0.3503_0.3764.png
                gene_name: ITGA7
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 17 percent done.
ITSN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.522044e-01	ci left: 5.744795e-02	ci right 6.700903e-02	k: 621	n:10000
Cons ci ratio: 4.676357e-02	ci left: 4.029277e-01	ci right 4.223232e-01	k: 4126	n:10000
KS ci ratio: 2.824171e-01	ci left: 1.622887e-02	ci right 2.165650e-02	k: 188	n:10000
ITSN1   10000 perm   2 sec   (4656 perm/sec)   p_kst 1.880000e-02   p_cons 4.126000e-01   p_joint 6.210000e-02

Joint ci ratio: 1.535677e-01	ci left: 2.912262e-02	ci right 3.401482e-02	k: 630	n:20000
Cons ci ratio: 3.299159e-02	ci left: 4.069123e-01	ci right 4.206128e-01	k: 8275	n:20000
KS ci ratio: 1.876616e-01	ci left: 1.934382e-02	ci right 2.339700e-02	k: 426	n:20000
ITSN1   20000 perm   5 sec   (4221 perm/sec)   p_kst 2.130000e-02   p_cons 4.137500e-01   p_joint 3.150000e-02

Joint ci ratio: 9.725848e-02	ci left: 4.886307e-02	ci right 5.389093e-02	k: 1540	n:30000
Cons ci ratio: 2.673304e-02	ci left: 4.118779e-01	ci right 4.230714e-01	k: 12524	n:30000
KS ci ratio: 1.491714e-01	ci left: 2.081941e-02	ci right 2.420727e-02	k: 674	n:30000
ITSN1   30000 perm   7 sec   (4063 perm/sec)   p_kst 2.246667e-02   p_cons 4.174667e-01   p_joint 5.133333e-02

Joint ci ratio: 7.089737e-02	ci left: 6.847728e-02	ci right 7.353521e-02	k: 2839	n:40000
Cons ci ratio: 2.314907e-02	ci left: 4.126858e-01	ci right 4.223761e-01	k: 16701	n:40000
KS ci ratio: 1.299271e-01	ci left: 2.080263e-02	ci right 2.371730e-02	k: 889	n:40000
ITSN1   40000 perm   10 sec   (3969 perm/sec)   p_kst 2.222500e-02   p_cons 4.175250e-01   p_joint 7.097500e-02

Joint ci ratio: 8.387103e-02	ci left: 4.010164e-02	ci right 4.363180e-02	k: 2092	n:50000
Cons ci ratio: 2.071578e-02	ci left: 4.129527e-01	ci right 4.216169e-01	k: 20864	n:50000
KS ci ratio: 1.147681e-01	ci left: 2.148998e-02	ci right 2.412583e-02	k: 1139	n:50000
ITSN1   50000 perm   13 sec   (3882 perm/sec)   p_kst 2.278000e-02   p_cons 4.172800e-01   p_joint 4.184000e-02

Joint ci ratio: 8.130143e-02	ci left: 3.578149e-02	ci right 3.883015e-02	k: 2237	n:60000
Cons ci ratio: 1.891341e-02	ci left: 4.132669e-01	ci right 4.211745e-01	k: 25033	n:60000
KS ci ratio: 1.048078e-01	ci left: 2.158796e-02	ci right 2.399184e-02	k: 1366	n:60000
ITSN1   60000 perm   16 sec   (3806 perm/sec)   p_kst 2.276667e-02   p_cons 4.172167e-01   p_joint 3.728333e-02

Joint ci ratio: 7.692297e-02	ci left: 3.439373e-02	ci right 3.715921e-02	k: 2503	n:70000
Cons ci ratio: 1.753169e-02	ci left: 4.129728e-01	ci right 4.202912e-01	k: 29164	n:70000
KS ci ratio: 9.702813e-02	ci left: 2.167902e-02	ci right 2.390363e-02	k: 1594	n:70000
ITSN1   70000 perm   19 sec   (3748 perm/sec)   p_kst 2.277143e-02   p_cons 4.166286e-01   p_joint 3.575714e-02

Outputting figure to mutsig2_images.part000000000087/ITSN1.3_5328_70000_0.022771_0.41663_0.035757.png
                gene_name: ITSN1
               theta_stop: 0.097 
                    nperm: 70000 
                     p_ks: 0.023 
        ci_ks_bounds_left: 0.022 
       ci_ks_bounds_right: 0.024 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.036 
     ci_joint_bounds_left: 0.034 
    ci_joint_bounds_right: 0.037 

Current progress: 33 percent done.
ITGA4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.155349e-02	ci left: 4.609766e-01	ci right 4.806404e-01	k: 4708	n:10000
KS ci ratio: 3.270107e-02	ci left: 5.798839e-01	ci right 5.992639e-01	k: 5896	n:10000
ITGA4   10000 perm   2 sec   (5249 perm/sec)   p_kst 5.896000e-01   p_cons 4.708000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000087/ITGA4.2_3211_10000_0.5896_0.4708_1.png
                gene_name: ITGA4
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
ITGA8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.409374e-01	ci left: 6.671876e-02	ci right 7.693236e-02	k: 717	n:10000
Cons ci ratio: 9.918711e-03	ci left: 9.350622e-01	ci right 9.444796e-01	k: 9399	n:10000
KS ci ratio: 3.900160e-01	ci left: 8.053309e-03	ci right 1.203990e-02	k: 99	n:10000
ITGA8   10000 perm   2 sec   (5499 perm/sec)   p_kst 9.900000e-03   p_cons 9.399000e-01   p_joint 7.170000e-02

Joint ci ratio: 5.532413e-02	ci left: 1.950690e-01	ci right 2.062182e-01	k: 4012	n:20000
Cons ci ratio: 6.663683e-03	ci left: 9.421609e-01	ci right 9.485088e-01	k: 18908	n:20000
KS ci ratio: 2.690752e-01	ci left: 9.087199e-03	ci right 1.195778e-02	k: 209	n:20000
ITGA8   20000 perm   4 sec   (4938 perm/sec)   p_kst 1.045000e-02   p_cons 9.454000e-01   p_joint 2.006000e-01

Joint ci ratio: 5.154968e-02	ci left: 1.574181e-01	ci right 1.657809e-01	k: 4847	n:30000
Cons ci ratio: 5.506622e-03	ci left: 9.414745e-01	ci right 9.467057e-01	k: 28324	n:30000
KS ci ratio: 2.214841e-01	ci left: 9.188445e-03	ci right 1.150785e-02	k: 309	n:30000
ITGA8   30000 perm   6 sec   (4744 perm/sec)   p_kst 1.030000e-02   p_cons 9.441333e-01   p_joint 1.615667e-01

Joint ci ratio: 4.517386e-02	ci left: 1.548343e-01	ci right 1.620153e-01	k: 6336	n:40000
Cons ci ratio: 4.749744e-03	ci left: 9.422623e-01	ci right 9.467729e-01	k: 37782	n:40000
KS ci ratio: 1.916555e-01	ci left: 9.357548e-03	ci right 1.136449e-02	k: 413	n:40000
ITGA8   40000 perm   9 sec   (4604 perm/sec)   p_kst 1.032500e-02   p_cons 9.445500e-01   p_joint 1.584000e-01

Joint ci ratio: 3.767251e-02	ci left: 1.746361e-01	ci right 1.813613e-01	k: 8899	n:50000
Cons ci ratio: 4.274440e-03	ci left: 9.418471e-01	ci right 9.459012e-01	k: 47195	n:50000
KS ci ratio: 1.721804e-01	ci left: 9.376099e-03	ci right 1.116145e-02	k: 512	n:50000
ITGA8   50000 perm   11 sec   (4491 perm/sec)   p_kst 1.024000e-02   p_cons 9.439000e-01   p_joint 1.779800e-01

Joint ci ratio: 3.362837e-02	ci left: 1.815357e-01	ci right 1.877615e-01	k: 11078	n:60000
Cons ci ratio: 3.874839e-03	ci left: 9.427735e-01	ci right 9.464500e-01	k: 56678	n:60000
KS ci ratio: 1.572562e-01	ci left: 9.443477e-03	ci right 1.107108e-02	k: 614	n:60000
ITGA8   60000 perm   14 sec   (4396 perm/sec)   p_kst 1.023333e-02   p_cons 9.446333e-01   p_joint 1.846333e-01

Joint ci ratio: 3.283260e-02	ci left: 1.664008e-01	ci right 1.719695e-01	k: 11842	n:70000
Cons ci ratio: 3.587507e-03	ci left: 9.429087e-01	ci right 9.463115e-01	k: 66124	n:70000
KS ci ratio: 1.467843e-01	ci left: 9.344964e-03	ci right 1.083892e-02	k: 705	n:70000
ITGA8   70000 perm   16 sec   (4306 perm/sec)   p_kst 1.007143e-02   p_cons 9.446286e-01   p_joint 1.691714e-01

Joint ci ratio: 3.729080e-02	ci left: 1.190948e-01	ci right 1.236327e-01	k: 9708	n:80000
Cons ci ratio: 3.352670e-03	ci left: 9.431190e-01	ci right 9.462986e-01	k: 75578	n:80000
KS ci ratio: 1.378104e-01	ci left: 9.322086e-03	ci right 1.071379e-02	k: 800	n:80000
ITGA8   80000 perm   19 sec   (4224 perm/sec)   p_kst 1.000000e-02   p_cons 9.447250e-01   p_joint 1.213500e-01

Joint ci ratio: 4.081685e-02	ci left: 9.105508e-02	ci right 9.486009e-02	k: 8365	n:90000
Cons ci ratio: 3.174742e-03	ci left: 9.427480e-01	ci right 9.457566e-01	k: 84984	n:90000
KS ci ratio: 1.290013e-01	ci left: 9.500038e-03	ci right 1.082071e-02	k: 913	n:90000
ITGA8   90000 perm   22 sec   (4146 perm/sec)   p_kst 1.014444e-02   p_cons 9.442667e-01   p_joint 9.294444e-02

Joint ci ratio: 4.360276e-02	ci left: 7.314717e-02	ci right 7.641755e-02	k: 7477	n:100000
Cons ci ratio: 3.025415e-03	ci left: 9.423445e-01	ci right 9.452097e-01	k: 94379	n:100000
KS ci ratio: 1.224762e-01	ci left: 9.518597e-03	ci right 1.077006e-02	k: 1013	n:100000
ITGA8   100000 perm   25 sec   (4070 perm/sec)   p_kst 1.013000e-02   p_cons 9.437900e-01   p_joint 7.477000e-02

Joint ci ratio: 4.203887e-02	ci left: 7.171252e-02	ci right 7.480094e-02	k: 8057	n:110000
Cons ci ratio: 2.890504e-03	ci left: 9.421929e-01	ci right 9.449292e-01	k: 103793	n:110000
KS ci ratio: 1.164815e-01	ci left: 9.596958e-03	ci right 1.079271e-02	k: 1120	n:110000
ITGA8   110000 perm   28 sec   (3998 perm/sec)   p_kst 1.018182e-02   p_cons 9.435727e-01   p_joint 7.324545e-02

Joint ci ratio: 3.981475e-02	ci left: 7.325164e-02	ci right 7.623561e-02	k: 8968	n:120000
Cons ci ratio: 2.763907e-03	ci left: 9.423893e-01	ci right 9.450058e-01	k: 113245	n:120000
KS ci ratio: 1.115645e-01	ci left: 9.614884e-03	ci right 1.075897e-02	k: 1221	n:120000
ITGA8   120000 perm   31 sec   (3928 perm/sec)   p_kst 1.017500e-02   p_cons 9.437083e-01   p_joint 7.473333e-02

Joint ci ratio: 3.219956e-02	ci left: 1.006883e-01	ci right 1.039910e-01	k: 13303	n:130000
Cons ci ratio: 2.652595e-03	ci left: 9.425576e-01	ci right 9.450687e-01	k: 122697	n:130000
KS ci ratio: 1.073449e-01	ci left: 9.608486e-03	ci right 1.070584e-02	k: 1319	n:130000
ITGA8   130000 perm   34 sec   (3863 perm/sec)   p_kst 1.014615e-02   p_cons 9.438231e-01   p_joint 1.023308e-01

Joint ci ratio: 3.099020e-02	ci left: 1.009726e-01	ci right 1.041581e-01	k: 14358	n:140000
Cons ci ratio: 2.549414e-03	ci left: 9.428838e-01	ci right 9.452977e-01	k: 132174	n:140000
KS ci ratio: 1.030941e-01	ci left: 9.694183e-03	ci right 1.075482e-02	k: 1430	n:140000
ITGA8   140000 perm   37 sec   (3803 perm/sec)   p_kst 1.021429e-02   p_cons 9.441000e-01   p_joint 1.025571e-01

Joint ci ratio: 2.678517e-02	ci left: 1.232706e-01	ci right 1.266239e-01	k: 18741	n:150000
Cons ci ratio: 2.462649e-03	ci left: 9.429390e-01	ci right 9.452705e-01	k: 141617	n:150000
KS ci ratio: 9.963824e-02	ci left: 9.704171e-03	ci right 1.072823e-02	k: 1531	n:150000
ITGA8   150000 perm   40 sec   (3743 perm/sec)   p_kst 1.020667e-02   p_cons 9.441133e-01   p_joint 1.249400e-01

Outputting figure to mutsig2_images.part000000000087/ITGA8.2_3312_150000_0.010207_0.94411_0.12494.png
                gene_name: ITGA8
               theta_stop: 0.100 
                    nperm: 150000 
                     p_ks: 0.010 
        ci_ks_bounds_left: 0.0097 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 67 percent done.
ITGAM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.620135e-01	ci left: 5.080410e-02	ci right 5.985714e-02	k: 552	n:10000
Cons ci ratio: 1.350161e-02	ci left: 8.878013e-01	ci right 8.999681e-01	k: 8940	n:10000
KS ci ratio: 4.509198e-01	ci left: 5.814929e-03	ci right 9.281233e-03	k: 74	n:10000
ITGAM   10000 perm   2 sec   (5498 perm/sec)   p_kst 7.400000e-03   p_cons 8.940000e-01   p_joint 5.520000e-02

Joint ci ratio: 1.474078e-01	ci left: 3.162770e-02	ci right 3.670891e-02	k: 682	n:20000
Cons ci ratio: 9.422003e-03	ci left: 8.921447e-01	ci right 9.006397e-01	k: 17929	n:20000
KS ci ratio: 3.029783e-01	ci left: 7.043292e-03	ci right 9.602748e-03	k: 165	n:20000
ITGAM   20000 perm   4 sec   (4902 perm/sec)   p_kst 8.250000e-03   p_cons 8.964500e-01   p_joint 3.410000e-02

Joint ci ratio: 1.320554e-01	ci left: 2.664618e-02	ci right 3.044585e-02	k: 855	n:30000
Cons ci ratio: 7.698890e-03	ci left: 8.927950e-01	ci right 8.997281e-01	k: 26889	n:30000
KS ci ratio: 2.425193e-01	ci left: 7.586271e-03	ci right 9.710531e-03	k: 258	n:30000
ITGAM   30000 perm   6 sec   (4655 perm/sec)   p_kst 8.600000e-03   p_cons 8.963000e-01   p_joint 2.850000e-02

Joint ci ratio: 1.315229e-01	ci left: 2.029445e-02	ci right 2.317557e-02	k: 868	n:40000
Cons ci ratio: 6.659210e-03	ci left: 8.934988e-01	ci right 8.994935e-01	k: 35861	n:40000
KS ci ratio: 2.119985e-01	ci left: 7.576304e-03	ci right 9.396133e-03	k: 338	n:40000
ITGAM   40000 perm   9 sec   (4410 perm/sec)   p_kst 8.450000e-03   p_cons 8.965250e-01   p_joint 2.170000e-02

Joint ci ratio: 1.174860e-01	ci left: 2.049898e-02	ci right 2.307695e-02	k: 1088	n:50000
Cons ci ratio: 5.953046e-03	ci left: 8.939183e-01	ci right 8.992755e-01	k: 44831	n:50000
KS ci ratio: 1.875639e-01	ci left: 7.847413e-03	ci right 9.490395e-03	k: 432	n:50000
ITGAM   50000 perm   12 sec   (4320 perm/sec)   p_kst 8.640000e-03   p_cons 8.966200e-01   p_joint 2.176000e-02

Joint ci ratio: 9.811050e-02	ci left: 2.464370e-02	ci right 2.720243e-02	k: 1554	n:60000
Cons ci ratio: 5.412892e-03	ci left: 8.948939e-01	ci right 8.997675e-01	k: 53841	n:60000
KS ci ratio: 1.695188e-01	ci left: 8.084167e-03	ci right 9.597249e-03	k: 529	n:60000
ITGAM   60000 perm   14 sec   (4239 perm/sec)   p_kst 8.816667e-03   p_cons 8.973500e-01   p_joint 2.590000e-02

Joint ci ratio: 9.749831e-02	ci left: 2.146984e-02	ci right 2.368427e-02	k: 1579	n:70000
Cons ci ratio: 4.994412e-03	ci left: 8.957055e-01	ci right 9.002043e-01	k: 62858	n:70000
KS ci ratio: 1.571151e-01	ci left: 8.121413e-03	ci right 9.519759e-03	k: 616	n:70000
ITGAM   70000 perm   17 sec   (4153 perm/sec)   p_kst 8.800000e-03   p_cons 8.979714e-01   p_joint 2.255714e-02

Joint ci ratio: 8.505765e-02	ci left: 2.476134e-02	ci right 2.697322e-02	k: 2068	n:80000
Cons ci ratio: 4.678419e-03	ci left: 8.955920e-01	ci right 8.998041e-01	k: 71817	n:80000
KS ci ratio: 1.466684e-01	ci left: 8.200565e-03	ci right 9.510425e-03	k: 707	n:80000
ITGAM   80000 perm   20 sec   (4090 perm/sec)   p_kst 8.837500e-03   p_cons 8.977125e-01   p_joint 2.585000e-02

Joint ci ratio: 7.073247e-02	ci left: 3.183152e-02	ci right 3.417648e-02	k: 2969	n:90000
Cons ci ratio: 4.415406e-03	ci left: 8.955225e-01	ci right 8.994963e-01	k: 80777	n:90000
KS ci ratio: 1.376281e-01	ci left: 8.318183e-03	ci right 9.558223e-03	k: 803	n:90000
ITGAM   90000 perm   22 sec   (4022 perm/sec)   p_kst 8.922222e-03   p_cons 8.975222e-01   p_joint 3.298889e-02

Joint ci ratio: 6.719757e-02	ci left: 3.180301e-02	ci right 3.402419e-02	k: 3290	n:100000
Cons ci ratio: 4.177010e-03	ci left: 8.961480e-01	ci right 8.999089e-01	k: 89804	n:100000
KS ci ratio: 1.309606e-01	ci left: 8.298147e-03	ci right 9.470605e-03	k: 887	n:100000
ITGAM   100000 perm   25 sec   (3960 perm/sec)   p_kst 8.870000e-03   p_cons 8.980400e-01   p_joint 3.290000e-02

Joint ci ratio: 7.270659e-02	ci left: 2.480858e-02	ci right 2.668927e-02	k: 2831	n:110000
Cons ci ratio: 3.972998e-03	ci left: 8.966820e-01	ci right 9.002606e-01	k: 98833	n:110000
KS ci ratio: 1.259636e-01	ci left: 8.177252e-03	ci right 9.285247e-03	k: 959	n:110000
ITGAM   110000 perm   28 sec   (3904 perm/sec)   p_kst 8.718182e-03   p_cons 8.984818e-01   p_joint 2.573636e-02

Joint ci ratio: 6.976738e-02	ci left: 2.473828e-02	ci right 2.653474e-02	k: 3075	n:120000
Cons ci ratio: 3.802600e-03	ci left: 8.968195e-01	ci right 9.002445e-01	k: 107825	n:120000
KS ci ratio: 1.205008e-01	ci left: 8.214633e-03	ci right 9.275979e-03	k: 1048	n:120000
ITGAM   120000 perm   31 sec   (3845 perm/sec)   p_kst 8.733333e-03   p_cons 8.985417e-01   p_joint 2.562500e-02

Joint ci ratio: 6.715801e-02	ci left: 2.468010e-02	ci right 2.640269e-02	k: 3319	n:130000
Cons ci ratio: 3.650856e-03	ci left: 8.970161e-01	ci right 9.003046e-01	k: 116827	n:130000
KS ci ratio: 1.158463e-01	ci left: 8.224727e-03	ci right 9.243522e-03	k: 1134	n:130000
ITGAM   130000 perm   34 sec   (3784 perm/sec)   p_kst 8.723077e-03   p_cons 8.986692e-01   p_joint 2.553077e-02

Joint ci ratio: 5.731149e-02	ci left: 3.140820e-02	ci right 3.326837e-02	k: 4526	n:140000
Cons ci ratio: 3.516349e-03	ci left: 8.971652e-01	ci right 9.003326e-01	k: 125826	n:140000
KS ci ratio: 1.110068e-01	ci left: 8.338239e-03	ci right 9.325123e-03	k: 1235	n:140000
ITGAM   140000 perm   38 sec   (3726 perm/sec)   p_kst 8.821429e-03   p_cons 8.987571e-01   p_joint 3.232857e-02

Joint ci ratio: 5.473210e-02	ci left: 3.216090e-02	ci right 3.397721e-02	k: 4959	n:150000
Cons ci ratio: 3.397805e-03	ci left: 8.971822e-01	ci right 9.002424e-01	k: 134808	n:150000
KS ci ratio: 1.080811e-01	ci left: 8.223242e-03	ci right 9.169229e-03	k: 1303	n:150000
ITGAM   150000 perm   41 sec   (3673 perm/sec)   p_kst 8.686667e-03   p_cons 8.987200e-01   p_joint 3.306000e-02

Joint ci ratio: 4.533101e-02	ci left: 4.363695e-02	ci right 4.566709e-02	k: 7143	n:160000
Cons ci ratio: 3.287105e-03	ci left: 8.973873e-01	ci right 9.003482e-01	k: 143820	n:160000
KS ci ratio: 1.050281e-01	ci left: 8.177704e-03	ci right 9.090235e-03	k: 1380	n:160000
ITGAM   160000 perm   44 sec   (3621 perm/sec)   p_kst 8.625000e-03   p_cons 8.988750e-01   p_joint 4.464375e-02

Joint ci ratio: 4.124286e-02	ci left: 4.941721e-02	ci right 5.150403e-02	k: 8577	n:170000
Cons ci ratio: 3.188724e-03	ci left: 8.974454e-01	ci right 9.003175e-01	k: 152811	n:170000
KS ci ratio: 1.019032e-01	ci left: 8.189457e-03	ci right 9.074481e-03	k: 1466	n:170000
ITGAM   170000 perm   48 sec   (3568 perm/sec)   p_kst 8.623529e-03   p_cons 8.988882e-01   p_joint 5.045294e-02

Joint ci ratio: 5.086290e-02	ci left: 3.113134e-02	ci right 3.276155e-02	k: 5749	n:180000
Cons ci ratio: 3.098585e-03	ci left: 8.975037e-01	ci right 9.002945e-01	k: 161803	n:180000
KS ci ratio: 9.975678e-02	ci left: 8.081053e-03	ci right 8.934890e-03	k: 1530	n:180000
ITGAM   180000 perm   51 sec   (3514 perm/sec)   p_kst 8.500000e-03   p_cons 8.989056e-01   p_joint 3.193889e-02

Outputting figure to mutsig2_images.part000000000087/ITGAM.2_3582_180000_0.0085_0.89891_0.031939.png
                gene_name: ITGAM
               theta_stop: 0.100 
                    nperm: 180000 
                     p_ks: 0.0085 
        ci_ks_bounds_left: 0.0081 
       ci_ks_bounds_right: 0.0089 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.032 
     ci_joint_bounds_left: 0.031 
    ci_joint_bounds_right: 0.033 

Current progress: 83 percent done.
IWS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.236922e-02	ci left: 3.495901e-01	ci right 3.684921e-01	k: 3590	n:10000
Cons ci ratio: 8.925190e-02	ci left: 1.544350e-01	ci right 1.689626e-01	k: 1616	n:10000
KS ci ratio: 3.597175e-02	ci left: 5.329749e-01	ci right 5.526002e-01	k: 5428	n:10000
IWS1   10000 perm   2 sec   (5911 perm/sec)   p_kst 5.428000e-01   p_cons 1.616000e-01   p_joint 3.590000e-01

Outputting figure to mutsig2_images.part000000000087/IWS1.2_2516_10000_0.5428_0.1616_0.359.png
                gene_name: IWS1
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000087
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 87 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 4398081: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000088> was used as the working directory.
Started at Wed Oct 24 16:13:03 2012
Results reported at Wed Oct 24 16:15:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000088.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000088.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 88  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000088.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    237.82 sec.
    Max Memory :      1300 MB
    Max Swap   :      3957 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
88
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 88
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 88: processing genes 7806 - 7894
Calculating significance of each gene.
Using projection method.
7806	JRK	1
7807	JRKL	9.416081e-02
7808	JSRP1	1
7809	JTB	1
7810	JUB	1
7811	JUN	1
7812	JUNB	1
7813	JUND	1
7814	JUP	1
7815	KAAG1	1
7816	KAL1	3.033849e-01
7817	KALRN	1
7818	KANK1	2.009385e-01
7819	KANK2	1
7820	KANK3	1
7821	KANK4	3.322444e-01
7822	KARS	1
7823	KAT2A	1
7824	KAT2B	1
7825	KAT5	1
7826	KATNA1	1
7827	KATNAL1	1
7828	KATNAL2	1
7829	KATNB1	1
7830	KAZ	1
7831	KAZALD1	1
7832	KBTBD10	1
7833	KBTBD12	1
7834	KBTBD2	1
7835	KBTBD3	1
7836	KBTBD4	1
7837	KBTBD5	1
7838	KBTBD6	1
7839	KBTBD7	1
7840	KBTBD8	1
7841	KCMF1	1
7842	KCNA1	1.595954e-01
7843	KCNA10	1
7844	KCNA2	1
7845	KCNA3	1
7846	KCNA4	1
7847	KCNA5	1
7848	KCNA6	1
7849	KCNA7	1
7850	KCNAB1	1.018665e-01
7851	KCNAB2	1
7852	KCNAB3	1
7853	KCNB1	1.774184e-01
7854	KCNB2	2.670678e-01
7855	KCNC1	1
7856	KCNC2	1
7857	KCNC3	1
7858	KCNC4	1.150209e-01
7859	KCND1	1
7860	KCND2	2.444198e-01
7861	KCND3	1.793414e-01
7862	KCNE1	1
7863	KCNE1L	1
7864	KCNE2	1
7865	KCNE3	1.131800e-02
7866	KCNE4	1
7867	KCNF1	1
7868	KCNG1	6.862293e-02
7869	KCNG2	1
7870	KCNG3	1
7871	KCNG4	1
7872	KCNH1	1.399949e-01
7873	KCNH2	3.489984e-01
7874	KCNH3	1
7875	KCNH4	1
7876	KCNH5	2.428385e-01
7877	KCNH6	2.145971e-01
7878	KCNH7	1
7879	KCNH8	1
7880	KCNIP1	8.273953e-02
7881	KCNIP2	1
7882	KCNIP3	1
7883	KCNIP4	1
7884	KCNJ1	1
7885	KCNJ10	1
7886	KCNJ11	1.470086e-01
7887	KCNJ12	1
7888	KCNJ13	1
7889	KCNJ14	1.451384e-01
7890	KCNJ15	1
7891	KCNJ16	1.528137e-01
7892	KCNJ2	1
7893	KCNJ3	1
7894	KCNJ4	1.035264e-01
Done

Running MutSig 2:
Scatter job 88: processing genes 7806 - 7894
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KALRN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.049740e-02	ci left: 6.133161e-01	ci right 6.324122e-01	k: 6229	n:10000
KS ci ratio: 1.435388e-01	ci left: 6.439839e-02	ci right 7.445420e-02	k: 693	n:10000
KALRN   10000 perm   3 sec   (3040 perm/sec)   p_kst 6.930000e-02   p_cons 6.229000e-01   p_joint 1

Joint ci ratio: 4.004513e-03	ci left: 9.775447e-01	ci right 9.815142e-01	k: 19592	n:20000
Cons ci ratio: 2.148572e-02	ci left: 6.178965e-01	ci right 6.313672e-01	k: 12493	n:20000
KS ci ratio: 1.020536e-01	ci left: 6.518352e-02	ci right 7.224249e-02	k: 1373	n:20000
KALRN   20000 perm   10 sec   (2040 perm/sec)   p_kst 6.865000e-02   p_cons 6.246500e-01   p_joint 9.796000e-01

Joint ci ratio: 3.319788e-03	ci left: 9.772791e-01	ci right 9.805606e-01	k: 29369	n:30000
Cons ci ratio: 1.833629e-02	ci left: 5.981386e-01	ci right 6.092413e-01	k: 18111	n:30000
KS ci ratio: 8.334871e-02	ci left: 6.579756e-02	ci right 7.155298e-02	k: 2059	n:30000
KALRN   30000 perm   14 sec   (2220 perm/sec)   p_kst 6.863333e-02   p_cons 6.037000e-01   p_joint 9.789667e-01

Outputting figure to mutsig2_images.part000000000088/KALRN.2_9357_30000_0.068633_0.6037_0.97897.png
                gene_name: KALRN
               theta_stop: 0.083 
                    nperm: 30000 
                     p_ks: 0.069 
        ci_ks_bounds_left: 0.066 
       ci_ks_bounds_right: 0.072 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 33 percent done.
KCND3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.341096e-02	ci left: 1.733008e-01	ci right 1.884856e-01	k: 1808	n:10000
KS ci ratio: 2.126700e-02	ci left: 7.642560e-01	ci right 7.807849e-01	k: 7726	n:10000
KCND3   10000 perm   2 sec   (5741 perm/sec)   p_kst 7.726000e-01   p_cons 1.808000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000088/KCND3.2_1996_10000_0.7726_0.1808_1.png
                gene_name: KCND3
               theta_stop: 0.083 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
KCNH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.309443e-02	ci left: 5.740655e-01	ci right 5.934856e-01	k: 5838	n:10000
Cons ci ratio: 4.653285e-02	ci left: 4.053188e-01	ci right 4.247308e-01	k: 4150	n:10000
KS ci ratio: 9.018502e-02	ci left: 1.516867e-01	ci right 1.661126e-01	k: 1588	n:10000
KCNH1   10000 perm   2 sec   (5346 perm/sec)   p_kst 1.588000e-01   p_cons 4.150000e-01   p_joint 5.838000e-01

Outputting figure to mutsig2_images.part000000000088/KCNH1.2_3014_10000_0.1588_0.415_0.5838.png
                gene_name: KCNH1
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000088
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 88 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4398084: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000089> was used as the working directory.
Started at Wed Oct 24 16:13:03 2012
Results reported at Wed Oct 24 16:14:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000089.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000089.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 89  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000089.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    133.28 sec.
    Max Memory :      1394 MB
    Max Swap   :      4078 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
89
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 89
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 89: processing genes 7895 - 7984
Calculating significance of each gene.
Using projection method.
7895	KCNJ5	1
7896	KCNJ6	1
7897	KCNJ8	8.040755e-03
7898	KCNJ9	1
7899	KCNK1	1
7900	KCNK10	1
7901	KCNK12	1
7902	KCNK13	1
7903	KCNK15	1
7904	KCNK16	1.128431e-02
7905	KCNK17	1
7906	KCNK18	1
7907	KCNK2	1
7908	KCNK3	1
7909	KCNK4	1
7910	KCNK5	1
7911	KCNK6	1
7912	KCNK7	1
7913	KCNK9	1
7914	KCNMA1	1.092132e-01
7915	KCNMB1	1
7916	KCNMB2	1
7917	KCNMB3	1
7918	KCNMB4	1
7919	KCNN1	1
7920	KCNN2	1
7921	KCNN3	1
7922	KCNN4	1
7923	KCNQ1	1
7924	KCNQ2	2.020258e-01
7925	KCNQ3	1
7926	KCNQ4	1
7927	KCNQ5	2.496381e-01
7928	KCNRG	1
7929	KCNS1	1
7930	KCNS2	1
7931	KCNS3	1
7932	KCNT1	1
7933	KCNT2	1
7934	KCNU1	1
7935	KCNV1	1
7936	KCNV2	1
7937	KCTD1	1
7938	KCTD10	1
7939	KCTD11	1
7940	KCTD12	1
7941	KCTD13	1.220974e-01
7942	KCTD14	1
7943	KCTD15	1
7944	KCTD16	1
7945	KCTD17	1
7946	KCTD18	5.647222e-02
7947	KCTD19	1
7948	KCTD2	4.552580e-02
7949	KCTD20	1
7950	KCTD21	1
7951	KCTD3	1
7952	KCTD4	1
7953	KCTD5	1
7954	KCTD6	1
7955	KCTD7	1
7956	KCTD8	1
7957	KCTD9	1
7958	KDELC1	1
7959	KDELC2	1
7960	KDELR1	7.627915e-02
7961	KDELR2	1
7962	KDELR3	1
7963	KDM1A	1
7964	KDM1B	1
7965	KDM2A	2.985624e-01
7966	KDM2B	1
7967	KDM3A	1
7968	KDM3B	4.796442e-01
7969	KDM4A	2.203850e-01
7970	KDM4B	1.539348e-01
7971	KDM4C	3.503801e-02
7972	KDM4D	1
7973	KDM5A	2.281964e-01
7974	KDM5B	2.874583e-01
7975	KDM5C	1
7976	KDM6A	1.974774e-01
7977	KDM6B	1
7978	KDR	1
7979	KDSR	1
7980	KEAP1	1
7981	KEL	1
7982	KERA	1
7983	KHDC1	1
7984	KHDRBS1	1
Done

Running MutSig 2:
Scatter job 89: processing genes 7895 - 7984
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KDM5A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.577984e-02	ci left: 3.212809e-01	ci right 3.398179e-01	k: 3305	n:10000
Cons ci ratio: 1.743342e-02	ci left: 8.274759e-01	ci right 8.421285e-01	k: 8349	n:10000
KS ci ratio: 7.041197e-02	ci left: 2.281991e-01	ci right 2.449546e-01	k: 2365	n:10000
KDM5A   10000 perm   2 sec   (4259 perm/sec)   p_kst 2.365000e-01   p_cons 8.349000e-01   p_joint 3.305000e-01

Outputting figure to mutsig2_images.part000000000089/KDM5A.3_5185_10000_0.2365_0.8349_0.3305.png
                gene_name: KDM5A
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 25 percent done.
KCNJ8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.172051e-01	ci left: 9.467402e-02	ci right 1.065598e-01	k: 1005	n:10000
KS ci ratio: 4.897433e-02	ci left: 3.808216e-01	ci right 4.000423e-01	k: 3904	n:10000
KCNJ8   10000 perm   2 sec   (6523 perm/sec)   p_kst 3.904000e-01   p_cons 1.005000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 8.222091e-02	ci left: 9.783865e-02	ci right 1.062774e-01	k: 2040	n:20000
KS ci ratio: 3.451735e-02	ci left: 3.852252e-01	ci right 3.988062e-01	k: 7840	n:20000
KCNJ8   20000 perm   3 sec   (5785 perm/sec)   p_kst 3.920000e-01   p_cons 1.020000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000089/KCNJ8.2_1283_20000_0.392_0.102_1.png
                gene_name: KCNJ8
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.098 
     ci_cons_bounds_right: 0.11 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
KCNMA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.426490e-02	ci left: 3.334940e-01	ci right 3.521976e-01	k: 3428	n:10000
KS ci ratio: 5.686859e-02	ci left: 3.128451e-01	ci right 3.312586e-01	k: 3220	n:10000
KCNMA1   10000 perm   2 sec   (5392 perm/sec)   p_kst 3.220000e-01   p_cons 3.428000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000089/KCNMA1.2_3995_10000_0.322_0.3428_1.png
                gene_name: KCNMA1
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
KDM4C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.931451e-02	ci left: 6.318096e-01	ci right 6.507081e-01	k: 6413	n:10000
KS ci ratio: 2.030862e-02	ci left: 7.802612e-01	ci right 7.963705e-01	k: 7884	n:10000
KDM4C   10000 perm   2 sec   (5198 perm/sec)   p_kst 7.884000e-01   p_cons 6.413000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000089/KDM4C.2_3497_10000_0.7884_0.6413_1.png
                gene_name: KDM4C
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000089
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 89 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4398086: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000090> was used as the working directory.
Started at Wed Oct 24 16:13:06 2012
Results reported at Wed Oct 24 16:15:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000090.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000090.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 90  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000090.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    215.94 sec.
    Max Memory :      1607 MB
    Max Swap   :      3940 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
90
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 90
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 90: processing genes 7985 - 8074
Calculating significance of each gene.
Using projection method.
7985	KHDRBS2	1
7986	KHDRBS3	1
7987	KHK	1
7988	KHNYN	1
7989	KHSRP	1
7990	KIAA0020	1.996579e-01
7991	KIAA0090	3.712357e-01
7992	KIAA0100	5.903650e-01
7993	KIAA0101	1
7994	KIAA0141	1
7995	KIAA0146	3.909077e-02
7996	KIAA0174	1
7997	KIAA0182	1
7998	KIAA0195	1
7999	KIAA0196	4.719063e-01
8000/17942 8000	KIAA0226	2.328256e-01
8001	KIAA0232	4.718130e-01
8002	KIAA0240	1
8003	KIAA0247	1
8004	KIAA0284	1
8005	KIAA0317	1.625421e-01
8006	KIAA0319	1
8007	KIAA0319L	1
8008	KIAA0355	1
8009	KIAA0368	1.738518e-01
8010	KIAA0391	1
8011	KIAA0406	3.623428e-01
8012	KIAA0408	1
8013	KIAA0415	1
8014	KIAA0427	7.552077e-02
8015	KIAA0430	2.274578e-01
8016	KIAA0467	1
8017	KIAA0494	1
8018	KIAA0495	1
8019	KIAA0513	1
8020	KIAA0528	1
8021	KIAA0556	4.052182e-01
8022	KIAA0562	3.939479e-01
8023	KIAA0564	1
8024	KIAA0586	1
8025	KIAA0649	1
8026	KIAA0652	1
8027	KIAA0664	1
8028	KIAA0748	1
8029	KIAA0753	1
8030	KIAA0754	2.284158e-01
8031	KIAA0776	6.055587e-02
8032	KIAA0802	1
8033	KIAA0831	1
8034	KIAA0892	1
8035	KIAA0895	1.038613e-01
8036	KIAA0895L	1
8037	KIAA0907	1
8038	KIAA0913	1
8039	KIAA0922	5.444464e-01
8040	KIAA0947	5.324007e-01
8041	KIAA1009	2.960543e-01
8042	KIAA1012	5.205066e-01
8043	KIAA1024	3.750115e-02
8044	KIAA1033	1.337414e-01
8045	KIAA1045	1
8046	KIAA1109	4.091359e-01
8047	KIAA1143	1
8048	KIAA1147	1
8049	KIAA1161	1
8050	KIAA1191	1
8051	KIAA1199	1
8052	KIAA1210	1
8053	KIAA1211	2.968043e-01
8054	KIAA1217	1
8055	KIAA1244	1
8056	KIAA1257	1
8057	KIAA1267	1.820722e-02
8058	KIAA1274	1.254514e-01
8059	KIAA1279	1
8060	KIAA1310	1
8061	KIAA1324	2.514730e-01
8062	KIAA1324L	1
8063	KIAA1328	1
8064	KIAA1370	1
8065	KIAA1377	1
8066	KIAA1383	3.244822e-01
8067	KIAA1407	2.037453e-01
8068	KIAA1409	6.168813e-01
8069	KIAA1429	1
8070	KIAA1430	1
8071	KIAA1432	5.160385e-01
8072	KIAA1462	3.107493e-01
8073	KIAA1467	1
8074	KIAA1468	1
Done

Running MutSig 2:
Scatter job 90: processing genes 7985 - 8074
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KIAA0146
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.972347e-02	ci left: 6.253754e-01	ci right 6.443460e-01	k: 6349	n:10000
KS ci ratio: 2.679039e-02	ci left: 6.723675e-01	ci right 6.907266e-01	k: 6816	n:10000
KIAA0146   10000 perm   2 sec   (5211 perm/sec)   p_kst 6.816000e-01   p_cons 6.349000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000090/KIAA0146.2_2828_10000_0.6816_0.6349_1.png
                gene_name: KIAA0146
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.64 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 17 percent done.
KIAA0368
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.340178e-02	ci left: 5.695523e-01	ci right 5.890015e-01	k: 5793	n:10000
KS ci ratio: 3.957213e-02	ci left: 4.853532e-01	ci right 5.050496e-01	k: 4952	n:10000
KIAA0368   10000 perm   2 sec   (4027 perm/sec)   p_kst 4.952000e-01   p_cons 5.793000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000090/KIAA0368.2_6258_10000_0.4952_0.5793_1.png
                gene_name: KIAA0368
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
KIAA1024
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.636482e-02	ci left: 5.275679e-01	ci right 5.472103e-01	k: 5374	n:10000
KS ci ratio: 3.594278e-02	ci left: 5.333754e-01	ci right 5.529994e-01	k: 5432	n:10000
KIAA1024   10000 perm   2 sec   (5559 perm/sec)   p_kst 5.432000e-01   p_cons 5.374000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000090/KIAA1024.2_2763_10000_0.5432_0.5374_1.png
                gene_name: KIAA1024
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
KIAA1109
Processing conservation and coverage...
65% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.222363e-02	ci left: 5.870082e-01	ci right 6.063355e-01	k: 5967	n:10000
KS ci ratio: 2.415983e-02	ci left: 7.158309e-01	ci right 7.334380e-01	k: 7247	n:10000
KIAA1109   10000 perm   4 sec   (2368 perm/sec)   p_kst 7.247000e-01   p_cons 5.967000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000090/KIAA1109.2_15354_10000_0.7247_0.5967_1.png
                gene_name: KIAA1109
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
KIAA1267
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.242059e-02	ci left: 7.449300e-01	ci right 7.619221e-01	k: 7535	n:10000
Cons ci ratio: 7.186508e-02	ci left: 2.209917e-01	ci right 2.375663e-01	k: 2292	n:10000
KS ci ratio: 1.079305e-02	ci left: 9.244098e-01	ci right 9.345383e-01	k: 9296	n:10000
KIAA1267   10000 perm   2 sec   (5312 perm/sec)   p_kst 9.296000e-01   p_cons 2.292000e-01   p_joint 7.535000e-01

Outputting figure to mutsig2_images.part000000000090/KIAA1267.2_3374_10000_0.9296_0.2292_0.7535.png
                gene_name: KIAA1267
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.74 
    ci_joint_bounds_right: 0.76 

Current progress: 83 percent done.
KIAA1409
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.104908e-02	ci left: 7.679013e-01	ci right 7.843376e-01	k: 7762	n:10000
Cons ci ratio: 5.530440e-02	ci left: 3.250533e-01	ci right 3.436433e-01	k: 3343	n:10000
KS ci ratio: 2.629179e-02	ci left: 6.805286e-01	ci right 6.987608e-01	k: 6897	n:10000
KIAA1409   10000 perm   3 sec   (3582 perm/sec)   p_kst 6.897000e-01   p_cons 3.343000e-01   p_joint 7.762000e-01

Outputting figure to mutsig2_images.part000000000090/KIAA1409.2_7565_10000_0.6897_0.3343_0.7762.png
                gene_name: KIAA1409
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.78 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000090
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 90 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4398089: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000091> was used as the working directory.
Started at Wed Oct 24 16:13:06 2012
Results reported at Wed Oct 24 16:19:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000091.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000091.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 91  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000091.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    420.07 sec.
    Max Memory :      1593 MB
    Max Swap   :      3950 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
91
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 91
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 91: processing genes 8075 - 8164
Calculating significance of each gene.
Using projection method.
8075	KIAA1486	1.619299e-01
8076	KIAA1522	1
8077	KIAA1524	1.406258e-01
8078	KIAA1529	1
8079	KIAA1530	1
8080	KIAA1539	1
8081	KIAA1543	1
8082	KIAA1549	1
8083	KIAA1586	1.776439e-01
8084	KIAA1598	1
8085	KIAA1609	1
8086	KIAA1614	1
8087	KIAA1632	1.236861e-01
8088	KIAA1644	1
8089	KIAA1683	1
8090	KIAA1704	1
8091	KIAA1712	1
8092	KIAA1715	1
8093	KIAA1737	1
8094	KIAA1751	1
8095	KIAA1755	1
8096	KIAA1797	1
8097	KIAA1804	1
8098	KIAA1826	1
8099	KIAA1841	1
8100	KIAA1919	1
8101	KIAA1949	1
8102	KIAA1958	1.376419e-01
8103	KIAA1967	1.843615e-01
8104	KIAA1984	1
8105	KIAA2013	1
8106	KIAA2018	1.550671e-01
8107	KIAA2022	2.318384e-02
8108	KIAA2026	1
8109	KIDINS220	5.518064e-01
8110	KIF11	1
8111	KIF12	1.524023e-01
8112	KIF13A	1
8113	KIF13B	1
8114	KIF14	2.755995e-01
8115	KIF15	5.542287e-01
8116	KIF16B	1.854472e-03
8117	KIF17	1.213949e-01
8118	KIF18A	1.713881e-01
8119	KIF18B	1
8120	KIF19	1
8121	KIF1A	1
8122	KIF1B	1
8123	KIF1C	1
8124	KIF20A	1
8125	KIF20B	2.771741e-01
8126	KIF21A	8.072902e-02
8127	KIF21B	1.424932e-01
8128	KIF22	2.634850e-01
8129	KIF23	3.237903e-01
8130	KIF24	1
8131	KIF25	1
8132	KIF26A	1.196628e-01
8133	KIF26B	1.103512e-01
8134	KIF27	3.949372e-01
8135	KIF2A	1
8136	KIF2B	1
8137	KIF2C	2.498077e-02
8138	KIF3A	1
8139	KIF3B	1.512083e-02
8140	KIF3C	1
8141	KIF4A	1.872200e-01
8142	KIF4B	3.533011e-01
8143	KIF5A	2.687212e-01
8144	KIF5B	1
8145	KIF5C	1
8146	KIF6	1
8147	KIF7	2.615501e-02
8148	KIF9	1
8149	KIFAP3	1
8150	KIFC1	6.420184e-02
8151	KIFC2	1.505010e-01
8152	KIFC3	1
8153	KIN	1
8154	KIR2DL1	1
8155	KIR2DL3	1
8156	KIR2DL4	1
8157	KIR2DS4	1
8158	KIR3DL1	5.111402e-02
8159	KIR3DL2	1
8160	KIR3DL3	1
8161	KIRREL	2.757042e-01
8162	KIRREL2	1
8163	KIRREL3	1
8164	KISS1	1
Done

Running MutSig 2:
Scatter job 91: processing genes 8075 - 8164
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KIF16B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.995174e-02	ci left: 1.265977e-01	ci right 1.400167e-01	k: 1332	n:10000
Cons ci ratio: 1.415757e-01	ci left: 6.613851e-02	ci right 7.631298e-02	k: 711	n:10000
KS ci ratio: 4.877944e-02	ci left: 3.827127e-01	ci right 4.019500e-01	k: 3923	n:10000
KIF16B   10000 perm   2 sec   (4466 perm/sec)   p_kst 3.923000e-01   p_cons 7.110000e-02   p_joint 1.332000e-01

Joint ci ratio: 6.968580e-02	ci left: 1.318193e-01	ci right 1.413866e-01	k: 2731	n:20000
Cons ci ratio: 1.002250e-01	ci left: 6.747821e-02	ci right 7.464710e-02	k: 1420	n:20000
KS ci ratio: 3.436218e-02	ci left: 3.873683e-01	ci right 4.009624e-01	k: 7883	n:20000
KIF16B   20000 perm   8 sec   (2454 perm/sec)   p_kst 3.941500e-01   p_cons 7.100000e-02   p_joint 1.365500e-01

Joint ci ratio: 4.900926e-02	ci left: 1.714415e-01	ci right 1.800881e-01	k: 5272	n:30000
Cons ci ratio: 8.167935e-02	ci left: 6.838039e-02	ci right 7.423629e-02	k: 2138	n:30000
KS ci ratio: 2.801936e-02	ci left: 3.892625e-01	ci right 4.003579e-01	k: 11844	n:30000
KIF16B   30000 perm   11 sec   (2718 perm/sec)   p_kst 3.948000e-01   p_cons 7.126667e-02   p_joint 1.757333e-01

Outputting figure to mutsig2_images.part000000000091/KIF16B.5_4058_30000_0.3948_0.071267_0.17573.png
                gene_name: KIF16B
               theta_stop: 0.082 
                    nperm: 30000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.071 
      ci_cons_bounds_left: 0.068 
     ci_cons_bounds_right: 0.074 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 8 percent done.
KIAA1632
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.895557e-02	ci left: 8.026788e-01	ci right 8.181399e-01	k: 8105	n:10000
Cons ci ratio: 9.742198e-03	ci left: 9.371348e-01	ci right 9.464058e-01	k: 9419	n:10000
KS ci ratio: 2.580158e-02	ci left: 6.885921e-01	ci right 7.066926e-01	k: 6977	n:10000
KIAA1632   10000 perm   3 sec   (2961 perm/sec)   p_kst 6.977000e-01   p_cons 9.419000e-01   p_joint 8.105000e-01

Outputting figure to mutsig2_images.part000000000091/KIAA1632.4_7916_10000_0.6977_0.9419_0.8105.png
                gene_name: KIAA1632
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.82 

Current progress: 15 percent done.
KIAA2022
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.131226e-01	ci left: 1.011041e-01	ci right 1.133258e-01	k: 1071	n:10000
Cons ci ratio: 2.221280e-01	ci left: 2.683859e-02	ci right 3.363872e-02	k: 301	n:10000
KS ci ratio: 4.113893e-02	ci left: 4.659699e-01	ci right 4.856442e-01	k: 4758	n:10000
KIAA2022   10000 perm   2 sec   (5101 perm/sec)   p_kst 4.758000e-01   p_cons 3.010000e-02   p_joint 1.071000e-01

Joint ci ratio: 6.023501e-02	ci left: 1.694601e-01	ci right 1.800346e-01	k: 3494	n:20000
Cons ci ratio: 1.487662e-01	ci left: 3.104924e-02	ci right 3.608756e-02	k: 670	n:20000
KS ci ratio: 2.950037e-02	ci left: 4.619139e-01	ci right 4.757952e-01	k: 9377	n:20000
KIAA2022   20000 perm   4 sec   (4616 perm/sec)   p_kst 4.688500e-01   p_cons 3.350000e-02   p_joint 1.747000e-01

Joint ci ratio: 5.900044e-02	ci left: 1.244693e-01	ci right 1.320695e-01	k: 3847	n:30000
Cons ci ratio: 1.210642e-01	ci left: 3.171894e-02	ci right 3.583866e-02	k: 1012	n:30000
KS ci ratio: 2.403528e-02	ci left: 4.642721e-01	ci right 4.756004e-01	k: 14098	n:30000
KIAA2022   30000 perm   7 sec   (4413 perm/sec)   p_kst 4.699333e-01   p_cons 3.373333e-02   p_joint 1.282333e-01

Joint ci ratio: 6.885703e-02	ci left: 7.236342e-02	ci right 7.754849e-02	k: 2997	n:40000
Cons ci ratio: 1.041948e-01	ci left: 3.239160e-02	ci right 3.597644e-02	k: 1366	n:40000
KS ci ratio: 2.086599e-02	ci left: 4.638246e-01	ci right 4.736299e-01	k: 18749	n:40000
KIAA2022   40000 perm   9 sec   (4278 perm/sec)   p_kst 4.687250e-01   p_cons 3.415000e-02   p_joint 7.492500e-02

Joint ci ratio: 6.169011e-02	ci left: 7.241030e-02	ci right 7.703922e-02	k: 3735	n:50000
Cons ci ratio: 9.352833e-02	ci left: 3.235040e-02	ci right 3.554401e-02	k: 1696	n:50000
KS ci ratio: 1.866795e-02	ci left: 4.642180e-01	ci right 4.729857e-01	k: 23430	n:50000
KIAA2022   50000 perm   12 sec   (4184 perm/sec)   p_kst 4.686000e-01   p_cons 3.392000e-02   p_joint 7.470000e-02

Outputting figure to mutsig2_images.part000000000091/KIAA2022.3_4563_50000_0.4686_0.03392_0.0747.png
                gene_name: KIAA2022
               theta_stop: 0.094 
                    nperm: 50000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.034 
      ci_cons_bounds_left: 0.032 
     ci_cons_bounds_right: 0.036 
                  p_joint: 0.075 
     ci_joint_bounds_left: 0.072 
    ci_joint_bounds_right: 0.077 

Current progress: 23 percent done.
KIF21A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.452937e-02	ci left: 7.096736e-01	ci right 7.273989e-01	k: 7186	n:10000
KS ci ratio: 2.980043e-02	ci left: 6.241692e-01	ci right 6.431529e-01	k: 6337	n:10000
KIF21A   10000 perm   2 sec   (4936 perm/sec)   p_kst 6.337000e-01   p_cons 7.186000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIF21A.3_5177_10000_0.6337_0.7186_1.png
                gene_name: KIF21A
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 31 percent done.
KIF26B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.044451e-02	ci left: 4.744608e-01	ci right 4.941484e-01	k: 4843	n:10000
Cons ci ratio: 2.542302e-02	ci left: 6.948436e-01	ci right 7.128375e-01	k: 7039	n:10000
KS ci ratio: 6.006440e-02	ci left: 2.896400e-01	ci right 3.076774e-01	k: 2986	n:10000
KIF26B   10000 perm   2 sec   (4501 perm/sec)   p_kst 2.986000e-01   p_cons 7.039000e-01   p_joint 4.843000e-01

Outputting figure to mutsig2_images.part000000000091/KIF26B.3_6387_10000_0.2986_0.7039_0.4843.png
                gene_name: KIF26B
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 38 percent done.
KIF3B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.080520e-01	ci left: 1.099814e-01	ci right 1.226430e-01	k: 1162	n:10000
Cons ci ratio: 2.272211e-01	ci left: 2.560990e-02	ci right 3.226830e-02	k: 288	n:10000
KS ci ratio: 8.876129e-02	ci left: 1.559077e-01	ci right 1.704891e-01	k: 1631	n:10000
KIF3B   10000 perm   2 sec   (5989 perm/sec)   p_kst 1.631000e-01   p_cons 2.880000e-02   p_joint 1.162000e-01

Joint ci ratio: 9.928795e-02	ci left: 6.869925e-02	ci right 7.592569e-02	k: 1445	n:20000
Cons ci ratio: 1.526953e-01	ci left: 2.945960e-02	ci right 3.437773e-02	k: 637	n:20000
KS ci ratio: 6.216256e-02	ci left: 1.606697e-01	ci right 1.710277e-01	k: 3316	n:20000
KIF3B   20000 perm   4 sec   (5349 perm/sec)   p_kst 1.658000e-01   p_cons 3.185000e-02   p_joint 7.225000e-02

Joint ci ratio: 6.489563e-02	ci left: 1.049034e-01	ci right 1.119726e-01	k: 3252	n:30000
Cons ci ratio: 1.268842e-01	ci left: 2.887377e-02	ci right 3.281777e-02	k: 924	n:30000
KS ci ratio: 5.046725e-02	ci left: 1.631911e-01	ci right 1.716734e-01	k: 5022	n:30000
KIF3B   30000 perm   6 sec   (5100 perm/sec)   p_kst 1.674000e-01   p_cons 3.080000e-02   p_joint 1.084000e-01

Joint ci ratio: 5.477640e-02	ci left: 1.103824e-01	ci right 1.166238e-01	k: 4539	n:40000
Cons ci ratio: 1.099007e-01	ci left: 2.912846e-02	ci right 3.254010e-02	k: 1232	n:40000
KS ci ratio: 4.403151e-02	ci left: 1.617213e-01	ci right 1.690274e-01	k: 6614	n:40000
KIF3B   40000 perm   8 sec   (4923 perm/sec)   p_kst 1.653500e-01   p_cons 3.080000e-02   p_joint 1.134750e-01

Joint ci ratio: 5.069218e-02	ci left: 1.041057e-01	ci right 1.095401e-01	k: 5340	n:50000
Cons ci ratio: 9.788146e-02	ci left: 2.955668e-02	ci right 3.261808e-02	k: 1553	n:50000
KS ci ratio: 3.946527e-02	ci left: 1.615378e-01	ci right 1.680612e-01	k: 8239	n:50000
KIF3B   50000 perm   10 sec   (4804 perm/sec)   p_kst 1.647800e-01   p_cons 3.106000e-02   p_joint 1.068000e-01

Outputting figure to mutsig2_images.part000000000091/KIF3B.3_2276_50000_0.16478_0.03106_0.1068.png
                gene_name: KIF3B
               theta_stop: 0.098 
                    nperm: 50000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.031 
      ci_cons_bounds_left: 0.030 
     ci_cons_bounds_right: 0.033 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 46 percent done.
KIAA2018
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.978354e-03	ci left: 9.877409e-01	ci right 9.917661e-01	k: 9899	n:10000
Cons ci ratio: 2.477813e-02	ci left: 7.055362e-01	ci right 7.233387e-01	k: 7145	n:10000
KS ci ratio: 1.964358e-02	ci left: 7.913132e-01	ci right 8.071121e-01	k: 7993	n:10000
KIAA2018   10000 perm   2 sec   (4624 perm/sec)   p_kst 7.993000e-01   p_cons 7.145000e-01   p_joint 9.899000e-01

Outputting figure to mutsig2_images.part000000000091/KIAA2018.2_6758_10000_0.7993_0.7145_0.9899.png
                gene_name: KIAA2018
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 54 percent done.
KIF13A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.230215e-02	ci left: 1.772353e-01	ci right 1.925487e-01	k: 1848	n:10000
KS ci ratio: 3.353212e-02	ci left: 5.676469e-01	ci right 5.871080e-01	k: 5774	n:10000
KIF13A   10000 perm   2 sec   (4821 perm/sec)   p_kst 5.774000e-01   p_cons 1.848000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIF13A.2_5599_10000_0.5774_0.1848_1.png
                gene_name: KIF13A
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.19 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 62 percent done.
KIF18A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.002490e-01	ci left: 7.602648e-03	ci right 1.149110e-02	k: 94	n:10000
Cons ci ratio: 2.693080e-03	ci left: 9.938690e-01	ci right 9.966303e-01	k: 9954	n:10000
KS ci ratio: 7.029257e-01	ci left: 2.024975e-03	ci right 4.279939e-03	k: 30	n:10000
KIF18A   10000 perm   2 sec   (5471 perm/sec)   p_kst 3.000000e-03   p_cons 9.954000e-01   p_joint 9.400000e-03

Joint ci ratio: 5.592997e-01	ci left: 1.770085e-03	ci right 3.180807e-03	k: 48	n:20000
Cons ci ratio: 1.863384e-03	ci left: 9.945267e-01	ci right 9.964248e-01	k: 19911	n:20000
KS ci ratio: 5.592997e-01	ci left: 1.770085e-03	ci right 3.180807e-03	k: 48	n:20000
KIF18A   20000 perm   4 sec   (5114 perm/sec)   p_kst 2.400000e-03   p_cons 9.955500e-01   p_joint 2.400000e-03

Joint ci ratio: 4.349599e-01	ci left: 2.115050e-03	ci right 3.317815e-03	k: 80	n:30000
Cons ci ratio: 1.538400e-03	ci left: 9.946037e-01	ci right 9.961646e-01	k: 29863	n:30000
KS ci ratio: 4.349599e-01	ci left: 2.115050e-03	ci right 3.317815e-03	k: 80	n:30000
KIF18A   30000 perm   6 sec   (4956 perm/sec)   p_kst 2.666667e-03   p_cons 9.954333e-01   p_joint 2.666667e-03

Joint ci ratio: 3.603281e-01	ci left: 2.419637e-03	ci right 3.504518e-03	k: 117	n:40000
Cons ci ratio: 1.325027e-03	ci left: 9.947675e-01	ci right 9.961090e-01	k: 39819	n:40000
KS ci ratio: 3.603281e-01	ci left: 2.419637e-03	ci right 3.504518e-03	k: 117	n:40000
KIF18A   40000 perm   8 sec   (4831 perm/sec)   p_kst 2.925000e-03   p_cons 9.954750e-01   p_joint 2.925000e-03

Joint ci ratio: 3.206569e-01	ci left: 2.502884e-03	ci right 3.476241e-03	k: 148	n:50000
Cons ci ratio: 1.122011e-03	ci left: 9.953428e-01	ci right 9.964784e-01	k: 49797	n:50000
KS ci ratio: 3.206569e-01	ci left: 2.502884e-03	ci right 3.476241e-03	k: 148	n:50000
KIF18A   50000 perm   11 sec   (4732 perm/sec)   p_kst 2.960000e-03   p_cons 9.959400e-01   p_joint 2.960000e-03

Joint ci ratio: 2.917385e-01	ci left: 2.562803e-03	ci right 3.453014e-03	k: 179	n:60000
Cons ci ratio: 1.033045e-03	ci left: 9.953202e-01	ci right 9.963643e-01	k: 59752	n:60000
KS ci ratio: 2.917385e-01	ci left: 2.562803e-03	ci right 3.453014e-03	k: 179	n:60000
KIF18A   60000 perm   13 sec   (4652 perm/sec)   p_kst 2.983333e-03   p_cons 9.958667e-01   p_joint 2.983333e-03

Joint ci ratio: 2.663085e-01	ci left: 2.675081e-03	ci right 3.509809e-03	k: 215	n:70000
Cons ci ratio: 9.472854e-04	ci left: 9.954436e-01	ci right 9.964002e-01	k: 69716	n:70000
KS ci ratio: 2.663085e-01	ci left: 2.675081e-03	ci right 3.509809e-03	k: 215	n:70000
KIF18A   70000 perm   15 sec   (4569 perm/sec)   p_kst 3.071429e-03   p_cons 9.959429e-01   p_joint 3.071429e-03

Joint ci ratio: 2.505677e-01	ci left: 2.668041e-03	ci right 3.443692e-03	k: 243	n:80000
Cons ci ratio: 8.905848e-04	ci left: 9.954325e-01	ci right 9.963310e-01	k: 79672	n:80000
KS ci ratio: 2.505677e-01	ci left: 2.668041e-03	ci right 3.443692e-03	k: 243	n:80000
KIF18A   80000 perm   18 sec   (4484 perm/sec)   p_kst 3.037500e-03   p_cons 9.959000e-01   p_joint 3.037500e-03

Joint ci ratio: 2.368878e-01	ci left: 2.674149e-03	ci right 3.402911e-03	k: 272	n:90000
Cons ci ratio: 8.372306e-04	ci left: 9.954839e-01	ci right 9.963281e-01	k: 89633	n:90000
KS ci ratio: 2.368878e-01	ci left: 2.674149e-03	ci right 3.402911e-03	k: 272	n:90000
KIF18A   90000 perm   20 sec   (4400 perm/sec)   p_kst 3.022222e-03   p_cons 9.959222e-01   p_joint 3.022222e-03

Joint ci ratio: 2.219358e-01	ci left: 2.764930e-03	ci right 3.464383e-03	k: 310	n:100000
Cons ci ratio: 7.904673e-04	ci left: 9.955471e-01	ci right 9.963437e-01	k: 99596	n:100000
KS ci ratio: 2.219358e-01	ci left: 2.764930e-03	ci right 3.464383e-03	k: 310	n:100000
KIF18A   100000 perm   23 sec   (4321 perm/sec)   p_kst 3.100000e-03   p_cons 9.959600e-01   p_joint 3.100000e-03

Joint ci ratio: 2.128911e-01	ci left: 2.745663e-03	ci right 3.408239e-03	k: 337	n:110000
Cons ci ratio: 7.481421e-04	ci left: 9.956281e-01	ci right 9.963818e-01	k: 109562	n:110000
KS ci ratio: 2.128911e-01	ci left: 2.745663e-03	ci right 3.408239e-03	k: 337	n:110000
KIF18A   110000 perm   26 sec   (4245 perm/sec)   p_kst 3.063636e-03   p_cons 9.960182e-01   p_joint 3.063636e-03

Joint ci ratio: 2.062912e-01	ci left: 2.690561e-03	ci right 3.317172e-03	k: 359	n:120000
Cons ci ratio: 7.193580e-04	ci left: 9.956090e-01	ci right 9.963333e-01	k: 119518	n:120000
KS ci ratio: 2.062912e-01	ci left: 2.690561e-03	ci right 3.317172e-03	k: 359	n:120000
KIF18A   120000 perm   29 sec   (4173 perm/sec)   p_kst 2.991667e-03   p_cons 9.959833e-01   p_joint 2.991667e-03

Joint ci ratio: 1.966864e-01	ci left: 2.746561e-03	ci right 3.352865e-03	k: 395	n:130000
Cons ci ratio: 6.883141e-04	ci left: 9.956578e-01	ci right 9.963506e-01	k: 129482	n:130000
KS ci ratio: 1.966864e-01	ci left: 2.746561e-03	ci right 3.352865e-03	k: 395	n:130000
KIF18A   130000 perm   32 sec   (4112 perm/sec)   p_kst 3.038462e-03   p_cons 9.960154e-01   p_joint 3.038462e-03

Joint ci ratio: 1.912171e-01	ci left: 2.706682e-03	ci right 3.285635e-03	k: 418	n:140000
Cons ci ratio: 6.645132e-04	ci left: 9.956553e-01	ci right 9.963239e-01	k: 139440	n:140000
KS ci ratio: 1.912171e-01	ci left: 2.706682e-03	ci right 3.285635e-03	k: 418	n:140000
KIF18A   140000 perm   35 sec   (4052 perm/sec)   p_kst 2.985714e-03   p_cons 9.960000e-01   p_joint 2.985714e-03

Joint ci ratio: 1.841027e-01	ci left: 2.735907e-03	ci right 3.296909e-03	k: 451	n:150000
Cons ci ratio: 6.403325e-04	ci left: 9.956883e-01	ci right 9.963323e-01	k: 149403	n:150000
KS ci ratio: 1.841027e-01	ci left: 2.735907e-03	ci right 3.296909e-03	k: 451	n:150000
KIF18A   150000 perm   38 sec   (3968 perm/sec)   p_kst 3.006667e-03   p_cons 9.960200e-01   p_joint 3.006667e-03

Joint ci ratio: 1.794049e-01	ci left: 2.708086e-03	ci right 3.247674e-03	k: 475	n:160000
Cons ci ratio: 6.254091e-04	ci left: 9.956265e-01	ci right 9.962553e-01	k: 159352	n:160000
KS ci ratio: 1.794049e-01	ci left: 2.708086e-03	ci right 3.247674e-03	k: 475	n:160000
KIF18A   160000 perm   41 sec   (3912 perm/sec)   p_kst 2.968750e-03   p_cons 9.959500e-01   p_joint 2.968750e-03

Joint ci ratio: 1.713096e-01	ci left: 2.807516e-03	ci right 3.339067e-03	k: 521	n:170000
Cons ci ratio: 6.060460e-04	ci left: 9.956457e-01	ci right 9.962549e-01	k: 169313	n:170000
KS ci ratio: 1.713096e-01	ci left: 2.807516e-03	ci right 3.339067e-03	k: 521	n:170000
KIF18A   170000 perm   44 sec   (3827 perm/sec)   p_kst 3.064706e-03   p_cons 9.959588e-01   p_joint 3.064706e-03

Joint ci ratio: 1.655402e-01	ci left: 2.848440e-03	ci right 3.367768e-03	k: 558	n:180000
Cons ci ratio: 5.904021e-04	ci left: 9.956342e-01	ci right 9.962275e-01	k: 179269	n:180000
KS ci ratio: 1.655402e-01	ci left: 2.848440e-03	ci right 3.367768e-03	k: 558	n:180000
KIF18A   180000 perm   48 sec   (3762 perm/sec)   p_kst 3.100000e-03   p_cons 9.959389e-01   p_joint 3.100000e-03

Joint ci ratio: 1.607233e-01	ci left: 2.870167e-03	ci right 3.376759e-03	k: 592	n:190000
Cons ci ratio: 5.818304e-04	ci left: 9.955370e-01	ci right 9.961214e-01	k: 189209	n:190000
KS ci ratio: 1.607233e-01	ci left: 2.870167e-03	ci right 3.376759e-03	k: 592	n:190000
KIF18A   190000 perm   51 sec   (3717 perm/sec)   p_kst 3.115789e-03   p_cons 9.958368e-01   p_joint 3.115789e-03

Joint ci ratio: 1.566802e-01	ci left: 2.875504e-03	ci right 3.369071e-03	k: 623	n:200000
Cons ci ratio: 5.685706e-04	ci left: 9.955223e-01	ci right 9.960932e-01	k: 199163	n:200000
KS ci ratio: 1.566802e-01	ci left: 2.875504e-03	ci right 3.369071e-03	k: 623	n:200000
KIF18A   200000 perm   55 sec   (3651 perm/sec)   p_kst 3.115000e-03   p_cons 9.958150e-01   p_joint 3.115000e-03

Joint ci ratio: 1.533982e-01	ci left: 2.862158e-03	ci right 3.342197e-03	k: 650	n:210000
Cons ci ratio: 5.561651e-04	ci left: 9.955091e-01	ci right 9.960675e-01	k: 209117	n:210000
KS ci ratio: 1.533982e-01	ci left: 2.862158e-03	ci right 3.342197e-03	k: 650	n:210000
KIF18A   210000 perm   59 sec   (3586 perm/sec)   p_kst 3.095238e-03   p_cons 9.957952e-01   p_joint 3.095238e-03

Joint ci ratio: 1.502031e-01	ci left: 2.854497e-03	ci right 3.322383e-03	k: 678	n:220000
Cons ci ratio: 5.415796e-04	ci left: 9.955443e-01	ci right 9.960880e-01	k: 219081	n:220000
KS ci ratio: 1.502031e-01	ci left: 2.854497e-03	ci right 3.322383e-03	k: 678	n:220000
KIF18A   220000 perm   62 sec   (3544 perm/sec)   p_kst 3.081818e-03   p_cons 9.958227e-01   p_joint 3.081818e-03

Joint ci ratio: 1.466803e-01	ci left: 2.868540e-03	ci right 3.326733e-03	k: 711	n:230000
Cons ci ratio: 5.302786e-04	ci left: 9.955406e-01	ci right 9.960728e-01	k: 229037	n:230000
KS ci ratio: 1.466803e-01	ci left: 2.868540e-03	ci right 3.326733e-03	k: 711	n:230000
KIF18A   230000 perm   66 sec   (3503 perm/sec)   p_kst 3.091304e-03   p_cons 9.958130e-01   p_joint 3.091304e-03

Joint ci ratio: 1.435878e-01	ci left: 2.873494e-03	ci right 3.321973e-03	k: 742	n:240000
Cons ci ratio: 5.199131e-04	ci left: 9.955331e-01	ci right 9.960548e-01	k: 238992	n:240000
KS ci ratio: 1.435878e-01	ci left: 2.873494e-03	ci right 3.321973e-03	k: 742	n:240000
KIF18A   240000 perm   69 sec   (3457 perm/sec)   p_kst 3.091667e-03   p_cons 9.958000e-01   p_joint 3.091667e-03

Joint ci ratio: 1.406829e-01	ci left: 2.878145e-03	ci right 3.317500e-03	k: 773	n:250000
Cons ci ratio: 5.089118e-04	ci left: 9.955469e-01	ci right 9.960575e-01	k: 248952	n:250000
KS ci ratio: 1.406829e-01	ci left: 2.878145e-03	ci right 3.317500e-03	k: 773	n:250000
KIF18A   250000 perm   73 sec   (3408 perm/sec)   p_kst 3.092000e-03   p_cons 9.958080e-01   p_joint 3.092000e-03

Joint ci ratio: 1.386403e-01	ci left: 2.852815e-03	ci right 3.281458e-03	k: 796	n:260000
Cons ci ratio: 4.997270e-04	ci left: 9.955399e-01	ci right 9.960412e-01	k: 258907	n:260000
KS ci ratio: 1.386403e-01	ci left: 2.852815e-03	ci right 3.281458e-03	k: 796	n:260000
KIF18A   260000 perm   77 sec   (3357 perm/sec)   p_kst 3.061538e-03   p_cons 9.957962e-01   p_joint 3.061538e-03

Joint ci ratio: 1.359378e-01	ci left: 2.861604e-03	ci right 3.282508e-03	k: 828	n:270000
Cons ci ratio: 4.899353e-04	ci left: 9.955526e-01	ci right 9.960441e-01	k: 268867	n:270000
KS ci ratio: 1.359378e-01	ci left: 2.861604e-03	ci right 3.282508e-03	k: 828	n:270000
KIF18A   270000 perm   81 sec   (3323 perm/sec)   p_kst 3.066667e-03   p_cons 9.958037e-01   p_joint 3.066667e-03

Joint ci ratio: 1.340923e-01	ci left: 2.838770e-03	ci right 3.250194e-03	k: 851	n:280000
Cons ci ratio: 4.811071e-04	ci left: 9.955571e-01	ci right 9.960397e-01	k: 278825	n:280000
KS ci ratio: 1.340923e-01	ci left: 2.838770e-03	ci right 3.250194e-03	k: 851	n:280000
KIF18A   280000 perm   85 sec   (3290 perm/sec)   p_kst 3.039286e-03   p_cons 9.958036e-01   p_joint 3.039286e-03

Joint ci ratio: 1.314191e-01	ci left: 2.857564e-03	ci right 3.262812e-03	k: 886	n:290000
Cons ci ratio: 4.748785e-04	ci left: 9.955224e-01	ci right 9.959986e-01	k: 288772	n:290000
KS ci ratio: 1.314191e-01	ci left: 2.857564e-03	ci right 3.262812e-03	k: 886	n:290000
KIF18A   290000 perm   89 sec   (3256 perm/sec)   p_kst 3.055172e-03   p_cons 9.957655e-01   p_joint 3.055172e-03

Joint ci ratio: 1.286897e-01	ci left: 2.884861e-03	ci right 3.284834e-03	k: 924	n:300000
Cons ci ratio: 4.651642e-04	ci left: 9.955586e-01	ci right 9.960250e-01	k: 298739	n:300000
KS ci ratio: 1.286897e-01	ci left: 2.884861e-03	ci right 3.284834e-03	k: 924	n:300000
KIF18A   300000 perm   93 sec   (3221 perm/sec)   p_kst 3.080000e-03   p_cons 9.957967e-01   p_joint 3.080000e-03

Joint ci ratio: 1.260580e-01	ci left: 2.913601e-03	ci right 3.308681e-03	k: 963	n:310000
Cons ci ratio: 4.559999e-04	ci left: 9.955925e-01	ci right 9.960497e-01	k: 308706	n:310000
KS ci ratio: 1.260580e-01	ci left: 2.913601e-03	ci right 3.308681e-03	k: 963	n:310000
KIF18A   310000 perm   97 sec   (3188 perm/sec)   p_kst 3.106452e-03   p_cons 9.958258e-01   p_joint 3.106452e-03

Joint ci ratio: 1.238294e-01	ci left: 2.928509e-03	ci right 3.318075e-03	k: 998	n:320000
Cons ci ratio: 4.478440e-04	ci left: 9.956147e-01	ci right 9.960637e-01	k: 318670	n:320000
KS ci ratio: 1.238294e-01	ci left: 2.928509e-03	ci right 3.318075e-03	k: 998	n:320000
KIF18A   320000 perm   101 sec   (3153 perm/sec)   p_kst 3.118750e-03   p_cons 9.958438e-01   p_joint 3.118750e-03

Joint ci ratio: 1.221900e-01	ci left: 2.919066e-03	ci right 3.301863e-03	k: 1025	n:330000
Cons ci ratio: 4.410720e-04	ci left: 9.956170e-01	ci right 9.960591e-01	k: 328628	n:330000
KS ci ratio: 1.221900e-01	ci left: 2.919066e-03	ci right 3.301863e-03	k: 1025	n:330000
KIF18A   330000 perm   106 sec   (3119 perm/sec)   p_kst 3.106061e-03   p_cons 9.958424e-01   p_joint 3.106061e-03

Joint ci ratio: 1.193139e-01	ci left: 2.975834e-03	ci right 3.356242e-03	k: 1075	n:340000
Cons ci ratio: 4.339808e-04	ci left: 9.956312e-01	ci right 9.960662e-01	k: 338590	n:340000
KS ci ratio: 1.193139e-01	ci left: 2.975834e-03	ci right 3.356242e-03	k: 1075	n:340000
KIF18A   340000 perm   110 sec   (3084 perm/sec)   p_kst 3.161765e-03   p_cons 9.958529e-01   p_joint 3.161765e-03

Joint ci ratio: 1.177918e-01	ci left: 2.968437e-03	ci right 3.342721e-03	k: 1103	n:350000
Cons ci ratio: 4.279579e-04	ci left: 9.956300e-01	ci right 9.960589e-01	k: 348547	n:350000
KS ci ratio: 1.177918e-01	ci left: 2.968437e-03	ci right 3.342721e-03	k: 1103	n:350000
KIF18A   350000 perm   115 sec   (3039 perm/sec)   p_kst 3.151429e-03   p_cons 9.958486e-01   p_joint 3.151429e-03

Joint ci ratio: 1.159673e-01	ci left: 2.980361e-03	ci right 3.349930e-03	k: 1138	n:360000
Cons ci ratio: 4.223203e-04	ci left: 9.956260e-01	ci right 9.960493e-01	k: 358503	n:360000
KS ci ratio: 1.159673e-01	ci left: 2.980361e-03	ci right 3.349930e-03	k: 1138	n:360000
KIF18A   360000 perm   120 sec   (3009 perm/sec)   p_kst 3.161111e-03   p_cons 9.958417e-01   p_joint 3.161111e-03

Joint ci ratio: 1.140789e-01	ci left: 2.999560e-03	ci right 3.365046e-03	k: 1176	n:370000
Cons ci ratio: 4.160834e-04	ci left: 9.956390e-01	ci right 9.960559e-01	k: 368465	n:370000
KS ci ratio: 1.140789e-01	ci left: 2.999560e-03	ci right 3.365046e-03	k: 1176	n:370000
KIF18A   370000 perm   124 sec   (2976 perm/sec)   p_kst 3.178378e-03   p_cons 9.958514e-01   p_joint 3.178378e-03

Joint ci ratio: 1.127933e-01	ci left: 2.989660e-03	ci right 3.349561e-03	k: 1203	n:380000
Cons ci ratio: 4.123308e-04	ci left: 9.956054e-01	ci right 9.960186e-01	k: 378410	n:380000
KS ci ratio: 1.127933e-01	ci left: 2.989660e-03	ci right 3.349561e-03	k: 1203	n:380000
KIF18A   380000 perm   129 sec   (2946 perm/sec)   p_kst 3.165789e-03   p_cons 9.958158e-01   p_joint 3.165789e-03

Joint ci ratio: 1.115501e-01	ci left: 2.980290e-03	ci right 3.334848e-03	k: 1230	n:390000
Cons ci ratio: 4.050194e-04	ci left: 9.956498e-01	ci right 9.960556e-01	k: 388384	n:390000
KS ci ratio: 1.115501e-01	ci left: 2.980290e-03	ci right 3.334848e-03	k: 1230	n:390000
KIF18A   390000 perm   134 sec   (2916 perm/sec)   p_kst 3.153846e-03   p_cons 9.958564e-01   p_joint 3.153846e-03

Joint ci ratio: 1.097363e-01	ci left: 3.005448e-03	ci right 3.356810e-03	k: 1271	n:400000
Cons ci ratio: 3.997477e-04	ci left: 9.956561e-01	ci right 9.960566e-01	k: 398344	n:400000
KS ci ratio: 1.097363e-01	ci left: 3.005448e-03	ci right 3.356810e-03	k: 1271	n:400000
KIF18A   400000 perm   139 sec   (2886 perm/sec)   p_kst 3.177500e-03   p_cons 9.958600e-01   p_joint 3.177500e-03

Joint ci ratio: 1.083398e-01	ci left: 3.010438e-03	ci right 3.357618e-03	k: 1304	n:410000
Cons ci ratio: 3.950265e-04	ci left: 9.956547e-01	ci right 9.960504e-01	k: 408301	n:410000
KS ci ratio: 1.083398e-01	ci left: 3.010438e-03	ci right 3.357618e-03	k: 1304	n:410000
KIF18A   410000 perm   144 sec   (2856 perm/sec)   p_kst 3.180488e-03   p_cons 9.958561e-01   p_joint 3.180488e-03

Joint ci ratio: 1.069552e-01	ci left: 3.017534e-03	ci right 3.360805e-03	k: 1338	n:420000
Cons ci ratio: 3.903559e-04	ci left: 9.956558e-01	ci right 9.960468e-01	k: 418259	n:420000
KS ci ratio: 1.069552e-01	ci left: 3.017534e-03	ci right 3.360805e-03	k: 1338	n:420000
KIF18A   420000 perm   149 sec   (2818 perm/sec)   p_kst 3.185714e-03   p_cons 9.958548e-01   p_joint 3.185714e-03

Joint ci ratio: 1.059714e-01	ci left: 3.003949e-03	ci right 3.342335e-03	k: 1363	n:430000
Cons ci ratio: 3.851951e-04	ci left: 9.956712e-01	ci right 9.960570e-01	k: 428223	n:430000
KS ci ratio: 1.059714e-01	ci left: 3.003949e-03	ci right 3.342335e-03	k: 1363	n:430000
KIF18A   430000 perm   154 sec   (2789 perm/sec)   p_kst 3.169767e-03   p_cons 9.958674e-01   p_joint 3.169767e-03

Joint ci ratio: 1.045995e-01	ci left: 3.015342e-03	ci right 3.350344e-03	k: 1399	n:440000
Cons ci ratio: 3.803355e-04	ci left: 9.956835e-01	ci right 9.960645e-01	k: 438186	n:440000
KS ci ratio: 1.045995e-01	ci left: 3.015342e-03	ci right 3.350344e-03	k: 1399	n:440000
KIF18A   440000 perm   159 sec   (2762 perm/sec)   p_kst 3.179545e-03   p_cons 9.958773e-01   p_joint 3.179545e-03

Joint ci ratio: 1.033518e-01	ci left: 3.021926e-03	ci right 3.353411e-03	k: 1433	n:450000
Cons ci ratio: 3.766703e-04	ci left: 9.956726e-01	ci right 9.960499e-01	k: 448139	n:450000
KS ci ratio: 1.033518e-01	ci left: 3.021926e-03	ci right 3.353411e-03	k: 1433	n:450000
KIF18A   450000 perm   165 sec   (2726 perm/sec)   p_kst 3.184444e-03   p_cons 9.958644e-01   p_joint 3.184444e-03

Joint ci ratio: 1.021477e-01	ci left: 3.028246e-03	ci right 3.356322e-03	k: 1467	n:460000
Cons ci ratio: 3.737920e-04	ci left: 9.956466e-01	ci right 9.960210e-01	k: 458085	n:460000
KS ci ratio: 1.021477e-01	ci left: 3.028246e-03	ci right 3.356322e-03	k: 1467	n:460000
KIF18A   460000 perm   170 sec   (2700 perm/sec)   p_kst 3.189130e-03   p_cons 9.958370e-01   p_joint 3.189130e-03

Joint ci ratio: 1.011537e-01	ci left: 3.023948e-03	ci right 3.348182e-03	k: 1496	n:470000
Cons ci ratio: 3.700167e-04	ci left: 9.956436e-01	ci right 9.960141e-01	k: 468041	n:470000
KS ci ratio: 1.011537e-01	ci left: 3.023948e-03	ci right 3.348182e-03	k: 1496	n:470000
KIF18A   470000 perm   176 sec   (2671 perm/sec)   p_kst 3.182979e-03   p_cons 9.958319e-01   p_joint 3.182979e-03

Joint ci ratio: 1.002212e-01	ci left: 3.017813e-03	ci right 3.338231e-03	k: 1524	n:480000
Cons ci ratio: 3.664449e-04	ci left: 9.956385e-01	ci right 9.960055e-01	k: 477996	n:480000
KS ci ratio: 1.002212e-01	ci left: 3.017813e-03	ci right 3.338231e-03	k: 1524	n:480000
KIF18A   480000 perm   182 sec   (2644 perm/sec)   p_kst 3.175000e-03   p_cons 9.958250e-01   p_joint 3.175000e-03

Joint ci ratio: 9.950704e-02	ci left: 3.000000e-03	ci right 3.316124e-03	k: 1546	n:490000
Cons ci ratio: 3.627958e-04	ci left: 9.956379e-01	ci right 9.960011e-01	k: 487953	n:490000
KS ci ratio: 9.950704e-02	ci left: 3.000000e-03	ci right 3.316124e-03	k: 1546	n:490000
KIF18A   490000 perm   187 sec   (2615 perm/sec)   p_kst 3.155102e-03   p_cons 9.958224e-01   p_joint 3.155102e-03

Outputting figure to mutsig2_images.part000000000091/KIF18A.2_2761_490000_0.0031551_0.99582_0.0031551.png
                gene_name: KIF18A
               theta_stop: 0.100 
                    nperm: 490000 
                     p_ks: 0.0032 
        ci_ks_bounds_left: 0.0030 
       ci_ks_bounds_right: 0.0033 
                   p_cons: 1.00 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.0032 
     ci_joint_bounds_left: 0.0030 
    ci_joint_bounds_right: 0.0033 

Current progress: 69 percent done.
KIF20B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.268230e-01	ci left: 8.164409e-02	ci right 9.279774e-02	k: 871	n:10000
Cons ci ratio: 1.016296e-01	ci left: 1.228802e-01	ci right 1.361365e-01	k: 1294	n:10000
KS ci ratio: 1.645486e-01	ci left: 4.926618e-02	ci right 5.819605e-02	k: 536	n:10000
KIF20B   10000 perm   2 sec   (5076 perm/sec)   p_kst 5.360000e-02   p_cons 1.294000e-01   p_joint 8.710000e-02

Joint ci ratio: 6.722610e-02	ci left: 1.403936e-01	ci right 1.502098e-01	k: 2905	n:20000
Cons ci ratio: 7.124930e-02	ci left: 1.267467e-01	ci right 1.361607e-01	k: 2628	n:20000
KS ci ratio: 1.195048e-01	ci left: 4.799150e-02	ci right 5.413986e-02	k: 1020	n:20000
KIF20B   20000 perm   4 sec   (4601 perm/sec)   p_kst 5.100000e-02   p_cons 1.314000e-01   p_joint 1.452500e-01

Joint ci ratio: 6.262937e-02	ci left: 1.118710e-01	ci right 1.191370e-01	k: 3464	n:30000
Cons ci ratio: 5.796800e-02	ci left: 1.284192e-01	ci right 1.361188e-01	k: 3967	n:30000
KS ci ratio: 9.786246e-02	ci left: 4.827697e-02	ci right 5.327714e-02	k: 1522	n:30000
KIF20B   30000 perm   7 sec   (4407 perm/sec)   p_kst 5.073333e-02   p_cons 1.322333e-01   p_joint 1.154667e-01

Outputting figure to mutsig2_images.part000000000091/KIF20B.2_5471_30000_0.050733_0.13223_0.11547.png
                gene_name: KIF20B
               theta_stop: 0.098 
                    nperm: 30000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.048 
       ci_ks_bounds_right: 0.053 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

Current progress: 77 percent done.
KIF21B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.057533e-02	ci left: 6.121106e-01	ci right 6.312185e-01	k: 6217	n:10000
KS ci ratio: 6.903667e-02	ci left: 2.353112e-01	ci right 2.522383e-01	k: 2437	n:10000
KIF21B   10000 perm   2 sec   (4981 perm/sec)   p_kst 2.437000e-01   p_cons 6.217000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIF21B.2_5011_10000_0.2437_0.6217_1.png
                gene_name: KIF21B
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.63 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 85 percent done.
KIF2C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.886211e-03	ci left: 9.467940e-01	ci right 9.553408e-01	k: 9512	n:10000
KS ci ratio: 8.790262e-03	ci left: 9.478349e-01	ci right 9.562992e-01	k: 9522	n:10000
KIF2C   10000 perm   2 sec   (5704 perm/sec)   p_kst 9.522000e-01   p_cons 9.512000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIF2C.2_2262_10000_0.9522_0.9512_1.png
                gene_name: KIF2C
               theta_stop: 0.0089 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 92 percent done.
KIF7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.088549e-02	ci left: 7.706358e-01	ci right 7.870015e-01	k: 7789	n:10000
KS ci ratio: 1.935551e-02	ci left: 7.960815e-01	ci right 8.117411e-01	k: 8040	n:10000
KIF7   10000 perm   2 sec   (5564 perm/sec)   p_kst 8.040000e-01   p_cons 7.789000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIF7.2_4104_10000_0.804_0.7789_1.png
                gene_name: KIF7
               theta_stop: 0.021 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000091
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 91 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4398093: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000092> was used as the working directory.
Started at Wed Oct 24 16:13:09 2012
Results reported at Wed Oct 24 16:15:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000092.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000092.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 92  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000092.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    137.70 sec.
    Max Memory :      1061 MB
    Max Swap   :      3881 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
92
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 92
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 92: processing genes 8165 - 8253
Calculating significance of each gene.
Using projection method.
8165	KIT	1
8166	KITLG	1
8167	KL	1
8168	KLB	1
8169	KLC1	1
8170	KLC2	1
8171	KLC3	1
8172	KLC4	1
8173	KLF1	1
8174	KLF10	2.305697e-01
8175	KLF11	1
8176	KLF12	1
8177	KLF13	1
8178	KLF14	1
8179	KLF15	1
8180	KLF17	1
8181	KLF3	1
8182	KLF4	1
8183	KLF5	1
8184	KLF6	1
8185	KLF7	1
8186	KLF8	1
8187	KLF9	1
8188	KLHDC1	1
8189	KLHDC10	1
8190	KLHDC2	1
8191	KLHDC3	1.424671e-02
8192	KLHDC4	1
8193	KLHDC5	1.377479e-01
8194	KLHDC7A	1
8195	KLHDC7B	5.054958e-02
8196	KLHDC8A	1
8197	KLHDC8B	1
8198	KLHDC9	1
8199	KLHL1	5.929826e-03
8200	KLHL10	2.280696e-01
8201	KLHL11	1
8202	KLHL12	1
8203	KLHL13	2.921257e-01
8204	KLHL14	1.888203e-01
8205	KLHL15	1
8206	KLHL17	1
8207	KLHL18	1
8208	KLHL2	2.512929e-02
8209	KLHL20	1
8210	KLHL21	1
8211	KLHL22	1
8212	KLHL23	1.353537e-01
8213	KLHL24	1
8214	KLHL25	1
8215	KLHL26	1
8216	KLHL28	1
8217	KLHL3	1
8218	KLHL30	1
8219	KLHL31	1
8220	KLHL32	1
8221	KLHL34	1
8222	KLHL35	1
8223	KLHL36	1
8224	KLHL38	1
8225	KLHL4	1.166727e-01
8226	KLHL5	1
8227	KLHL6	1.146611e-01
8228	KLHL7	2.176392e-01
8229	KLHL8	1
8230	KLHL9	1
8231	KLK1	1
8232	KLK10	1
8233	KLK11	1
8234	KLK12	1
8235	KLK13	1
8236	KLK14	1
8237	KLK15	1
8238	KLK2	1
8239	KLK3	5.182087e-02
8240	KLK4	1
8241	KLK5	1
8242	KLK6	1
8243	KLK7	1
8244	KLK8	1
8245	KLK9	1
8246	KLKB1	1
8247	KLRAQ1	1
8248	KLRB1	1
8249	KLRC1	1
8250	KLRC2	1
8251	KLRC3	1
8252	KLRC4	1
8253	KLRD1	1
Done

Running MutSig 2:
Scatter job 92: processing genes 8165 - 8253
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KLHDC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.581213e-03	ci left: 9.390015e-01	ci right 9.481380e-01	k: 9437	n:10000
Cons ci ratio: 6.954595e-02	ci left: 2.326438e-01	ci right 2.495073e-01	k: 2410	n:10000
KS ci ratio: 1.404356e-02	ci left: 8.799154e-01	ci right 8.924587e-01	k: 8863	n:10000
KLHDC3   10000 perm   2 sec   (6244 perm/sec)   p_kst 8.863000e-01   p_cons 2.410000e-01   p_joint 9.437000e-01

Outputting figure to mutsig2_images.part000000000092/KLHDC3.2_1189_10000_0.8863_0.241_0.9437.png
                gene_name: KLHDC3
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 33 percent done.
KLHL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.513066e-02	ci left: 6.996848e-01	ci right 7.175935e-01	k: 7087	n:10000
KS ci ratio: 2.045457e-02	ci left: 7.778289e-01	ci right 7.940042e-01	k: 7860	n:10000
KLHL1   10000 perm   3 sec   (3421 perm/sec)   p_kst 7.860000e-01   p_cons 7.087000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000092/KLHL1.2_2291_10000_0.786_0.7087_1.png
                gene_name: KLHL1
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
KLHL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.252316e-02	ci left: 7.432110e-01	ci right 7.602421e-01	k: 7518	n:10000
Cons ci ratio: 7.764659e-02	ci left: 1.951537e-01	ci right 2.110196e-01	k: 2030	n:10000
KS ci ratio: 5.276977e-02	ci left: 3.461116e-01	ci right 3.649727e-01	k: 3555	n:10000
KLHL2   10000 perm   3 sec   (3654 perm/sec)   p_kst 3.555000e-01   p_cons 2.030000e-01   p_joint 7.518000e-01

Outputting figure to mutsig2_images.part000000000092/KLHL2.2_1884_10000_0.3555_0.203_0.7518.png
                gene_name: KLHL2
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.74 
    ci_joint_bounds_right: 0.76 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000092
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 92 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1553>
Subject: Job 4398096: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1553>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000093> was used as the working directory.
Started at Wed Oct 24 16:13:28 2012
Results reported at Wed Oct 24 16:16:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000093.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000093.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 93  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000093.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    284.33 sec.
    Max Memory :      1324 MB
    Max Swap   :      3978 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
93
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 93
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 93: processing genes 8254 - 8343
Calculating significance of each gene.
Using projection method.
8254	KLRF1	1
8255	KLRG1	1
8256	KLRG2	1
8257	KLRK1	1
8258	KMO	1.622912e-01
8259	KNCN	1
8260	KNDC1	1
8261	KNG1	1
8262	KNTC1	1.603684e-01
8263	KPNA1	2.183852e-01
8264	KPNA2	6.047348e-04
8265	KPNA3	2.511264e-01
8266	KPNA4	1
8267	KPNA5	1
8268	KPNA6	1.040561e-01
8269	KPNB1	1
8270	KPRP	1
8271	KPTN	1
8272	KRAS	3.000750e-02
8273	KRBA1	1
8274	KRBA2	1
8275	KRCC1	1.403024e-01
8276	KREMEN1	1
8277	KREMEN2	1
8278	KRI1	1
8279	KRIT1	1
8280	KRR1	1
8281	KRT1	2.789268e-01
8282	KRT10	1
8283	KRT12	1
8284	KRT13	1
8285	KRT14	1
8286	KRT15	1.864408e-01
8287	KRT16	1
8288	KRT17	1.172950e-01
8289	KRT18	1
8290	KRT19	1
8291	KRT2	4.909209e-03
8292	KRT20	1
8293	KRT222	1
8294	KRT23	1
8295	KRT24	1
8296	KRT25	1
8297	KRT26	1
8298	KRT27	1
8299	KRT28	1.332503e-01
8300	KRT3	1
8301	KRT31	8.384351e-03
8302	KRT32	1
8303	KRT33A	1
8304	KRT33B	1
8305	KRT34	1
8306	KRT35	8.445990e-02
8307	KRT36	1
8308	KRT37	1
8309	KRT38	1
8310	KRT39	1
8311	KRT4	1
8312	KRT40	1
8313	KRT5	1
8314	KRT6A	1
8315	KRT6B	1.608671e-02
In gene KRT6C the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 1501    n = 1	mu =   4.43e-07
8316	KRT6C	5.089437e-02
8317	KRT7	1
8318	KRT71	1
8319	KRT72	1
8320	KRT73	1
8321	KRT74	1
8322	KRT75	1
8323	KRT76	1
8324	KRT77	1
8325	KRT78	1
8326	KRT79	1
8327	KRT8	1
8328	KRT80	1
8329	KRT81	1
8330	KRT82	1
8331	KRT83	1
8332	KRT84	1.212909e-01
8333	KRT85	1
8334	KRT86	1.690753e-01
8335	KRT9	1
8336	KRTAP1-1	1
8337	KRTAP1-3	3.809949e-02
8338	KRTAP1-5	1
8339	KRTAP10-1	1
8340	KRTAP10-10	1
8341	KRTAP10-11	1
8342	KRTAP10-12	1
8343	KRTAP10-2	1
Done

Running MutSig 2:
Scatter job 93: processing genes 8254 - 8343
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KPNA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.968229e-02	ci left: 1.531589e-01	ci right 1.676395e-01	k: 1603	n:10000
Cons ci ratio: 6.293718e-02	ci left: 2.706208e-01	ci right 2.883078e-01	k: 2794	n:10000
KS ci ratio: 8.624746e-02	ci left: 1.637654e-01	ci right 1.786266e-01	k: 1711	n:10000
KPNA2   10000 perm   2 sec   (5311 perm/sec)   p_kst 1.711000e-01   p_cons 2.794000e-01   p_joint 1.603000e-01

Outputting figure to mutsig2_images.part000000000093/KPNA2.3_1630_10000_0.1711_0.2794_0.1603.png
                gene_name: KPNA2
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.16 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.17 

Current progress: 20 percent done.
KNTC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.039475e-01	ci left: 1.179914e-01	ci right 1.310282e-01	k: 1244	n:10000
Cons ci ratio: 2.290929e-02	ci left: 7.367410e-01	ci right 7.539159e-01	k: 7454	n:10000
KS ci ratio: 2.772291e-01	ci left: 1.688052e-02	ci right 2.240432e-02	k: 195	n:10000
KNTC1   10000 perm   3 sec   (3864 perm/sec)   p_kst 1.950000e-02   p_cons 7.454000e-01   p_joint 1.244000e-01

Joint ci ratio: 2.891467e-02	ci left: 4.719052e-01	ci right 4.858010e-01	k: 9577	n:20000
Cons ci ratio: 1.610134e-02	ci left: 7.416198e-01	ci right 7.537081e-01	k: 14954	n:20000
KS ci ratio: 1.925569e-01	ci left: 1.834288e-02	ci right 2.229831e-02	k: 405	n:20000
KNTC1   20000 perm   6 sec   (3554 perm/sec)   p_kst 2.025000e-02   p_cons 7.477000e-01   p_joint 4.788500e-01

Joint ci ratio: 1.132799e-02	ci left: 7.950919e-01	ci right 8.041833e-01	k: 23990	n:30000
Cons ci ratio: 1.365104e-02	ci left: 7.281896e-01	ci right 7.382319e-01	k: 21997	n:30000
KS ci ratio: 1.561795e-01	ci left: 1.895846e-02	ci right 2.220199e-02	k: 616	n:30000
KNTC1   30000 perm   9 sec   (3441 perm/sec)   p_kst 2.053333e-02   p_cons 7.332333e-01   p_joint 7.996667e-01

Joint ci ratio: 2.031594e-02	ci left: 4.771422e-01	ci right 4.869604e-01	k: 19282	n:40000
Cons ci ratio: 1.187607e-02	ci left: 7.270775e-01	ci right 7.357889e-01	k: 29258	n:40000
KS ci ratio: 1.354803e-01	ci left: 1.910956e-02	ci right 2.191066e-02	k: 819	n:40000
KNTC1   40000 perm   12 sec   (3369 perm/sec)   p_kst 2.047500e-02   p_cons 7.314500e-01   p_joint 4.820500e-01

Joint ci ratio: 2.637611e-02	ci left: 3.023407e-01	ci right 3.104418e-01	k: 15319	n:50000
Cons ci ratio: 1.059662e-02	ci left: 7.284961e-01	ci right 7.362769e-01	k: 36620	n:50000
KS ci ratio: 1.214197e-01	ci left: 1.917881e-02	ci right 2.167730e-02	k: 1020	n:50000
KNTC1   50000 perm   15 sec   (3307 perm/sec)   p_kst 2.040000e-02   p_cons 7.324000e-01   p_joint 3.063800e-01

Joint ci ratio: 2.251047e-02	ci left: 3.319377e-01	ci right 3.395115e-01	k: 20143	n:60000
Cons ci ratio: 9.686515e-03	ci left: 7.283026e-01	ci right 7.354083e-01	k: 43912	n:60000
KS ci ratio: 1.116433e-01	ci left: 1.900818e-02	ci right 2.127190e-02	k: 1207	n:60000
KNTC1   60000 perm   18 sec   (3255 perm/sec)   p_kst 2.011667e-02   p_cons 7.318667e-01   p_joint 3.357167e-01

Joint ci ratio: 2.975456e-02	ci left: 1.957210e-01	ci right 2.016468e-01	k: 13907	n:70000
Cons ci ratio: 8.973091e-03	ci left: 7.283437e-01	ci right 7.349228e-01	k: 51215	n:70000
KS ci ratio: 1.033368e-01	ci left: 1.910098e-02	ci right 2.119621e-02	k: 1409	n:70000
KNTC1   70000 perm   22 sec   (3204 perm/sec)   p_kst 2.012857e-02   p_cons 7.316429e-01   p_joint 1.986714e-01

Joint ci ratio: 2.789514e-02	ci left: 1.952061e-01	ci right 2.007408e-01	k: 15837	n:80000
Cons ci ratio: 8.384594e-03	ci left: 7.289789e-01	ci right 7.351293e-01	k: 58565	n:80000
KS ci ratio: 9.640146e-02	ci left: 1.927292e-02	ci right 2.123709e-02	k: 1619	n:80000
KNTC1   80000 perm   25 sec   (3155 perm/sec)   p_kst 2.023750e-02   p_cons 7.320625e-01   p_joint 1.979625e-01

Outputting figure to mutsig2_images.part000000000093/KNTC1.2_6882_80000_0.020237_0.73206_0.19796.png
                gene_name: KNTC1
               theta_stop: 0.096 
                    nperm: 80000 
                     p_ks: 0.020 
        ci_ks_bounds_left: 0.019 
       ci_ks_bounds_right: 0.021 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.20 

Current progress: 40 percent done.
KRT2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.459463e-02	ci left: 4.260512e-01	ci right 4.455862e-01	k: 4358	n:10000
Cons ci ratio: 7.735992e-02	ci left: 1.963361e-01	ci right 2.122365e-01	k: 2042	n:10000
KS ci ratio: 8.609581e-02	ci left: 1.642567e-01	ci right 1.791350e-01	k: 1716	n:10000
KRT2   10000 perm   2 sec   (5136 perm/sec)   p_kst 1.716000e-01   p_cons 2.042000e-01   p_joint 4.358000e-01

Outputting figure to mutsig2_images.part000000000093/KRT2.2_1956_10000_0.1716_0.2042_0.4358.png
                gene_name: KRT2
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 60 percent done.
KRT31
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.251928e-02	ci left: 9.016521e-01	ci right 9.131093e-01	k: 9075	n:10000
KS ci ratio: 1.257135e-02	ci left: 9.009330e-01	ci right 9.124288e-01	k: 9068	n:10000
KRT31   10000 perm   2 sec   (6536 perm/sec)   p_kst 9.068000e-01   p_cons 9.075000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000093/KRT31.2_1279_10000_0.9068_0.9075_1.png
                gene_name: KRT31
               theta_stop: 0.013 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
KRT6B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.904749e-02	ci left: 6.360330e-01	ci right 6.548822e-01	k: 6455	n:10000
KS ci ratio: 3.460899e-02	ci left: 5.521087e-01	ci right 5.716552e-01	k: 5619	n:10000
KRT6B   10000 perm   2 sec   (6337 perm/sec)   p_kst 5.619000e-01   p_cons 6.455000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000093/KRT6B.2_1731_10000_0.5619_0.6455_1.png
                gene_name: KRT6B
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000093
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 93 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1547>
Subject: Job 4398098: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000094> was used as the working directory.
Started at Wed Oct 24 16:13:27 2012
Results reported at Wed Oct 24 16:15:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000094.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000094.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 94  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000094.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    148.97 sec.
    Max Memory :       689 MB
    Max Swap   :      3457 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
94
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 94
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 94: processing genes 8344 - 8433
Calculating significance of each gene.
Using projection method.
8344	KRTAP10-3	1
8345	KRTAP10-4	1
8346	KRTAP10-5	1
8347	KRTAP10-6	1
8348	KRTAP10-7	1
8349	KRTAP10-8	1
8350	KRTAP10-9	1
8351	KRTAP11-1	5.283724e-03
8352	KRTAP12-1	1
8353	KRTAP12-2	1
8354	KRTAP12-3	1
8355	KRTAP12-4	1
8356	KRTAP13-1	1
8357	KRTAP13-2	1
8358	KRTAP13-3	1
8359	KRTAP13-4	1
8360	KRTAP15-1	1
8361	KRTAP17-1	1
8362	KRTAP19-1	1.901668e-02
8363	KRTAP19-2	1
8364	KRTAP19-3	1
8365	KRTAP19-4	1
8366	KRTAP19-5	1
8367	KRTAP19-6	1
8368	KRTAP19-7	1
8369	KRTAP19-8	1
8370	KRTAP20-1	1
8371	KRTAP20-2	1
8372	KRTAP21-1	1
8373	KRTAP21-2	1
8374	KRTAP22-1	1
8375	KRTAP23-1	1
8376	KRTAP24-1	1
8377	KRTAP26-1	1
8378	KRTAP27-1	1
8379	KRTAP3-1	1
8380	KRTAP3-2	1
8381	KRTAP3-3	1
8382	KRTAP4-1	1
8383	KRTAP4-12	5.090839e-02
8384	KRTAP4-2	1
8385	KRTAP4-3	1
8386	KRTAP4-4	1
8387	KRTAP4-5	1
8388	KRTAP5-1	1
8389	KRTAP5-10	1
8390	KRTAP5-11	1
8391	KRTAP5-2	1
8392	KRTAP5-3	1
8393	KRTAP5-5	1
8394	KRTAP5-6	1
8395	KRTAP5-7	1
8396	KRTAP5-8	5.971777e-02
8397	KRTAP5-9	1
8398	KRTAP6-1	1
8399	KRTAP6-2	1
8400	KRTAP6-3	1
8401	KRTAP8-1	1
8402	KRTAP9-2	1
8403	KRTAP9-3	1
8404	KRTAP9-4	8.356814e-03
8405	KRTAP9-8	3.810371e-02
8406	KRTAP9-9	1
8407	KRTCAP2	1
8408	KRTCAP3	1
8409	KRTDAP	1
8410	KSR1	1.120796e-01
8411	KSR2	1
8412	KTELC1	1
8413	KTI12	1
8414	KTN1	1
8415	KY	2.362571e-01
8416	KYNU	1
8417	L1CAM	2.018833e-01
8418	L1TD1	1
8419	L2HGDH	1
8420	L3MBTL	1
8421	L3MBTL2	1
8422	L3MBTL3	1
8423	L3MBTL4	1
8424	LACE1	1
8425	LACRT	1
8426	LACTB	1
8427	LACTB2	1
8428	LAD1	1
8429	LAG3	1
8430	LAGE3	1
8431	LAIR1	5.224271e-02
8432	LAIR2	1
8433	LALBA	1
Done

Running MutSig 2:
Scatter job 94: processing genes 8344 - 8433
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000094
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 94 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4398100: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000095> was used as the working directory.
Started at Wed Oct 24 16:13:30 2012
Results reported at Wed Oct 24 16:16:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000095.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000095.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 95  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000095.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    181.99 sec.
    Max Memory :      1494 MB
    Max Swap   :      4080 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
95
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 95
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 95: processing genes 8434 - 8522
Calculating significance of each gene.
Using projection method.
8434	LAMA1	5.753654e-01
8435	LAMA2	6.099772e-01
8436	LAMA3	6.347700e-01
8437	LAMA4	5.022234e-01
8438	LAMA5	5.011020e-01
8439	LAMB1	2.709845e-01
8440	LAMB2	1.040836e-01
8441	LAMB3	2.447293e-01
8442	LAMB4	1
8443	LAMC1	4.053965e-01
8444	LAMC2	1
8445	LAMC3	1
8446	LAMP1	1.105055e-01
8447	LAMP2	1
8448	LAMP3	1.831151e-01
8449	LANCL1	1
8450	LANCL2	1
8451	LANCL3	1
8452	LAP3	1
8453	LAPTM4A	1
8454	LAPTM4B	1
8455	LAPTM5	1
8456	LARGE	1
8457	LARP1	1
8458	LARP1B	3.399512e-01
8459	LARP4	1
8460	LARP4B	1
8461	LARP6	2.388080e-01
8462	LARP7	1
8463	LARS	2.707873e-01
8464	LARS2	1
8465	LAS1L	1
8466	LASP1	1
8467	LASS1	1
8468	LASS2	1
8469	LASS3	1
8470	LASS4	1
8471	LASS5	1.048992e-01
8472	LASS6	1
8473	LAT	1
8474	LAT2	1
8475	LATS1	4.590510e-01
8476	LATS2	1
8477	LAX1	1
8478	LAYN	1
8479	LBH	1
8480	LBP	1
8481	LBR	7.460887e-02
8482	LBX1	1
8483	LBX2	1
8484	LBXCOR1	1
8485	LCA5	1
8486	LCA5L	1.642788e-01
8487	LCAT	1
8488	LCE1A	1
8489	LCE1B	5.863992e-02
8490	LCE1C	1
8491	LCE1D	1
8492	LCE1E	1
8493	LCE1F	1
8494	LCE2A	1
8495	LCE2B	1
8496	LCE2C	1
8497	LCE2D	1
8498	LCE3A	1
8499	LCE3B	1
8500	LCE3C	1
8501	LCE3D	1
8502	LCE3E	1
8503	LCE4A	1
8504	LCE5A	1
8505	LCK	1
8506	LCLAT1	1.113262e-01
8507	LCMT1	4.249426e-03
8508	LCMT2	1
8509	LCN1	1
8510	LCN10	4.472547e-02
8511	LCN12	1
8512	LCN15	1
8513	LCN2	1
8514	LCN6	1
8515	LCN8	1
8516	LCN9	1
8517	LCNL1	1
8518	LCOR	1
8519	LCORL	1
8520	LCP1	1
8521	LCP2	1.538421e-01
8522	LCT	1.246800e-01
Done

Running MutSig 2:
Scatter job 95: processing genes 8434 - 8522
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LAMA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.705609e-02	ci left: 6.680363e-01	ci right 6.864603e-01	k: 6773	n:10000
Cons ci ratio: 5.390563e-02	ci left: 3.364739e-01	ci right 3.552160e-01	k: 3458	n:10000
KS ci ratio: 3.275514e-02	ci left: 5.790813e-01	ci right 5.984670e-01	k: 5888	n:10000
LAMA1   10000 perm   3 sec   (3878 perm/sec)   p_kst 5.888000e-01   p_cons 3.458000e-01   p_joint 6.773000e-01

Outputting figure to mutsig2_images.part000000000095/LAMA1.2_9480_10000_0.5888_0.3458_0.6773.png
                gene_name: LAMA1
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.69 

Current progress: 17 percent done.
LAMB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.379586e-01	ci left: 6.952474e-02	ci right 7.992463e-02	k: 746	n:10000
Cons ci ratio: 1.278700e-01	ci left: 8.038196e-02	ci right 9.146065e-02	k: 858	n:10000
KS ci ratio: 6.798590e-02	ci left: 2.409439e-01	ci right 2.580023e-01	k: 2494	n:10000
LAMB2   10000 perm   2 sec   (4763 perm/sec)   p_kst 2.494000e-01   p_cons 8.580000e-02   p_joint 7.460000e-02

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 9.088334e-02	ci left: 8.121946e-02	ci right 8.900166e-02	k: 1701	n:20000
KS ci ratio: 4.768535e-02	ci left: 2.464903e-01	ci right 2.585817e-01	k: 5050	n:20000
LAMB2   20000 perm   5 sec   (4327 perm/sec)   p_kst 2.525000e-01   p_cons 8.505000e-02   p_joint 1

Outputting figure to mutsig2_images.part000000000095/LAMB2.2_5525_20000_0.2525_0.08505_1.png
                gene_name: LAMB2
               theta_stop: 0.091 
                    nperm: 20000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.085 
      ci_cons_bounds_left: 0.081 
     ci_cons_bounds_right: 0.089 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
LCAT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.051180e-02	ci left: 2.865679e-01	ci right 3.045513e-01	k: 2955	n:10000
Cons ci ratio: 6.742779e-02	ci left: 2.440081e-01	ci right 2.611363e-01	k: 2525	n:10000
KS ci ratio: 1.288571e-01	ci left: 7.921726e-02	ci right 9.022608e-02	k: 846	n:10000
LCAT   10000 perm   2 sec   (6458 perm/sec)   p_kst 8.460000e-02   p_cons 2.525000e-01   p_joint 2.955000e-01

Joint ci ratio: 3.979696e-02	ci left: 3.201011e-01	ci right 3.331493e-01	k: 6532	n:20000
Cons ci ratio: 4.744031e-02	ci left: 2.484247e-01	ci right 2.605467e-01	k: 5089	n:20000
KS ci ratio: 8.996207e-02	ci left: 8.278644e-02	ci right 9.063420e-02	k: 1733	n:20000
LCAT   20000 perm   3 sec   (5719 perm/sec)   p_kst 8.665000e-02   p_cons 2.544500e-01   p_joint 3.266000e-01

Outputting figure to mutsig2_images.part000000000095/LCAT.2_1347_20000_0.08665_0.25445_0.3266.png
                gene_name: LCAT
               theta_stop: 0.090 
                    nperm: 20000 
                     p_ks: 0.087 
        ci_ks_bounds_left: 0.083 
       ci_ks_bounds_right: 0.091 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.33 

Current progress: 50 percent done.
LCLAT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.494084e-02	ci left: 4.222622e-01	ci right 4.417774e-01	k: 4320	n:10000
Cons ci ratio: 1.554271e-01	ci left: 5.513502e-02	ci right 6.452344e-02	k: 597	n:10000
KS ci ratio: 3.045107e-01	ci left: 1.381734e-02	ci right 1.887010e-02	k: 162	n:10000
LCLAT1   10000 perm   1 sec   (6837 perm/sec)   p_kst 1.620000e-02   p_cons 5.970000e-02   p_joint 4.320000e-01

Joint ci ratio: 3.199326e-01	ci left: 6.259271e-03	ci right 8.687225e-03	k: 148	n:20000
Cons ci ratio: 1.455428e-01	ci left: 3.244754e-02	ci right 3.758880e-02	k: 699	n:20000
KS ci ratio: 2.180628e-01	ci left: 1.416473e-02	ci right 1.767805e-02	k: 317	n:20000
LCLAT1   20000 perm   3 sec   (6028 perm/sec)   p_kst 1.585000e-02   p_cons 3.495000e-02   p_joint 7.400000e-03

Joint ci ratio: 2.259452e-01	ci left: 8.810667e-03	ci right 1.108575e-02	k: 297	n:30000
Cons ci ratio: 1.197851e-01	ci left: 3.239853e-02	ci right 3.655893e-02	k: 1033	n:30000
KS ci ratio: 1.791977e-01	ci left: 1.429182e-02	ci right 1.713642e-02	k: 470	n:30000
LCLAT1   30000 perm   5 sec   (5715 perm/sec)   p_kst 1.566667e-02   p_cons 3.443333e-02   p_joint 9.900000e-03

Joint ci ratio: 2.001318e-01	ci left: 8.548862e-03	ci right 1.047335e-02	k: 379	n:40000
Cons ci ratio: 1.023112e-01	ci left: 3.358602e-02	ci right 3.723183e-02	k: 1415	n:40000
KS ci ratio: 1.541956e-01	ci left: 1.467284e-02	ci right 1.714816e-02	k: 635	n:40000
LCLAT1   40000 perm   7 sec   (5500 perm/sec)   p_kst 1.587500e-02   p_cons 3.537500e-02   p_joint 9.475000e-03

Joint ci ratio: 1.528701e-01	ci left: 1.198699e-02	ci right 1.399014e-02	k: 648	n:50000
Cons ci ratio: 9.124323e-02	ci left: 3.397333e-02	ci right 3.724087e-02	k: 1779	n:50000
KS ci ratio: 1.352616e-01	ci left: 1.540155e-02	ci right 1.765509e-02	k: 825	n:50000
LCLAT1   50000 perm   9 sec   (5339 perm/sec)   p_kst 1.650000e-02   p_cons 3.558000e-02   p_joint 1.296000e-02

Joint ci ratio: 1.612787e-01	ci left: 8.963225e-03	ci right 1.055140e-02	k: 584	n:60000
Cons ci ratio: 8.339468e-02	ci left: 3.403357e-02	ci right 3.701158e-02	k: 2130	n:60000
KS ci ratio: 1.234893e-01	ci left: 1.549580e-02	ci right 1.755134e-02	k: 990	n:60000
LCLAT1   60000 perm   12 sec   (5196 perm/sec)   p_kst 1.650000e-02   p_cons 3.550000e-02   p_joint 9.733333e-03

Joint ci ratio: 1.652829e-01	ci left: 7.312283e-03	ci right 8.643274e-03	k: 557	n:70000
Cons ci ratio: 7.769863e-02	ci left: 3.372081e-02	ci right 3.646076e-02	k: 2455	n:70000
KS ci ratio: 1.142369e-01	ci left: 1.559702e-02	ci right 1.750050e-02	k: 1157	n:70000
LCLAT1   70000 perm   14 sec   (5070 perm/sec)   p_kst 1.652857e-02   p_cons 3.507143e-02   p_joint 7.957143e-03

Joint ci ratio: 1.532471e-01	ci left: 7.490514e-03	ci right 8.745550e-03	k: 648	n:80000
Cons ci ratio: 7.242491e-02	ci left: 3.404415e-02	ci right 3.661469e-02	k: 2825	n:80000
KS ci ratio: 1.064276e-01	ci left: 1.578681e-02	ci right 1.757349e-02	k: 1333	n:80000
LCLAT1   80000 perm   16 sec   (4949 perm/sec)   p_kst 1.666250e-02   p_cons 3.531250e-02   p_joint 8.100000e-03

Joint ci ratio: 1.427318e-01	ci left: 7.717606e-03	ci right 8.914410e-03	k: 747	n:90000
Cons ci ratio: 6.750806e-02	ci left: 3.489072e-02	ci right 3.733930e-02	k: 3249	n:90000
KS ci ratio: 9.999422e-02	ci left: 1.594871e-02	ci right 1.763820e-02	k: 1510	n:90000
LCLAT1   90000 perm   19 sec   (4838 perm/sec)   p_kst 1.677778e-02   p_cons 3.610000e-02   p_joint 8.300000e-03

Joint ci ratio: 1.346829e-01	ci left: 7.833968e-03	ci right 8.974821e-03	k: 839	n:100000
Cons ci ratio: 6.412778e-02	ci left: 3.486370e-02	ci right 3.718331e-02	k: 3601	n:100000
KS ci ratio: 9.457366e-02	ci left: 1.609060e-02	ci right 1.769759e-02	k: 1688	n:100000
LCLAT1   100000 perm   21 sec   (4742 perm/sec)   p_kst 1.688000e-02   p_cons 3.601000e-02   p_joint 8.390000e-03

Joint ci ratio: 1.274451e-01	ci left: 7.983541e-03	ci right 9.078972e-03	k: 937	n:110000
Cons ci ratio: 6.131383e-02	ci left: 3.472768e-02	ci right 3.693324e-02	k: 3940	n:110000
KS ci ratio: 9.029368e-02	ci left: 1.608427e-02	ci right 1.761408e-02	k: 1852	n:110000
LCLAT1   110000 perm   24 sec   (4651 perm/sec)   p_kst 1.683636e-02   p_cons 3.581818e-02   p_joint 8.518182e-03

Joint ci ratio: 1.009202e-01	ci left: 1.178964e-02	ci right 1.305075e-02	k: 1489	n:120000
Cons ci ratio: 5.857136e-02	ci left: 3.492840e-02	ci right 3.704411e-02	k: 4317	n:120000
KS ci ratio: 8.641605e-02	ci left: 1.612930e-02	ci right 1.759418e-02	k: 2022	n:120000
LCLAT1   120000 perm   26 sec   (4561 perm/sec)   p_kst 1.685000e-02   p_cons 3.597500e-02   p_joint 1.240833e-02

Joint ci ratio: 9.687495e-02	ci left: 1.183552e-02	ci right 1.304791e-02	k: 1616	n:130000
Cons ci ratio: 5.625382e-02	ci left: 3.499385e-02	ci right 3.702692e-02	k: 4680	n:130000
KS ci ratio: 8.303713e-02	ci left: 1.615352e-02	ci right 1.756046e-02	k: 2190	n:130000
LCLAT1   130000 perm   29 sec   (4481 perm/sec)   p_kst 1.684615e-02   p_cons 3.600000e-02   p_joint 1.243077e-02

Outputting figure to mutsig2_images.part000000000095/LCLAT1.2_1269_130000_0.016846_0.036_0.012431.png
                gene_name: LCLAT1
               theta_stop: 0.097 
                    nperm: 130000 
                     p_ks: 0.017 
        ci_ks_bounds_left: 0.016 
       ci_ks_bounds_right: 0.018 
                   p_cons: 0.036 
      ci_cons_bounds_left: 0.035 
     ci_cons_bounds_right: 0.037 
                  p_joint: 0.012 
     ci_joint_bounds_left: 0.012 
    ci_joint_bounds_right: 0.013 

Current progress: 67 percent done.
LCMT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.752814e-02	ci left: 8.259500e-01	ci right 8.406553e-01	k: 8334	n:10000
Cons ci ratio: 3.221694e-02	ci left: 5.871085e-01	ci right 6.064351e-01	k: 5968	n:10000
KS ci ratio: 2.956342e-02	ci left: 6.278885e-01	ci right 6.468314e-01	k: 6374	n:10000
LCMT1   10000 perm   1 sec   (6874 perm/sec)   p_kst 6.374000e-01   p_cons 5.968000e-01   p_joint 8.334000e-01

Outputting figure to mutsig2_images.part000000000095/LCMT1.2_1049_10000_0.6374_0.5968_0.8334.png
                gene_name: LCMT1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.84 

Current progress: 83 percent done.
LCT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.918628e-02	ci left: 4.902514e-01	ci right 5.099486e-01	k: 5001	n:10000
KS ci ratio: 2.264382e-02	ci left: 7.411889e-01	ci right 7.582654e-01	k: 7498	n:10000
LCT   10000 perm   2 sec   (4705 perm/sec)   p_kst 7.498000e-01   p_cons 5.001000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000095/LCT.2_5852_10000_0.7498_0.5001_1.png
                gene_name: LCT
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000095
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 95 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4398103: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000096> was used as the working directory.
Started at Wed Oct 24 16:13:30 2012
Results reported at Wed Oct 24 16:14:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000096.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000096.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 96  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000096.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     69.89 sec.
    Max Memory :      1214 MB
    Max Swap   :      4010 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
96
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 96
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 96: processing genes 8523 - 8612
Calculating significance of each gene.
Using projection method.
8523	LCTL	1
8524	LDB1	1
8525	LDB2	1
8526	LDB3	1
8527	LDHA	1
8528	LDHAL6A	1
8529	LDHAL6B	1
8530	LDHB	1
8531	LDHC	1
8532	LDHD	1
8533	LDLR	1
8534	LDLRAD1	1
8535	LDLRAD2	1
8536	LDLRAD3	1
8537	LDLRAP1	1
8538	LDOC1	1
8539	LDOC1L	1
8540	LEAP2	1
8541	LECT1	1
8542	LECT2	1
8543	LEF1	1
8544	LEFTY1	1.332297e-01
8545	LEFTY2	9.244174e-02
8546	LEKR1	1
8547	LELP1	1
8548	LEMD1	1
8549	LEMD2	7.577928e-02
8550	LEMD3	1
8551	LENEP	1
8552	LENG1	2.737351e-02
8553	LENG8	1.883756e-01
8554	LENG9	5.444529e-02
8555	LEO1	1
8556	LEP	4.551323e-03
8557	LEPR	2.333450e-01
8558	LEPRE1	9.574455e-03
8559	LEPREL1	2.118765e-01
8560	LEPREL2	7.551438e-02
8561	LEPROT	1
8562	LEPROTL1	1
8563	LETM1	1
8564	LETM2	1
8565	LETMD1	1.014007e-01
8566	LFNG	1
8567	LGALS1	1
8568	LGALS12	8.994071e-02
8569	LGALS13	1
8570	LGALS14	1
8571	LGALS2	1
8572	LGALS3	1
8573	LGALS3BP	1
8574	LGALS4	1
8575	LGALS7B	1
8576	LGALS8	1
8577	LGALS9	1
8578	LGALS9B	1
8579	LGALS9C	1
8580	LGI1	1
8581	LGI2	1
8582	LGI3	1
8583	LGI4	1
8584	LGMN	1
8585	LGR4	1
8586	LGR5	1
8587	LGR6	1.173078e-01
8588	LGSN	1
8589	LGTN	1
8590	LHB	1
8591	LHCGR	1
8592	LHFP	1
8593	LHFPL1	1
8594	LHFPL2	1
8595	LHFPL3	1
8596	LHFPL4	1
8597	LHFPL5	1
8598	LHPP	1
8599	LHX1	1
8600	LHX2	1
8601	LHX3	1
8602	LHX4	1
8603	LHX5	1
8604	LHX6	1
8605	LHX8	1
8606	LHX9	1
8607	LIAS	1
8608	LIF	1
8609	LIFR	1
8610	LIG1	4.038351e-01
8611	LIG3	1.259778e-01
8612	LIG4	3.488098e-02
Done

Running MutSig 2:
Scatter job 96: processing genes 8523 - 8612
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LEPRE1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.634954e-03	ci left: 9.495015e-01	ci right 9.578316e-01	k: 9538	n:10000
Cons ci ratio: 1.830504e-02	ci left: 8.133433e-01	ci right 8.284693e-01	k: 8210	n:10000
KS ci ratio: 4.435967e-02	ci left: 4.286440e-01	ci right 4.481919e-01	k: 4384	n:10000
LEPRE1   10000 perm   2 sec   (6532 perm/sec)   p_kst 4.384000e-01   p_cons 8.210000e-01   p_joint 9.538000e-01

Outputting figure to mutsig2_images.part000000000096/LEPRE1.2_2290_10000_0.4384_0.821_0.9538.png
                gene_name: LEPRE1
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 50 percent done.
LIG4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.039732e-03	ci left: 9.737631e-01	ci right 9.797547e-01	k: 9769	n:10000
KS ci ratio: 7.363547e-03	ci left: 9.622595e-01	ci right 9.694658e-01	k: 9660	n:10000
LIG4   10000 perm   2 sec   (6648 perm/sec)   p_kst 9.660000e-01   p_cons 9.769000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000096/LIG4.2_2740_10000_0.966_0.9769_1.png
                gene_name: LIG4
               theta_stop: 0.0074 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000096
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 96 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4398106: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000097> was used as the working directory.
Started at Wed Oct 24 16:13:30 2012
Results reported at Wed Oct 24 16:14:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000097.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000097.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 97  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000097.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     66.43 sec.
    Max Memory :      1013 MB
    Max Swap   :      3839 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
97
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 97
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 97: processing genes 8613 - 8702
Calculating significance of each gene.
Using projection method.
8613	LILRA1	1
8614	LILRA2	1
8615	LILRA3	1
8616	LILRA4	1
8617	LILRA5	1
8618	LILRA6	1
8619	LILRB1	1
8620	LILRB2	4.607106e-02
8621	LILRB3	1
8622	LILRB4	1.501316e-01
8623	LILRB5	1
8624	LIM2	1
8625	LIMA1	1.717268e-01
8626	LIMCH1	1
8627	LIMD1	1
8628	LIMD2	1.126229e-02
8629	LIME1	1
8630	LIMK1	2.774900e-01
8631	LIMK2	1
8632	LIMS1	1
8633	LIMS2	1
8634	LIN28A	7.460367e-02
8635	LIN28B	1
8636	LIN37	1
8637	LIN52	1
8638	LIN54	1
8639	LIN7A	1
8640	LIN7B	1
8641	LIN7C	1
8642	LIN9	5.684656e-02
8643	LINGO1	6.339326e-02
8644	LINGO2	1
8645	LINGO3	1
8646	LINGO4	2.733164e-01
8647	LINS1	2.061353e-01
8648	LIPA	4.389460e-02
8649	LIPC	1
8650	LIPE	1
8651	LIPF	1.266886e-01
8652	LIPG	1
8653	LIPH	7.690883e-02
8654	LIPI	1
8655	LIPJ	1
8656	LIPK	1
8657	LIPN	1
8658	LIPT1	1
8659	LITAF	1
8660	LIX1	1
8661	LIX1L	1
8662	LLGL1	1
8663	LLGL2	2.998099e-01
8664	LLPH	5.150237e-03
8665	LMAN1	1
8666	LMAN1L	1
8667	LMAN2	1
8668	LMAN2L	1
8669	LMBR1	1
8670	LMBR1L	1.260200e-01
8671	LMBRD1	2.194104e-01
8672	LMBRD2	1
8673	LMCD1	1
8674	LMF1	1
8675	LMF2	1.664466e-01
8676	LMLN	1
8677	LMNA	1
8678	LMNB1	1
8679	LMNB2	1
8680	LMO1	1
8681	LMO2	1
8682	LMO3	1
8683	LMO4	1
8684	LMO7	1
8685	LMOD1	1
8686	LMOD2	1
8687	LMOD3	1
8688	LMTK2	1
8689	LMTK3	1.739738e-01
8690	LMX1A	1.378240e-01
8691	LMX1B	1
8692	LNP1	4.001818e-02
8693	LNPEP	1
8694	LNX1	1
8695	LNX2	3.065613e-01
8696	LOC100302652	1
8697	LOC150786	1
8698	LOC153328	1
8699	LOC200726	1
8700	LOC285033	1
8701	LOC286238	1
8702	LOC401052	1
Done

Running MutSig 2:
Scatter job 97: processing genes 8613 - 8702
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LMX1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.404887e-02	ci left: 3.352819e-01	ci right 3.540087e-01	k: 3446	n:10000
Cons ci ratio: 1.027259e-01	ci left: 1.205332e-01	ci right 1.336849e-01	k: 1270	n:10000
KS ci ratio: 7.032931e-03	ci left: 9.653082e-01	ci right 9.722151e-01	k: 9689	n:10000
LMX1A   10000 perm   1 sec   (6863 perm/sec)   p_kst 9.689000e-01   p_cons 1.270000e-01   p_joint 3.446000e-01

Joint ci ratio: 3.813383e-02	ci left: 3.390567e-01	ci right 3.522881e-01	k: 6913	n:20000
Cons ci ratio: 7.308482e-02	ci left: 1.211352e-01	ci right 1.303739e-01	k: 2514	n:20000
KS ci ratio: 4.874060e-03	ci left: 9.675933e-01	ci right 9.723687e-01	k: 19401	n:20000
LMX1A   20000 perm   6 sec   (3511 perm/sec)   p_kst 9.700500e-01   p_cons 1.257000e-01   p_joint 3.456500e-01

Outputting figure to mutsig2_images.part000000000097/LMX1A.2_1181_20000_0.97005_0.1257_0.34565.png
                gene_name: LMX1A
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.35 
     ci_joint_bounds_left: 0.34 
    ci_joint_bounds_right: 0.35 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000097
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 97 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4398109: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000098> was used as the working directory.
Started at Wed Oct 24 16:13:34 2012
Results reported at Wed Oct 24 19:25:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000098.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000098.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 98  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000098.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :  11640.71 sec.
    Max Memory :      1819 MB
    Max Swap   :      4043 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
98
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 98
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 98: processing genes 8703 - 8792
Calculating significance of each gene.
Using projection method.
8703	LOC55908	1
8704	LOC642587	1
8705	LOC646498	1
8706	LOC649330	1.057578e-01
8707	LOC653486	1
8708	LOC728819	1
8709	LOC729991-MEF2B	1
8710	LOC81691	1
8711	LOH12CR1	1
8712	LONP1	1
8713	LONP2	1
8714	LONRF1	1
8715	LONRF2	7.107474e-03
8716	LONRF3	2.010301e-01
8717	LOX	1
8718	LOXL1	1
8719	LOXL2	1
8720	LOXL3	2.665747e-01
8721	LOXL4	1
8722	LPA	1
8723	LPAR1	6.988411e-02
8724	LPAR2	1
8725	LPAR3	1
8726	LPAR4	1
8727	LPAR5	1
8728	LPAR6	1
8729	LPCAT1	1
8730	LPCAT2	1
8731	LPCAT3	1
8732	LPCAT4	1
8733	LPGAT1	1.110101e-01
8734	LPHN1	3.961878e-01
8735	LPHN2	1
8736	LPHN3	1
8737	LPIN1	1
8738	LPIN2	1
8739	LPIN3	1.480379e-02
8740	LPL	1
8741	LPO	3.378156e-01
8742	LPP	1
8743	LPPR1	1
8744	LPPR2	1
8745	LPPR3	1
8746	LPPR4	1
8747	LPPR5	1
8748	LPXN	1
8749	LRAT	1
8750	LRBA	3.073541e-01
8751	LRCH1	1
8752	LRCH2	1
8753	LRCH3	1
8754	LRCH4	1
8755	LRDD	1
8756	LRFN1	4.870490e-03
8757	LRFN2	1
8758	LRFN3	1.748578e-01
8759	LRFN4	1
8760	LRFN5	2.228641e-01
8761	LRG1	1
8762	LRGUK	1
8763	LRIG1	2.419157e-01
8764	LRIG2	3.279875e-01
8765	LRIG3	1
8766	LRIT1	1
8767	LRIT2	9.896218e-02
8768	LRIT3	1.112477e-01
8769	LRMP	1
8770	LRP1	1
8771	LRP10	1
8772	LRP11	2.889063e-03
8773	LRP12	1
8774	LRP1B	7.063643e-01
8775	LRP2	2.544608e-01
8776	LRP2BP	1
8777	LRP3	1
8778	LRP4	1
8779	LRP5	4.279019e-03
8780	LRP5L	1
8781	LRP6	1.191546e-03
8782	LRP8	1
8783	LRPAP1	1
8784	LRPPRC	2.043850e-01
8785	LRRC1	1.416944e-01
8786	LRRC10	1
8787	LRRC14	1
8788	LRRC14B	1
8789	LRRC15	1.098584e-01
8790	LRRC16A	3.850931e-01
8791	LRRC16B	1.621979e-01
8792	LRRC17	1
Done

Running MutSig 2:
Scatter job 98: processing genes 8703 - 8792
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LRP6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.291093e-02	ci left: 5.767739e-01	ci right 5.961757e-01	k: 5865	n:10000
Cons ci ratio: 8.856681e-02	ci left: 1.564968e-01	ci right 1.710996e-01	k: 1637	n:10000
KS ci ratio: 2.869303e-02	ci left: 6.416654e-01	ci right 6.604465e-01	k: 6511	n:10000
LRP6   10000 perm   2 sec   (4343 perm/sec)   p_kst 6.511000e-01   p_cons 1.637000e-01   p_joint 5.865000e-01

Outputting figure to mutsig2_images.part000000000098/LRP6.5_4934_10000_0.6511_0.1637_0.5865.png
                gene_name: LRP6
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 9 percent done.
LRP5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.272375e-02	ci left: 3.465091e-01	ci right 3.653749e-01	k: 3559	n:10000
Cons ci ratio: 5.380435e-03	ci left: 9.787712e-01	ci right 9.841431e-01	k: 9816	n:10000
KS ci ratio: 7.074492e-02	ci left: 2.265204e-01	ci right 2.432343e-01	k: 2348	n:10000
LRP5   10000 perm   3 sec   (3125 perm/sec)   p_kst 2.348000e-01   p_cons 9.816000e-01   p_joint 3.559000e-01

Outputting figure to mutsig2_images.part000000000098/LRP5.4_4940_10000_0.2348_0.9816_0.3559.png
                gene_name: LRP5
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 18 percent done.
LONRF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.437765e-02	ci left: 5.554160e-01	ci right 5.749460e-01	k: 5652	n:10000
Cons ci ratio: 1.664326e-02	ci left: 8.400990e-01	ci right 8.542981e-01	k: 8473	n:10000
KS ci ratio: 1.064023e-01	ci left: 1.131062e-01	ci right 1.259164e-01	k: 1194	n:10000
LONRF2   10000 perm   3 sec   (3796 perm/sec)   p_kst 1.194000e-01   p_cons 8.473000e-01   p_joint 5.652000e-01

Joint ci ratio: 2.547089e-02	ci left: 5.352144e-01	ci right 5.490733e-01	k: 10843	n:20000
Cons ci ratio: 1.181557e-02	ci left: 8.411756e-01	ci right 8.512235e-01	k: 16925	n:20000
KS ci ratio: 7.567130e-02	ci left: 1.138056e-01	ci right 1.228057e-01	k: 2365	n:20000
LONRF2   20000 perm   5 sec   (4062 perm/sec)   p_kst 1.182500e-01   p_cons 8.462500e-01   p_joint 5.421500e-01

Outputting figure to mutsig2_images.part000000000098/LONRF2.2_2313_20000_0.11825_0.84625_0.54215.png
                gene_name: LONRF2
               theta_stop: 0.076 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.54 
    ci_joint_bounds_right: 0.55 

Current progress: 27 percent done.
LPHN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.031728e-02	ci left: 3.680851e-01	ci right 3.871862e-01	k: 3776	n:10000
KS ci ratio: 2.385736e-02	ci left: 7.208794e-01	ci right 7.383866e-01	k: 7297	n:10000
LPHN1   10000 perm   2 sec   (4109 perm/sec)   p_kst 7.297000e-01   p_cons 3.776000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000098/LPHN1.2_4517_10000_0.7297_0.3776_1.png
                gene_name: LPHN1
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 36 percent done.
LPIN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.057512e-02	ci left: 3.656978e-01	ci right 3.847749e-01	k: 3752	n:10000
Cons ci ratio: 1.261114e-01	ci left: 8.251809e-02	ci right 9.372320e-02	k: 880	n:10000
KS ci ratio: 4.739627e-02	ci left: 3.964531e-01	ci right 4.158017e-01	k: 4061	n:10000
LPIN3   10000 perm   3 sec   (3470 perm/sec)   p_kst 4.061000e-01   p_cons 8.800000e-02   p_joint 3.752000e-01

Joint ci ratio: 8.715687e-02	ci left: 8.783284e-02	ci right 9.588628e-02	k: 1836	n:20000
Cons ci ratio: 9.292732e-02	ci left: 7.789098e-02	ci right 8.553115e-02	k: 1633	n:20000
KS ci ratio: 3.363579e-02	ci left: 3.975876e-01	ci right 4.112402e-01	k: 8088	n:20000
LPIN3   20000 perm   6 sec   (3195 perm/sec)   p_kst 4.044000e-01   p_cons 8.165000e-02   p_joint 9.180000e-02

Outputting figure to mutsig2_images.part000000000098/LPIN3.2_2632_20000_0.4044_0.08165_0.0918.png
                gene_name: LPIN3
               theta_stop: 0.093 
                    nperm: 20000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.082 
      ci_cons_bounds_left: 0.078 
     ci_cons_bounds_right: 0.086 
                  p_joint: 0.092 
     ci_joint_bounds_left: 0.088 
    ci_joint_bounds_right: 0.096 

Current progress: 45 percent done.
LRBA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.491369e-02	ci left: 8.669281e-01	ci right 8.800535e-01	k: 8736	n:10000
KS ci ratio: 9.854893e-02	ci left: 1.298276e-01	ci right 1.433848e-01	k: 1365	n:10000
LRBA   10000 perm   2 sec   (4153 perm/sec)   p_kst 1.365000e-01   p_cons 8.736000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000098/LRBA.2_8820_10000_0.1365_0.8736_1.png
                gene_name: LRBA
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.88 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 55 percent done.
LRFN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.758343e-02	ci left: 3.945608e-01	ci right 4.138950e-01	k: 4042	n:10000
KS ci ratio: 2.708704e-02	ci left: 6.675328e-01	ci right 6.859641e-01	k: 6768	n:10000
LRFN1   10000 perm   2 sec   (5837 perm/sec)   p_kst 6.768000e-01   p_cons 4.042000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000098/LRFN1.2_2324_10000_0.6768_0.4042_1.png
                gene_name: LRFN1
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 64 percent done.
LRP1
Processing conservation and coverage...
71% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.160103e-01	ci left: 6.974044e-03	ci right 1.072050e-02	k: 87	n:10000
Cons ci ratio: 5.964782e-01	ci left: 3.028617e-03	ci right 5.672985e-03	k: 42	n:10000
KS ci ratio: 3.769094e-01	ci left: 8.686342e-03	ci right 1.280614e-02	k: 106	n:10000
LRP1   10000 perm   3 sec   (3317 perm/sec)   p_kst 1.060000e-02   p_cons 4.200000e-03   p_joint 8.700000e-03

Joint ci ratio: 2.478726e-01	ci left: 1.081866e-02	ci right 1.392552e-02	k: 246	n:20000
Cons ci ratio: 4.193426e-01	ci left: 3.440841e-03	ci right 5.307780e-03	k: 86	n:20000
KS ci ratio: 2.703794e-01	ci left: 8.993904e-03	ci right 1.185112e-02	k: 207	n:20000
LRP1   20000 perm   7 sec   (3061 perm/sec)   p_kst 1.035000e-02   p_cons 4.300000e-03   p_joint 1.230000e-02

Joint ci ratio: 3.457367e-01	ci left: 3.530325e-03	ci right 5.034838e-03	k: 127	n:30000
Cons ci ratio: 3.571231e-01	ci left: 3.287119e-03	ci right 4.744855e-03	k: 119	n:30000
KS ci ratio: 2.251832e-01	ci left: 8.873598e-03	ci right 1.115613e-02	k: 299	n:30000
LRP1   30000 perm   10 sec   (2955 perm/sec)   p_kst 9.966667e-03   p_cons 3.966667e-03   p_joint 4.233333e-03

Joint ci ratio: 2.991247e-01	ci left: 3.636202e-03	ci right 4.937384e-03	k: 170	n:40000
Cons ci ratio: 3.092789e-01	ci left: 3.382116e-03	ci right 4.641571e-03	k: 159	n:40000
KS ci ratio: 1.977807e-01	ci left: 8.762746e-03	ci right 1.070942e-02	k: 388	n:40000
LRP1   40000 perm   14 sec   (2890 perm/sec)   p_kst 9.700000e-03   p_cons 3.975000e-03   p_joint 4.250000e-03

Joint ci ratio: 2.661428e-01	ci left: 3.745401e-03	ci right 4.913300e-03	k: 215	n:50000
Cons ci ratio: 2.738917e-01	ci left: 3.521589e-03	ci right 4.657178e-03	k: 203	n:50000
KS ci ratio: 1.776867e-01	ci left: 8.783002e-03	ci right 1.051464e-02	k: 481	n:50000
LRP1   50000 perm   18 sec   (2840 perm/sec)   p_kst 9.620000e-03   p_cons 4.060000e-03   p_joint 4.300000e-03

Joint ci ratio: 2.430487e-01	ci left: 3.792199e-03	ci right 4.856624e-03	k: 258	n:60000
Cons ci ratio: 2.509563e-01	ci left: 3.541977e-03	ci right 4.573571e-03	k: 242	n:60000
KS ci ratio: 1.605871e-01	ci left: 9.043231e-03	ci right 1.063805e-02	k: 589	n:60000
LRP1   60000 perm   21 sec   (2795 perm/sec)   p_kst 9.816667e-03   p_cons 4.033333e-03   p_joint 4.300000e-03

Joint ci ratio: 2.239674e-01	ci left: 3.869229e-03	ci right 4.858263e-03	k: 304	n:70000
Cons ci ratio: 2.329603e-01	ci left: 3.559389e-03	ci right 4.511020e-03	k: 281	n:70000
KS ci ratio: 1.469947e-01	ci left: 9.317433e-03	ci right 1.080931e-02	k: 703	n:70000
LRP1   70000 perm   25 sec   (2754 perm/sec)   p_kst 1.004286e-02   p_cons 4.014286e-03   p_joint 4.342857e-03

Joint ci ratio: 2.090727e-01	ci left: 3.917612e-03	ci right 4.843897e-03	k: 349	n:80000
Cons ci ratio: 2.169990e-01	ci left: 3.621719e-03	ci right 4.514837e-03	k: 324	n:80000
KS ci ratio: 1.366096e-01	ci left: 9.491134e-03	ci right 1.089473e-02	k: 814	n:80000
LRP1   80000 perm   29 sec   (2718 perm/sec)   p_kst 1.017500e-02   p_cons 4.050000e-03   p_joint 4.362500e-03

Joint ci ratio: 1.948304e-01	ci left: 4.041488e-03	ci right 4.924252e-03	k: 402	n:90000
Cons ci ratio: 2.022757e-01	ci left: 3.735220e-03	ci right 4.586117e-03	k: 373	n:90000
KS ci ratio: 1.305247e-01	ci left: 9.274209e-03	ci right 1.057989e-02	k: 892	n:90000
LRP1   90000 perm   34 sec   (2685 perm/sec)   p_kst 9.911111e-03   p_cons 4.144444e-03   p_joint 4.466667e-03

Joint ci ratio: 1.839632e-01	ci left: 4.104133e-03	ci right 4.945004e-03	k: 451	n:100000
Cons ci ratio: 1.915616e-01	ci left: 3.770516e-03	ci right 4.578660e-03	k: 416	n:100000
KS ci ratio: 1.235266e-01	ci left: 9.353780e-03	ci right 1.059489e-02	k: 996	n:100000
LRP1   100000 perm   38 sec   (2654 perm/sec)   p_kst 9.960000e-03   p_cons 4.160000e-03   p_joint 4.510000e-03

Joint ci ratio: 1.757932e-01	ci left: 4.104344e-03	ci right 4.903945e-03	k: 494	n:110000
Cons ci ratio: 1.840013e-01	ci left: 3.730963e-03	ci right 4.495547e-03	k: 451	n:110000
KS ci ratio: 1.174916e-01	ci left: 9.429238e-03	ci right 1.061499e-02	k: 1101	n:110000
LRP1   110000 perm   42 sec   (2603 perm/sec)   p_kst 1.000909e-02   p_cons 4.100000e-03   p_joint 4.490909e-03

Joint ci ratio: 1.675319e-01	ci left: 4.161098e-03	ci right 4.929815e-03	k: 544	n:120000
Cons ci ratio: 1.751173e-01	ci left: 3.794131e-03	ci right 4.530149e-03	k: 498	n:120000
KS ci ratio: 1.120285e-01	ci left: 9.533859e-03	ci right 1.067334e-02	k: 1211	n:120000
LRP1   120000 perm   47 sec   (2571 perm/sec)   p_kst 1.009167e-02   p_cons 4.150000e-03   p_joint 4.533333e-03

Joint ci ratio: 1.621245e-01	ci left: 4.113881e-03	ci right 4.846954e-03	k: 581	n:130000
Cons ci ratio: 1.691266e-01	ci left: 3.767265e-03	ci right 4.470522e-03	k: 534	n:130000
KS ci ratio: 1.079663e-01	ci left: 9.496179e-03	ci right 1.058738e-02	k: 1304	n:130000
LRP1   130000 perm   51 sec   (2544 perm/sec)   p_kst 1.003077e-02   p_cons 4.107692e-03   p_joint 4.469231e-03

Joint ci ratio: 1.560732e-01	ci left: 4.135529e-03	ci right 4.842378e-03	k: 627	n:140000
Cons ci ratio: 1.625718e-01	ci left: 3.799424e-03	ci right 4.478509e-03	k: 578	n:140000
KS ci ratio: 1.037183e-01	ci left: 9.575865e-03	ci right 1.063029e-02	k: 1413	n:140000
LRP1   140000 perm   56 sec   (2516 perm/sec)   p_kst 1.009286e-02   p_cons 4.128571e-03   p_joint 4.478571e-03

Joint ci ratio: 1.509906e-01	ci left: 4.135482e-03	ci right 4.817224e-03	k: 670	n:150000
Cons ci ratio: 1.574878e-01	ci left: 3.789317e-03	ci right 4.443413e-03	k: 616	n:150000
KS ci ratio: 9.993524e-02	ci left: 9.645654e-03	ci right 1.066675e-02	k: 1522	n:150000
LRP1   150000 perm   60 sec   (2491 perm/sec)   p_kst 1.014667e-02   p_cons 4.106667e-03   p_joint 4.466667e-03

Joint ci ratio: 1.316285e-01	ci left: 5.149518e-03	ci right 5.881076e-03	k: 881	n:160000
Cons ci ratio: 1.511249e-01	ci left: 3.870960e-03	ci right 4.509712e-03	k: 669	n:160000
KS ci ratio: 9.735493e-02	ci left: 9.542631e-03	ci right 1.052525e-02	k: 1604	n:160000
LRP1   160000 perm   65 sec   (2466 perm/sec)   p_kst 1.002500e-02   p_cons 4.181250e-03   p_joint 5.506250e-03

Joint ci ratio: 1.288176e-01	ci left: 5.068529e-03	ci right 5.772029e-03	k: 920	n:170000
Cons ci ratio: 1.478563e-01	ci left: 3.813118e-03	ci right 4.427512e-03	k: 699	n:170000
KS ci ratio: 9.490777e-02	ci left: 9.463520e-03	ci right 1.041213e-02	k: 1688	n:170000
LRP1   170000 perm   70 sec   (2443 perm/sec)   p_kst 9.929412e-03   p_cons 4.111765e-03   p_joint 5.411765e-03

Joint ci ratio: 1.173484e-01	ci left: 5.799419e-03	ci right 6.527735e-03	k: 1108	n:180000
Cons ci ratio: 1.435133e-01	ci left: 3.831462e-03	ci right 4.429126e-03	k: 742	n:180000
KS ci ratio: 9.274197e-02	ci left: 9.371763e-03	ci right 1.028857e-02	k: 1768	n:180000
LRP1   180000 perm   74 sec   (2420 perm/sec)   p_kst 9.822222e-03   p_cons 4.122222e-03   p_joint 6.155556e-03

Joint ci ratio: 1.141015e-01	ci left: 5.821282e-03	ci right 6.530753e-03	k: 1172	n:190000
Cons ci ratio: 1.390884e-01	ci left: 3.873514e-03	ci right 4.457564e-03	k: 790	n:190000
KS ci ratio: 9.061896e-02	ci left: 9.310467e-03	ci right 1.019932e-02	k: 1852	n:190000
LRP1   190000 perm   79 sec   (2396 perm/sec)   p_kst 9.747368e-03   p_cons 4.157895e-03   p_joint 6.168421e-03

Joint ci ratio: 1.105716e-01	ci left: 5.899555e-03	ci right 6.594873e-03	k: 1248	n:200000
Cons ci ratio: 1.346466e-01	ci left: 3.935774e-03	ci right 4.508743e-03	k: 843	n:200000
KS ci ratio: 8.835937e-02	ci left: 9.314202e-03	ci right 1.018010e-02	k: 1948	n:200000
LRP1   200000 perm   84 sec   (2375 perm/sec)   p_kst 9.740000e-03   p_cons 4.215000e-03   p_joint 6.240000e-03

Joint ci ratio: 7.793176e-02	ci left: 1.144059e-02	ci right 1.237296e-02	k: 2499	n:210000
Cons ci ratio: 1.317905e-01	ci left: 3.918672e-03	ci right 4.476103e-03	k: 880	n:210000
KS ci ratio: 8.550400e-02	ci left: 9.485612e-03	ci right 1.033752e-02	k: 2080	n:210000
LRP1   210000 perm   89 sec   (2353 perm/sec)   p_kst 9.904762e-03   p_cons 4.190476e-03   p_joint 1.190000e-02

Joint ci ratio: 1.056156e-01	ci left: 5.893944e-03	ci right 6.555530e-03	k: 1368	n:220000
Cons ci ratio: 1.292502e-01	ci left: 3.894444e-03	ci right 4.436930e-03	k: 915	n:220000
KS ci ratio: 8.328952e-02	ci left: 9.552808e-03	ci right 1.038745e-02	k: 2192	n:220000
LRP1   220000 perm   94 sec   (2332 perm/sec)   p_kst 9.963636e-03   p_cons 4.159091e-03   p_joint 6.218182e-03

Joint ci ratio: 5.942239e-02	ci left: 1.801746e-02	ci right 1.912515e-02	k: 4270	n:230000
Cons ci ratio: 1.260552e-01	ci left: 3.922946e-03	ci right 4.454885e-03	k: 962	n:230000
KS ci ratio: 8.134563e-02	ci left: 9.588857e-03	ci right 1.040617e-02	k: 2298	n:230000
LRP1   230000 perm   100 sec   (2311 perm/sec)   p_kst 9.991304e-03   p_cons 4.182609e-03   p_joint 1.856522e-02

Joint ci ratio: 1.087181e+00	ci left: 2.583599e-05	ci right 8.733831e-05	k: 12	n:240000
Cons ci ratio: 6.823361e-01	ci left: 9.120163e-05	ci right 1.882217e-04	k: 32	n:240000
KS ci ratio: 7.951508e-02	ci left: 9.626195e-03	ci right 1.042737e-02	k: 2405	n:240000
LRP1   240000 perm   105 sec   (2291 perm/sec)   p_kst 1.002083e-02   p_cons 1.333333e-04   p_joint 5.000000e-05

Joint ci ratio: 1.087182e+00	ci left: 2.480254e-05	ci right 8.384484e-05	k: 12	n:250000
Cons ci ratio: 6.722274e-01	ci left: 9.086441e-05	ci right 1.853721e-04	k: 33	n:250000
KS ci ratio: 7.778716e-02	ci left: 9.664658e-03	ci right 1.045076e-02	k: 2513	n:250000
LRP1   250000 perm   110 sec   (2270 perm/sec)   p_kst 1.005200e-02   p_cons 1.320000e-04   p_joint 4.800000e-05

Joint ci ratio: 1.047634e+00	ci left: 2.662315e-05	ci right 8.550001e-05	k: 13	n:260000
Cons ci ratio: 6.625551e-01	ci left: 9.056314e-05	ci right 1.827321e-04	k: 34	n:260000
KS ci ratio: 7.637343e-02	ci left: 9.647506e-03	ci right 1.041732e-02	k: 2607	n:260000
LRP1   260000 perm   116 sec   (2243 perm/sec)   p_kst 1.002692e-02   p_cons 1.307692e-04   p_joint 5.000000e-05

Joint ci ratio: 1.047635e+00	ci left: 2.563710e-05	ci right 8.233339e-05	k: 13	n:270000
Cons ci ratio: 6.625568e-01	ci left: 8.720889e-05	ci right 1.759645e-04	k: 34	n:270000
KS ci ratio: 7.509025e-02	ci left: 9.617206e-03	ci right 1.037115e-02	k: 2697	n:270000
LRP1   270000 perm   121 sec   (2223 perm/sec)   p_kst 9.988889e-03   p_cons 1.259259e-04   p_joint 4.814815e-05

Joint ci ratio: 1.047636e+00	ci left: 2.472148e-05	ci right 7.939296e-05	k: 13	n:280000
Cons ci ratio: 6.532902e-01	ci left: 8.706858e-05	ci right 1.738405e-04	k: 35	n:280000
KS ci ratio: 7.380281e-02	ci left: 9.606701e-03	ci right 1.034635e-02	k: 2792	n:280000
LRP1   280000 perm   127 sec   (2204 perm/sec)   p_kst 9.971429e-03   p_cons 1.250000e-04   p_joint 4.642857e-05

Joint ci ratio: 1.047637e+00	ci left: 2.386901e-05	ci right 7.665532e-05	k: 13	n:290000
Cons ci ratio: 6.358652e-01	ci left: 8.983400e-05	ci right 1.758565e-04	k: 37	n:290000
KS ci ratio: 7.247808e-02	ci left: 9.624115e-03	ci right 1.035124e-02	k: 2895	n:290000
LRP1   290000 perm   133 sec   (2185 perm/sec)   p_kst 9.982759e-03   p_cons 1.275862e-04   p_joint 4.482759e-05

Joint ci ratio: 1.047638e+00	ci left: 2.307337e-05	ci right 7.410018e-05	k: 13	n:300000
Cons ci ratio: 6.197641e-01	ci left: 9.244429e-05	ci right 1.777100e-04	k: 39	n:300000
KS ci ratio: 7.113840e-02	ci left: 9.663401e-03	ci right 1.037945e-02	k: 3005	n:300000
LRP1   300000 perm   139 sec   (2166 perm/sec)   p_kst 1.001667e-02   p_cons 1.300000e-04   p_joint 4.333333e-05

Joint ci ratio: 1.012114e+00	ci left: 2.469031e-05	ci right 7.577181e-05	k: 14	n:310000
Cons ci ratio: 6.121597e-01	ci left: 9.218409e-05	ci right 1.757012e-04	k: 40	n:310000
KS ci ratio: 6.993840e-02	ci left: 9.681247e-03	ci right 1.038602e-02	k: 3109	n:310000
LRP1   310000 perm   144 sec   (2146 perm/sec)   p_kst 1.002903e-02   p_cons 1.290323e-04   p_joint 4.516129e-05

Joint ci ratio: 1.012114e+00	ci left: 2.391873e-05	ci right 7.340398e-05	k: 14	n:320000
Cons ci ratio: 6.121610e-01	ci left: 8.930329e-05	ci right 1.702107e-04	k: 40	n:320000
KS ci ratio: 6.885127e-02	ci left: 9.682715e-03	ci right 1.037620e-02	k: 3208	n:320000
LRP1   320000 perm   150 sec   (2128 perm/sec)   p_kst 1.002500e-02   p_cons 1.250000e-04   p_joint 4.375000e-05

Joint ci ratio: 1.012115e+00	ci left: 2.319392e-05	ci right 7.117965e-05	k: 14	n:330000
Cons ci ratio: 6.121622e-01	ci left: 8.659708e-05	ci right 1.650529e-04	k: 40	n:330000
KS ci ratio: 6.772032e-02	ci left: 9.710988e-03	ci right 1.039463e-02	k: 3316	n:330000
LRP1   330000 perm   156 sec   (2109 perm/sec)   p_kst 1.004848e-02   p_cons 1.212121e-04   p_joint 4.242424e-05

Joint ci ratio: 1.012116e+00	ci left: 2.251174e-05	ci right 6.908616e-05	k: 14	n:340000
Cons ci ratio: 6.121633e-01	ci left: 8.405007e-05	ci right 1.601985e-04	k: 40	n:340000
KS ci ratio: 6.657463e-02	ci left: 9.757934e-03	ci right 1.043281e-02	k: 3431	n:340000
LRP1   340000 perm   162 sec   (2093 perm/sec)   p_kst 1.009118e-02   p_cons 1.176471e-04   p_joint 4.117647e-05

Joint ci ratio: 9.799762e-01	ci left: 2.398701e-05	ci right 7.068536e-05	k: 15	n:350000
Cons ci ratio: 5.977568e-01	ci left: 8.648677e-05	ci right 1.622017e-04	k: 42	n:350000
KS ci ratio: 6.557863e-02	ci left: 9.774182e-03	ci right 1.043968e-02	k: 3536	n:350000
LRP1   350000 perm   169 sec   (2076 perm/sec)   p_kst 1.010286e-02   p_cons 1.200000e-04   p_joint 4.285714e-05

Joint ci ratio: 9.799769e-01	ci left: 2.332070e-05	ci right 6.872190e-05	k: 15	n:360000
Cons ci ratio: 5.909253e-01	ci left: 8.644384e-05	ci right 1.608875e-04	k: 43	n:360000
KS ci ratio: 6.467090e-02	ci left: 9.775931e-03	ci right 1.043199e-02	k: 3636	n:360000
LRP1   360000 perm   175 sec   (2059 perm/sec)   p_kst 1.010000e-02   p_cons 1.194444e-04   p_joint 4.166667e-05

Joint ci ratio: 9.799775e-01	ci left: 2.269040e-05	ci right 6.686458e-05	k: 15	n:370000
Cons ci ratio: 5.843228e-01	ci left: 8.640796e-05	ci right 1.596398e-04	k: 44	n:370000
KS ci ratio: 6.395562e-02	ci left: 9.729767e-03	ci right 1.037524e-02	k: 3718	n:370000
LRP1   370000 perm   181 sec   (2042 perm/sec)   p_kst 1.004865e-02   p_cons 1.189189e-04   p_joint 4.054054e-05

Joint ci ratio: 9.799781e-01	ci left: 2.209328e-05	ci right 6.510500e-05	k: 15	n:380000
Cons ci ratio: 5.779367e-01	ci left: 8.637840e-05	ci right 1.584535e-04	k: 45	n:380000
KS ci ratio: 6.312113e-02	ci left: 9.730107e-03	ci right 1.036687e-02	k: 3817	n:380000
LRP1   380000 perm   188 sec   (2026 perm/sec)   p_kst 1.004474e-02   p_cons 1.184211e-04   p_joint 3.947368e-05

Joint ci ratio: 9.799786e-01	ci left: 2.152679e-05	ci right 6.343567e-05	k: 15	n:390000
Cons ci ratio: 5.779376e-01	ci left: 8.416354e-05	ci right 1.543907e-04	k: 45	n:390000
KS ci ratio: 6.233455e-02	ci left: 9.725433e-03	ci right 1.035367e-02	k: 3914	n:390000
LRP1   390000 perm   194 sec   (2009 perm/sec)   p_kst 1.003590e-02   p_cons 1.153846e-04   p_joint 3.846154e-05

Joint ci ratio: 9.799792e-01	ci left: 2.098861e-05	ci right 6.184979e-05	k: 15	n:400000
Cons ci ratio: 5.717565e-01	ci left: 8.419565e-05	ci right 1.533909e-04	k: 46	n:400000
KS ci ratio: 6.166210e-02	ci left: 9.693959e-03	ci right 1.031317e-02	k: 4000	n:400000
LRP1   400000 perm   201 sec   (1992 perm/sec)   p_kst 1.000000e-02   p_cons 1.150000e-04   p_joint 3.750000e-05

Joint ci ratio: 9.799797e-01	ci left: 2.047669e-05	ci right 6.034128e-05	k: 15	n:410000
Cons ci ratio: 5.599659e-01	ci left: 8.632174e-05	ci right 1.552191e-04	k: 48	n:410000
KS ci ratio: 6.092818e-02	ci left: 9.690480e-03	ci right 1.030184e-02	k: 4097	n:410000
LRP1   410000 perm   207 sec   (1976 perm/sec)   p_kst 9.992683e-03   p_cons 1.170732e-04   p_joint 3.658537e-05

Joint ci ratio: 9.799802e-01	ci left: 1.998915e-05	ci right 5.890460e-05	k: 15	n:420000
Cons ci ratio: 5.435719e-01	ci left: 9.041284e-05	ci right 1.596531e-04	k: 51	n:420000
KS ci ratio: 6.020537e-02	ci left: 9.691899e-03	ci right 1.029584e-02	k: 4196	n:420000
LRP1   420000 perm   214 sec   (1961 perm/sec)   p_kst 9.990476e-03   p_cons 1.214286e-04   p_joint 3.571429e-05

Joint ci ratio: 9.507198e-01	ci left: 2.126848e-05	ci right 6.042487e-05	k: 16	n:430000
Cons ci ratio: 5.285383e-01	ci left: 9.434197e-05	ci right 1.638533e-04	k: 54	n:430000
KS ci ratio: 5.946576e-02	ci left: 9.707040e-03	ci right 1.030424e-02	k: 4301	n:430000
LRP1   430000 perm   221 sec   (1947 perm/sec)   p_kst 1.000233e-02   p_cons 1.255814e-04   p_joint 3.720930e-05

Joint ci ratio: 9.239329e-01	ci left: 2.250726e-05	ci right 6.185984e-05	k: 17	n:440000
Cons ci ratio: 5.237981e-01	ci left: 9.416845e-05	ci right 1.627016e-04	k: 55	n:440000
KS ci ratio: 5.878644e-02	ci left: 9.710339e-03	ci right 1.030069e-02	k: 4401	n:440000
LRP1   440000 perm   228 sec   (1933 perm/sec)   p_kst 1.000227e-02   p_cons 1.250000e-04   p_joint 3.863636e-05

Joint ci ratio: 1.087195e+00	ci left: 1.377913e-05	ci right 4.658084e-05	k: 12	n:450000
Cons ci ratio: 5.237989e-01	ci left: 9.207579e-05	ci right 1.590861e-04	k: 55	n:450000
KS ci ratio: 5.819521e-02	ci left: 9.691625e-03	ci right 1.027471e-02	k: 4491	n:450000
LRP1   450000 perm   234 sec   (1920 perm/sec)   p_kst 9.980000e-03   p_cons 1.222222e-04   p_joint 2.666667e-05

Joint ci ratio: 1.087196e+00	ci left: 1.347958e-05	ci right 4.556822e-05	k: 12	n:460000
Cons ci ratio: 5.018707e-01	ci left: 9.953691e-05	ci right 1.678923e-04	k: 60	n:460000
KS ci ratio: 5.750116e-02	ci left: 9.714470e-03	ci right 1.029173e-02	k: 4600	n:460000
LRP1   460000 perm   241 sec   (1908 perm/sec)   p_kst 1.000000e-02   p_cons 1.304348e-04   p_joint 2.608696e-05

Joint ci ratio: 1.047647e+00	ci left: 1.472764e-05	ci right 4.729825e-05	k: 13	n:470000
Cons ci ratio: 4.938400e-01	ci left: 1.011398e-04	ci right 1.691058e-04	k: 62	n:470000
KS ci ratio: 5.692300e-02	ci left: 9.704917e-03	ci right 1.027562e-02	k: 4694	n:470000
LRP1   470000 perm   248 sec   (1895 perm/sec)   p_kst 9.987234e-03   p_cons 1.319149e-04   p_joint 2.765957e-05

Joint ci ratio: 1.047648e+00	ci left: 1.442081e-05	ci right 4.631288e-05	k: 13	n:480000
Cons ci ratio: 4.938407e-01	ci left: 9.903273e-05	ci right 1.655828e-04	k: 62	n:480000
KS ci ratio: 5.635598e-02	ci left: 9.697843e-03	ci right 1.026226e-02	k: 4789	n:480000
LRP1   480000 perm   255 sec   (1882 perm/sec)   p_kst 9.977083e-03   p_cons 1.291667e-04   p_joint 2.708333e-05

Joint ci ratio: 1.047648e+00	ci left: 1.412651e-05	ci right 4.536773e-05	k: 13	n:490000
Cons ci ratio: 4.824857e-01	ci left: 1.023803e-04	ci right 1.690741e-04	k: 65	n:490000
KS ci ratio: 5.577676e-02	ci left: 9.701149e-03	ci right 1.025977e-02	k: 4889	n:490000
LRP1   490000 perm   262 sec   (1869 perm/sec)   p_kst 9.977551e-03   p_cons 1.326531e-04   p_joint 2.653061e-05

Joint ci ratio: 1.047648e+00	ci left: 1.384398e-05	ci right 4.446038e-05	k: 13	n:500000
Cons ci ratio: 4.753370e-01	ci left: 1.038496e-04	ci right 1.701722e-04	k: 67	n:500000
KS ci ratio: 5.514810e-02	ci left: 9.728023e-03	ci right 1.028168e-02	k: 5001	n:500000
LRP1   500000 perm   269 sec   (1856 perm/sec)   p_kst 1.000200e-02   p_cons 1.340000e-04   p_joint 2.600000e-05

Joint ci ratio: 1.047649e+00	ci left: 1.357252e-05	ci right 4.358862e-05	k: 13	n:510000
Cons ci ratio: 4.718802e-01	ci left: 1.035400e-04	ci right 1.690288e-04	k: 68	n:510000
KS ci ratio: 5.458876e-02	ci left: 9.736469e-03	ci right 1.028481e-02	k: 5104	n:510000
LRP1   510000 perm   277 sec   (1843 perm/sec)   p_kst 1.000784e-02   p_cons 1.333333e-04   p_joint 2.549020e-05

Joint ci ratio: 1.047649e+00	ci left: 1.331151e-05	ci right 4.275038e-05	k: 13	n:520000
Cons ci ratio: 4.619440e-01	ci left: 1.066392e-04	ci right 1.722216e-04	k: 71	n:520000
KS ci ratio: 5.402515e-02	ci left: 9.752206e-03	ci right 1.029558e-02	k: 5211	n:520000
LRP1   520000 perm   284 sec   (1829 perm/sec)   p_kst 1.002115e-02   p_cons 1.365385e-04   p_joint 2.500000e-05

Joint ci ratio: 1.012124e+00	ci left: 1.444145e-05	ci right 4.431964e-05	k: 14	n:530000
Cons ci ratio: 4.526102e-01	ci left: 1.096353e-04	ci right 1.752803e-04	k: 74	n:530000
KS ci ratio: 5.356518e-02	ci left: 9.735727e-03	ci right 1.027342e-02	k: 5301	n:530000
LRP1   530000 perm   292 sec   (1817 perm/sec)   p_kst 1.000189e-02   p_cons 1.396226e-04   p_joint 2.641509e-05

Joint ci ratio: 1.012125e+00	ci left: 1.417402e-05	ci right 4.349892e-05	k: 14	n:540000
Cons ci ratio: 4.466932e-01	ci left: 1.108892e-04	ci right 1.761549e-04	k: 76	n:540000
KS ci ratio: 5.300269e-02	ci left: 9.761910e-03	ci right 1.029522e-02	k: 5414	n:540000
LRP1   540000 perm   299 sec   (1806 perm/sec)   p_kst 1.002593e-02   p_cons 1.407407e-04   p_joint 2.592593e-05

Joint ci ratio: 9.799849e-01	ci left: 1.526442e-05	ci right 4.498182e-05	k: 15	n:550000
Cons ci ratio: 4.355231e-01	ci left: 1.153380e-04	ci right 1.810276e-04	k: 80	n:550000
KS ci ratio: 5.246715e-02	ci left: 9.783581e-03	ci right 1.031251e-02	k: 5525	n:550000
LRP1   550000 perm   307 sec   (1793 perm/sec)   p_kst 1.004545e-02   p_cons 1.454545e-04   p_joint 2.727273e-05

Joint ci ratio: 1.012125e+00	ci left: 1.366780e-05	ci right 4.194540e-05	k: 14	n:560000
Cons ci ratio: 4.328595e-01	ci left: 1.148689e-04	ci right 1.797747e-04	k: 81	n:560000
KS ci ratio: 5.197546e-02	ci left: 9.793927e-03	ci right 1.031830e-02	k: 5630	n:560000
LRP1   560000 perm   315 sec   (1780 perm/sec)   p_kst 1.005357e-02   p_cons 1.446429e-04   p_joint 2.500000e-05

Joint ci ratio: 1.012125e+00	ci left: 1.342801e-05	ci right 4.120952e-05	k: 14	n:570000
Cons ci ratio: 4.328601e-01	ci left: 1.128536e-04	ci right 1.766208e-04	k: 81	n:570000
KS ci ratio: 5.153821e-02	ci left: 9.788345e-03	ci right 1.030788e-02	k: 5726	n:570000
LRP1   570000 perm   322 sec   (1768 perm/sec)   p_kst 1.004561e-02   p_cons 1.421053e-04   p_joint 2.456140e-05

Joint ci ratio: 1.012126e+00	ci left: 1.319649e-05	ci right 4.049902e-05	k: 14	n:580000
Cons ci ratio: 4.276757e-01	ci left: 1.139827e-04	ci right 1.773952e-04	k: 83	n:580000
KS ci ratio: 5.105869e-02	ci left: 9.803400e-03	ci right 1.031875e-02	k: 5834	n:580000
LRP1   580000 perm   330 sec   (1756 perm/sec)   p_kst 1.005862e-02   p_cons 1.431034e-04   p_joint 2.413793e-05

Joint ci ratio: 1.047651e+00	ci left: 1.173217e-05	ci right 3.767834e-05	k: 13	n:590000
Cons ci ratio: 4.251527e-01	ci left: 1.135637e-04	ci right 1.762643e-04	k: 84	n:590000
KS ci ratio: 5.059230e-02	ci left: 9.817967e-03	ci right 1.032923e-02	k: 5942	n:590000
LRP1   590000 perm   338 sec   (1744 perm/sec)   p_kst 1.007119e-02   p_cons 1.423729e-04   p_joint 2.203390e-05

Joint ci ratio: 1.047651e+00	ci left: 1.153664e-05	ci right 3.705037e-05	k: 13	n:600000
Cons ci ratio: 4.202373e-01	ci left: 1.146497e-04	ci right 1.770125e-04	k: 86	n:600000
KS ci ratio: 5.021818e-02	ci left: 9.800796e-03	ci right 1.030728e-02	k: 6031	n:600000
LRP1   600000 perm   346 sec   (1732 perm/sec)   p_kst 1.005167e-02   p_cons 1.433333e-04   p_joint 2.166667e-05

Joint ci ratio: 1.047651e+00	ci left: 1.134751e-05	ci right 3.644300e-05	k: 13	n:610000
Cons ci ratio: 4.178429e-01	ci left: 1.142367e-04	ci right 1.759220e-04	k: 87	n:610000
KS ci ratio: 4.988105e-02	ci left: 9.772868e-03	ci right 1.027443e-02	k: 6113	n:610000
LRP1   610000 perm   354 sec   (1722 perm/sec)   p_kst 1.002131e-02   p_cons 1.426230e-04   p_joint 2.131148e-05

Joint ci ratio: 1.047651e+00	ci left: 1.116449e-05	ci right 3.585521e-05	k: 13	n:620000
Cons ci ratio: 4.154890e-01	ci left: 1.138379e-04	ci right 1.748656e-04	k: 88	n:620000
KS ci ratio: 4.955061e-02	ci left: 9.745851e-03	ci right 1.024261e-02	k: 6195	n:620000
LRP1   620000 perm   363 sec   (1710 perm/sec)   p_kst 9.991935e-03   p_cons 1.419355e-04   p_joint 2.096774e-05

Joint ci ratio: 1.047652e+00	ci left: 1.098727e-05	ci right 3.528608e-05	k: 13	n:630000
Cons ci ratio: 4.131744e-01	ci left: 1.134528e-04	ci right 1.738419e-04	k: 89	n:630000
KS ci ratio: 4.906508e-02	ci left: 9.783991e-03	ci right 1.027767e-02	k: 6318	n:630000
LRP1   630000 perm   371 sec   (1699 perm/sec)   p_kst 1.002857e-02   p_cons 1.412698e-04   p_joint 2.063492e-05

Joint ci ratio: 1.047652e+00	ci left: 1.081559e-05	ci right 3.473474e-05	k: 13	n:640000
Cons ci ratio: 4.086586e-01	ci left: 1.144820e-04	ci right 1.745719e-04	k: 91	n:640000
KS ci ratio: 4.865462e-02	ci left: 9.796263e-03	ci right 1.028631e-02	k: 6425	n:640000
LRP1   640000 perm   379 sec   (1688 perm/sec)   p_kst 1.003906e-02   p_cons 1.421875e-04   p_joint 2.031250e-05

Joint ci ratio: 1.012127e+00	ci left: 1.177533e-05	ci right 3.613761e-05	k: 14	n:650000
Cons ci ratio: 4.042876e-01	ci left: 1.154830e-04	ci right 1.752761e-04	k: 93	n:650000
KS ci ratio: 4.825428e-02	ci left: 9.808173e-03	ci right 1.029467e-02	k: 6532	n:650000
LRP1   650000 perm   388 sec   (1677 perm/sec)   p_kst 1.004923e-02   p_cons 1.430769e-04   p_joint 2.153846e-05

Joint ci ratio: 1.012127e+00	ci left: 1.159691e-05	ci right 3.559008e-05	k: 14	n:660000
Cons ci ratio: 4.000539e-01	ci left: 1.164571e-04	ci right 1.759556e-04	k: 95	n:660000
KS ci ratio: 4.792934e-02	ci left: 9.792790e-03	ci right 1.027516e-02	k: 6621	n:660000
LRP1   660000 perm   396 sec   (1666 perm/sec)   p_kst 1.003182e-02   p_cons 1.439394e-04   p_joint 2.121212e-05

Joint ci ratio: 1.239603e+00	ci left: 6.142366e-06	ci right 2.549955e-05	k: 9	n:670000
Cons ci ratio: 3.979866e-01	ci left: 1.160617e-04	ci right 1.749710e-04	k: 96	n:670000
KS ci ratio: 4.756793e-02	ci left: 9.795575e-03	ci right 1.027435e-02	k: 6722	n:670000
LRP1   670000 perm   405 sec   (1656 perm/sec)   p_kst 1.003284e-02   p_cons 1.432836e-04   p_joint 1.343284e-05

Joint ci ratio: 1.239603e+00	ci left: 6.052037e-06	ci right 2.512456e-05	k: 9	n:680000
Cons ci ratio: 3.979870e-01	ci left: 1.143548e-04	ci right 1.723979e-04	k: 96	n:680000
KS ci ratio: 4.722856e-02	ci left: 9.792479e-03	ci right 1.026759e-02	k: 6819	n:680000
LRP1   680000 perm   413 sec   (1645 perm/sec)   p_kst 1.002794e-02   p_cons 1.411765e-04   p_joint 1.323529e-05

Joint ci ratio: 7.156747e-01	ci left: 2.814765e-05	ci right 6.036008e-05	k: 29	n:690000
Cons ci ratio: 3.881089e-01	ci left: 1.192278e-04	ci right 1.778583e-04	k: 101	n:690000
KS ci ratio: 4.691006e-02	ci left: 9.783754e-03	ci right 1.025516e-02	k: 6912	n:690000
LRP1   690000 perm   422 sec   (1635 perm/sec)   p_kst 1.001739e-02   p_cons 1.463768e-04   p_joint 4.202899e-05

Joint ci ratio: 7.040367e-01	ci left: 2.891572e-05	ci right 6.118068e-05	k: 30	n:700000
Cons ci ratio: 3.862204e-01	ci left: 1.188141e-04	ci right 1.768844e-04	k: 102	n:700000
KS ci ratio: 4.659791e-02	ci left: 9.775289e-03	ci right 1.024306e-02	k: 7005	n:700000
LRP1   700000 perm   431 sec   (1624 perm/sec)   p_kst 1.000714e-02   p_cons 1.457143e-04   p_joint 4.285714e-05

Joint ci ratio: 7.040369e-01	ci left: 2.850845e-05	ci right 6.031898e-05	k: 30	n:710000
Cons ci ratio: 3.862208e-01	ci left: 1.171406e-04	ci right 1.743932e-04	k: 102	n:710000
KS ci ratio: 4.630838e-02	ci left: 9.760111e-03	ci right 1.022418e-02	k: 7093	n:710000
LRP1   710000 perm   440 sec   (1614 perm/sec)   p_kst 9.990141e-03   p_cons 1.436620e-04   p_joint 4.225352e-05

Joint ci ratio: 6.929488e-01	ci left: 2.925434e-05	ci right 6.111337e-05	k: 31	n:720000
Cons ci ratio: 3.843596e-01	ci left: 1.167680e-04	ci right 1.734938e-04	k: 103	n:720000
KS ci ratio: 4.603714e-02	ci left: 9.739872e-03	ci right 1.020019e-02	k: 7177	n:720000
LRP1   720000 perm   449 sec   (1604 perm/sec)   p_kst 9.968056e-03   p_cons 1.430556e-04   p_joint 4.305556e-05

Joint ci ratio: 6.823685e-01	ci left: 2.998372e-05	ci right 6.188225e-05	k: 32	n:730000
Cons ci ratio: 3.825251e-01	ci left: 1.164063e-04	ci right 1.726185e-04	k: 104	n:730000
KS ci ratio: 4.574834e-02	ci left: 9.729675e-03	ci right 1.018656e-02	k: 7268	n:730000
LRP1   730000 perm   458 sec   (1595 perm/sec)   p_kst 9.956164e-03   p_cons 1.424658e-04   p_joint 4.383562e-05

Joint ci ratio: 6.358912e-01	ci left: 3.520485e-05	ci right 6.891776e-05	k: 37	n:740000
Cons ci ratio: 3.771744e-01	ci left: 1.185002e-04	ci right 1.747251e-04	k: 107	n:740000
KS ci ratio: 4.539954e-02	ci left: 9.747821e-03	ci right 1.020197e-02	k: 7380	n:740000
LRP1   740000 perm   467 sec   (1585 perm/sec)   p_kst 9.972973e-03   p_cons 1.445946e-04   p_joint 5.000000e-05

Joint ci ratio: 6.358914e-01	ci left: 3.473545e-05	ci right 6.799887e-05	k: 37	n:750000
Cons ci ratio: 3.771748e-01	ci left: 1.169202e-04	ci right 1.723955e-04	k: 107	n:750000
KS ci ratio: 4.509203e-02	ci left: 9.750994e-03	ci right 1.020214e-02	k: 7481	n:750000
LRP1   750000 perm   476 sec   (1576 perm/sec)   p_kst 9.974667e-03   p_cons 1.426667e-04   p_joint 4.933333e-05

Joint ci ratio: 6.358917e-01	ci left: 3.427840e-05	ci right 6.710415e-05	k: 37	n:760000
Cons ci ratio: 3.754407e-01	ci left: 1.165731e-04	ci right 1.715668e-04	k: 108	n:760000
KS ci ratio: 4.483251e-02	ci left: 9.735876e-03	ci right 1.018366e-02	k: 7568	n:760000
LRP1   760000 perm   485 sec   (1567 perm/sec)   p_kst 9.957895e-03   p_cons 1.421053e-04   p_joint 4.868421e-05

Joint ci ratio: 6.358919e-01	ci left: 3.383322e-05	ci right 6.623268e-05	k: 37	n:770000
Cons ci ratio: 3.754411e-01	ci left: 1.150592e-04	ci right 1.693387e-04	k: 108	n:770000
KS ci ratio: 4.456273e-02	ci left: 9.727581e-03	ci right 1.017222e-02	k: 7660	n:770000
LRP1   770000 perm   494 sec   (1557 perm/sec)   p_kst 9.948052e-03   p_cons 1.402597e-04   p_joint 4.805195e-05

Joint ci ratio: 6.358921e-01	ci left: 3.339946e-05	ci right 6.538355e-05	k: 37	n:780000
Cons ci ratio: 3.703784e-01	ci left: 1.170698e-04	ci right 1.713727e-04	k: 111	n:780000
KS ci ratio: 4.429199e-02	ci left: 9.722042e-03	ci right 1.016366e-02	k: 7754	n:780000
LRP1   780000 perm   504 sec   (1548 perm/sec)   p_kst 9.941026e-03   p_cons 1.423077e-04   p_joint 4.743590e-05

Joint ci ratio: 6.276865e-01	ci left: 3.403954e-05	ci right 6.602215e-05	k: 38	n:790000
Cons ci ratio: 3.687360e-01	ci left: 1.167361e-04	ci right 1.705863e-04	k: 112	n:790000
KS ci ratio: 4.403178e-02	ci left: 9.714147e-03	ci right 1.015275e-02	k: 7846	n:790000
LRP1   790000 perm   513 sec   (1539 perm/sec)   p_kst 9.931646e-03   p_cons 1.417722e-04   p_joint 4.810127e-05

Joint ci ratio: 6.276867e-01	ci left: 3.361404e-05	ci right 6.519688e-05	k: 38	n:800000
Cons ci ratio: 3.639362e-01	ci left: 1.186818e-04	ci right 1.725476e-04	k: 115	n:800000
KS ci ratio: 4.375664e-02	ci left: 9.715112e-03	ci right 1.015095e-02	k: 7945	n:800000
LRP1   800000 perm   523 sec   (1530 perm/sec)   p_kst 9.931250e-03   p_cons 1.437500e-04   p_joint 4.750000e-05

Joint ci ratio: 6.276869e-01	ci left: 3.319905e-05	ci right 6.439199e-05	k: 38	n:810000
Cons ci ratio: 3.639366e-01	ci left: 1.172166e-04	ci right 1.704174e-04	k: 115	n:810000
KS ci ratio: 4.348931e-02	ci left: 9.714840e-03	ci right 1.014793e-02	k: 8043	n:810000
LRP1   810000 perm   532 sec   (1522 perm/sec)   p_kst 9.929630e-03   p_cons 1.419753e-04   p_joint 4.691358e-05

Joint ci ratio: 6.276871e-01	ci left: 3.279418e-05	ci right 6.360673e-05	k: 38	n:820000
Cons ci ratio: 3.623781e-01	ci left: 1.168953e-04	ci right 1.696695e-04	k: 116	n:820000
KS ci ratio: 4.322951e-02	ci left: 9.713376e-03	ci right 1.014375e-02	k: 8140	n:820000
LRP1   820000 perm   542 sec   (1513 perm/sec)   p_kst 9.926829e-03   p_cons 1.414634e-04   p_joint 4.634146e-05

Joint ci ratio: 6.276872e-01	ci left: 3.239907e-05	ci right 6.284039e-05	k: 38	n:830000
Cons ci ratio: 3.593198e-01	ci left: 1.176781e-04	ci right 1.702525e-04	k: 118	n:830000
KS ci ratio: 4.299012e-02	ci left: 9.704804e-03	ci right 1.013236e-02	k: 8231	n:830000
LRP1   830000 perm   552 sec   (1504 perm/sec)   p_kst 9.916867e-03   p_cons 1.421687e-04   p_joint 4.578313e-05

Joint ci ratio: 6.276874e-01	ci left: 3.201336e-05	ci right 6.209230e-05	k: 38	n:840000
Cons ci ratio: 3.578196e-01	ci left: 1.173604e-04	ci right 1.695229e-04	k: 119	n:840000
KS ci ratio: 4.273134e-02	ci left: 9.707042e-03	ci right 1.013206e-02	k: 8331	n:840000
LRP1   840000 perm   562 sec   (1495 perm/sec)   p_kst 9.917857e-03   p_cons 1.416667e-04   p_joint 4.523810e-05

Joint ci ratio: 6.197915e-01	ci left: 3.262704e-05	ci right 6.272216e-05	k: 39	n:850000
Cons ci ratio: 3.563381e-01	ci left: 1.170507e-04	ci right 1.688101e-04	k: 120	n:850000
KS ci ratio: 4.249245e-02	ci left: 9.702251e-03	ci right 1.012463e-02	k: 8425	n:850000
LRP1   850000 perm   572 sec   (1486 perm/sec)   p_kst 9.911765e-03   p_cons 1.411765e-04   p_joint 4.588235e-05

Joint ci ratio: 6.197916e-01	ci left: 3.224765e-05	ci right 6.199284e-05	k: 39	n:860000
Cons ci ratio: 3.520008e-01	ci left: 1.188677e-04	ci right 1.706446e-04	k: 123	n:860000
KS ci ratio: 4.230017e-02	ci left: 9.678018e-03	ci right 1.009739e-02	k: 8502	n:860000
LRP1   860000 perm   582 sec   (1478 perm/sec)   p_kst 9.886047e-03   p_cons 1.430233e-04   p_joint 4.534884e-05

Joint ci ratio: 6.197918e-01	ci left: 3.187698e-05	ci right 6.128028e-05	k: 39	n:870000
Cons ci ratio: 3.520011e-01	ci left: 1.175014e-04	ci right 1.686832e-04	k: 123	n:870000
KS ci ratio: 4.209808e-02	ci left: 9.660033e-03	ci right 1.007657e-02	k: 8584	n:870000
LRP1   870000 perm   592 sec   (1470 perm/sec)   p_kst 9.866667e-03   p_cons 1.413793e-04   p_joint 4.482759e-05

Joint ci ratio: 6.197920e-01	ci left: 3.151474e-05	ci right 6.058392e-05	k: 39	n:880000
Cons ci ratio: 3.491962e-01	ci left: 1.182387e-04	ci right 1.692384e-04	k: 125	n:880000
KS ci ratio: 4.186229e-02	ci left: 9.659330e-03	ci right 1.007345e-02	k: 8681	n:880000
LRP1   880000 perm   602 sec   (1462 perm/sec)   p_kst 9.864773e-03   p_cons 1.420455e-04   p_joint 4.431818e-05

Joint ci ratio: 6.197921e-01	ci left: 3.116064e-05	ci right 5.990321e-05	k: 39	n:890000
Cons ci ratio: 3.437814e-01	ci left: 1.210135e-04	ci right 1.722208e-04	k: 129	n:890000
KS ci ratio: 4.159454e-02	ci left: 9.675329e-03	ci right 1.008742e-02	k: 8793	n:890000
LRP1   890000 perm   612 sec   (1453 perm/sec)   p_kst 9.879775e-03   p_cons 1.449438e-04   p_joint 4.382022e-05

Joint ci ratio: 6.048547e-01	ci left: 3.269165e-05	ci right 6.180075e-05	k: 41	n:900000
Cons ci ratio: 3.437817e-01	ci left: 1.196689e-04	ci right 1.703073e-04	k: 129	n:900000
KS ci ratio: 4.140235e-02	ci left: 9.657990e-03	ci right 1.006740e-02	k: 8875	n:900000
LRP1   900000 perm   623 sec   (1445 perm/sec)   p_kst 9.861111e-03   p_cons 1.433333e-04   p_joint 4.555556e-05

Joint ci ratio: 5.977799e-01	ci left: 3.326383e-05	ci right 6.238609e-05	k: 42	n:910000
Cons ci ratio: 3.424671e-01	ci left: 1.193581e-04	ci right 1.696290e-04	k: 130	n:910000
KS ci ratio: 4.117800e-02	ci left: 9.657351e-03	ci right 1.006446e-02	k: 8972	n:910000
LRP1   910000 perm   633 sec   (1437 perm/sec)   p_kst 9.859341e-03   p_cons 1.428571e-04   p_joint 4.615385e-05

Joint ci ratio: 5.977801e-01	ci left: 3.290226e-05	ci right 6.170798e-05	k: 42	n:920000
Cons ci ratio: 3.373549e-01	ci left: 1.220375e-04	ci right 1.725027e-04	k: 134	n:920000
KS ci ratio: 4.095497e-02	ci left: 9.657807e-03	ci right 1.006268e-02	k: 9070	n:920000
LRP1   920000 perm   644 sec   (1429 perm/sec)   p_kst 9.858696e-03   p_cons 1.456522e-04   p_joint 4.565217e-05

Joint ci ratio: 5.843446e-01	ci left: 3.437705e-05	ci right 6.351341e-05	k: 44	n:930000
Cons ci ratio: 3.312754e-01	ci left: 1.256505e-04	ci right 1.764737e-04	k: 139	n:930000
KS ci ratio: 4.074675e-02	ci left: 9.652938e-03	ci right 1.005550e-02	k: 9163	n:930000
LRP1   930000 perm   654 sec   (1421 perm/sec)   p_kst 9.852688e-03   p_cons 1.494624e-04   p_joint 4.731183e-05

Joint ci ratio: 5.843448e-01	ci left: 3.401134e-05	ci right 6.283774e-05	k: 44	n:940000
Cons ci ratio: 3.300986e-01	ci left: 1.252893e-04	ci right 1.757482e-04	k: 140	n:940000
KS ci ratio: 4.052178e-02	ci left: 9.657656e-03	ci right 1.005814e-02	k: 9265	n:940000
LRP1   940000 perm   665 sec   (1414 perm/sec)   p_kst 9.856383e-03   p_cons 1.489362e-04   p_joint 4.680851e-05

Joint ci ratio: 5.843450e-01	ci left: 3.365332e-05	ci right 6.217629e-05	k: 44	n:950000
Cons ci ratio: 3.266417e-01	ci left: 1.268680e-04	ci right 1.773155e-04	k: 143	n:950000
KS ci ratio: 4.033313e-02	ci left: 9.646649e-03	ci right 1.004477e-02	k: 9352	n:950000
LRP1   950000 perm   676 sec   (1404 perm/sec)   p_kst 9.844211e-03   p_cons 1.505263e-04   p_joint 4.631579e-05

Joint ci ratio: 5.843451e-01	ci left: 3.330276e-05	ci right 6.152863e-05	k: 44	n:960000
Cons ci ratio: 3.255135e-01	ci left: 1.265029e-04	ci right 1.765951e-04	k: 144	n:960000
KS ci ratio: 4.013420e-02	ci left: 9.642063e-03	ci right 1.003799e-02	k: 9445	n:960000
LRP1   960000 perm   688 sec   (1395 perm/sec)   p_kst 9.838542e-03   p_cons 1.500000e-04   p_joint 4.583333e-05

Joint ci ratio: 5.843452e-01	ci left: 3.295943e-05	ci right 6.089432e-05	k: 44	n:970000
Cons ci ratio: 3.232915e-01	ci left: 1.270927e-04	ci right 1.770037e-04	k: 146	n:970000
KS ci ratio: 3.993608e-02	ci left: 9.638597e-03	ci right 1.003238e-02	k: 9539	n:970000
LRP1   970000 perm   699 sec   (1387 perm/sec)   p_kst 9.834021e-03   p_cons 1.505155e-04   p_joint 4.536082e-05

Joint ci ratio: 5.843454e-01	ci left: 3.262311e-05	ci right 6.027295e-05	k: 44	n:980000
Cons ci ratio: 3.189803e-01	ci left: 1.295486e-04	ci right 1.796070e-04	k: 150	n:980000
KS ci ratio: 3.969719e-02	ci left: 9.656424e-03	ci right 1.004852e-02	k: 9654	n:980000
LRP1   980000 perm   710 sec   (1380 perm/sec)   p_kst 9.851020e-03   p_cons 1.530612e-04   p_joint 4.489796e-05

Joint ci ratio: 5.843455e-01	ci left: 3.229358e-05	ci right 5.966414e-05	k: 44	n:990000
Cons ci ratio: 3.179294e-01	ci left: 1.291694e-04	ci right 1.788833e-04	k: 151	n:990000
KS ci ratio: 3.952592e-02	ci left: 9.642891e-03	ci right 1.003271e-02	k: 9738	n:990000
LRP1   990000 perm   721 sec   (1372 perm/sec)   p_kst 9.836364e-03   p_cons 1.525253e-04   p_joint 4.444444e-05

Joint ci ratio: 6.722627e-01	ci left: 2.271579e-05	ci right 4.634396e-05	k: 33	n:1000000
Cons ci ratio: 3.168888e-01	ci left: 1.287980e-04	ci right 1.781739e-04	k: 152	n:1000000
KS ci ratio: 3.931644e-02	ci left: 9.649438e-03	ci right 1.003741e-02	k: 9842	n:1000000
LRP1   1000000 perm   733 sec   (1365 perm/sec)   p_kst 9.842000e-03   p_cons 1.520000e-04   p_joint 3.300000e-05

Joint ci ratio: 6.533214e-01	ci left: 2.413752e-05	ci right 4.819426e-05	k: 35	n:1010000
Cons ci ratio: 3.158584e-01	ci left: 1.284343e-04	ci right 1.774783e-04	k: 153	n:1010000
KS ci ratio: 3.909834e-02	ci left: 9.661743e-03	ci right 1.004801e-02	k: 9952	n:1010000
LRP1   1010000 perm   744 sec   (1358 perm/sec)   p_kst 9.853465e-03   p_cons 1.514851e-04   p_joint 3.465347e-05

Joint ci ratio: 6.533215e-01	ci left: 2.390088e-05	ci right 4.772177e-05	k: 35	n:1020000
Cons ci ratio: 3.148379e-01	ci left: 1.280779e-04	ci right 1.767960e-04	k: 154	n:1020000
KS ci ratio: 3.888775e-02	ci left: 9.671871e-03	ci right 1.005641e-02	k: 10060	n:1020000
LRP1   1020000 perm   755 sec   (1351 perm/sec)   p_kst 9.862745e-03   p_cons 1.509804e-04   p_joint 3.431373e-05

Joint ci ratio: 6.823731e-01	ci left: 2.125056e-05	ci right 4.385841e-05	k: 32	n:1030000
Cons ci ratio: 3.138273e-01	ci left: 1.277287e-04	ci right 1.761268e-04	k: 155	n:1030000
KS ci ratio: 3.869012e-02	ci left: 9.677000e-03	ci right 1.005974e-02	k: 10163	n:1030000
LRP1   1030000 perm   766 sec   (1344 perm/sec)   p_kst 9.866990e-03   p_cons 1.504854e-04   p_joint 3.106796e-05

Joint ci ratio: 6.823733e-01	ci left: 2.104622e-05	ci right 4.343670e-05	k: 32	n:1040000
Cons ci ratio: 3.118346e-01	ci left: 1.282727e-04	ci right 1.765068e-04	k: 157	n:1040000
KS ci ratio: 3.846900e-02	ci left: 9.695369e-03	ci right 1.007660e-02	k: 10280	n:1040000
LRP1   1040000 perm   778 sec   (1337 perm/sec)   p_kst 9.884615e-03   p_cons 1.509615e-04   p_joint 3.076923e-05

Joint ci ratio: 6.722632e-01	ci left: 2.163408e-05	ci right 4.413712e-05	k: 33	n:1050000
Cons ci ratio: 3.108525e-01	ci left: 1.279290e-04	ci right 1.758523e-04	k: 158	n:1050000
KS ci ratio: 3.828138e-02	ci left: 9.698300e-03	ci right 1.007774e-02	k: 10381	n:1050000
LRP1   1050000 perm   789 sec   (1330 perm/sec)   p_kst 9.886667e-03   p_cons 1.504762e-04   p_joint 3.142857e-05

Joint ci ratio: 6.722634e-01	ci left: 2.142998e-05	ci right 4.372073e-05	k: 33	n:1060000
Cons ci ratio: 3.098797e-01	ci left: 1.275921e-04	ci right 1.752100e-04	k: 159	n:1060000
KS ci ratio: 3.810383e-02	ci left: 9.697442e-03	ci right 1.007505e-02	k: 10478	n:1060000
LRP1   1060000 perm   801 sec   (1323 perm/sec)   p_kst 9.884906e-03   p_cons 1.500000e-04   p_joint 3.113208e-05

Joint ci ratio: 6.722635e-01	ci left: 2.122970e-05	ci right 4.331213e-05	k: 33	n:1070000
Cons ci ratio: 3.098799e-01	ci left: 1.263996e-04	ci right 1.735726e-04	k: 159	n:1070000
KS ci ratio: 3.791605e-02	ci left: 9.703085e-03	ci right 1.007901e-02	k: 10582	n:1070000
LRP1   1070000 perm   813 sec   (1317 perm/sec)   p_kst 9.889720e-03   p_cons 1.485981e-04   p_joint 3.084112e-05

Joint ci ratio: 6.722636e-01	ci left: 2.103313e-05	ci right 4.291110e-05	k: 33	n:1080000
Cons ci ratio: 3.070148e-01	ci left: 1.277921e-04	ci right 1.749575e-04	k: 162	n:1080000
KS ci ratio: 3.774529e-02	ci left: 9.701289e-03	ci right 1.007542e-02	k: 10678	n:1080000
LRP1   1080000 perm   824 sec   (1310 perm/sec)   p_kst 9.887037e-03   p_cons 1.500000e-04   p_joint 3.055556e-05

Joint ci ratio: 6.722637e-01	ci left: 2.084016e-05	ci right 4.251742e-05	k: 33	n:1090000
Cons ci ratio: 3.033153e-01	ci left: 1.300085e-04	ci right 1.773022e-04	k: 166	n:1090000
KS ci ratio: 3.758034e-02	ci left: 9.697713e-03	ci right 1.007004e-02	k: 10772	n:1090000
LRP1   1090000 perm   836 sec   (1303 perm/sec)   p_kst 9.882569e-03   p_cons 1.522936e-04   p_joint 3.027523e-05

Joint ci ratio: 6.722638e-01	ci left: 2.065071e-05	ci right 4.213090e-05	k: 33	n:1100000
Cons ci ratio: 3.024113e-01	ci left: 1.296666e-04	ci right 1.766683e-04	k: 167	n:1100000
KS ci ratio: 3.739669e-02	ci left: 9.705013e-03	ci right 1.007576e-02	k: 10878	n:1100000
LRP1   1100000 perm   848 sec   (1297 perm/sec)   p_kst 9.889091e-03   p_cons 1.518182e-04   p_joint 3.000000e-05

Joint ci ratio: 6.722639e-01	ci left: 2.046466e-05	ci right 4.175134e-05	k: 33	n:1110000
Cons ci ratio: 3.015154e-01	ci left: 1.293311e-04	ci right 1.760456e-04	k: 168	n:1110000
KS ci ratio: 3.724139e-02	ci left: 9.698797e-03	ci right 1.006773e-02	k: 10969	n:1110000
LRP1   1110000 perm   860 sec   (1290 perm/sec)   p_kst 9.881982e-03   p_cons 1.513514e-04   p_joint 2.972973e-05

Joint ci ratio: 6.722639e-01	ci left: 2.028194e-05	ci right 4.137857e-05	k: 33	n:1120000
Cons ci ratio: 3.006273e-01	ci left: 1.290017e-04	ci right 1.754339e-04	k: 169	n:1120000
KS ci ratio: 3.705081e-02	ci left: 9.712157e-03	ci right 1.007967e-02	k: 11082	n:1120000
LRP1   1120000 perm   873 sec   (1283 perm/sec)   p_kst 9.894643e-03   p_cons 1.508929e-04   p_joint 2.946429e-05

Joint ci ratio: 6.625904e-01	ci left: 2.083725e-05	ci right 4.204541e-05	k: 34	n:1130000
Cons ci ratio: 3.006275e-01	ci left: 1.278601e-04	ci right 1.738814e-04	k: 169	n:1130000
KS ci ratio: 3.688976e-02	ci left: 9.711256e-03	ci right 1.007710e-02	k: 11179	n:1130000
LRP1   1130000 perm   885 sec   (1277 perm/sec)   p_kst 9.892920e-03   p_cons 1.495575e-04   p_joint 3.008850e-05

Joint ci ratio: 6.625905e-01	ci left: 2.065446e-05	ci right 4.167659e-05	k: 34	n:1140000
Cons ci ratio: 2.988745e-01	ci left: 1.283610e-04	ci right 1.742421e-04	k: 171	n:1140000
KS ci ratio: 3.670943e-02	ci left: 9.721674e-03	ci right 1.008609e-02	k: 11289	n:1140000
LRP1   1140000 perm   897 sec   (1270 perm/sec)   p_kst 9.902632e-03   p_cons 1.500000e-04   p_joint 2.982456e-05

Joint ci ratio: 6.625906e-01	ci left: 2.047486e-05	ci right 4.131419e-05	k: 34	n:1150000
Cons ci ratio: 2.963015e-01	ci left: 1.296588e-04	ci right 1.755298e-04	k: 174	n:1150000
KS ci ratio: 3.654467e-02	ci left: 9.725021e-03	ci right 1.008789e-02	k: 11391	n:1150000
LRP1   1150000 perm   910 sec   (1264 perm/sec)   p_kst 9.905217e-03   p_cons 1.513043e-04   p_joint 2.956522e-05

Joint ci ratio: 6.625907e-01	ci left: 2.029835e-05	ci right 4.095803e-05	k: 34	n:1160000
Cons ci ratio: 2.946226e-01	ci left: 1.301374e-04	ci right 1.758681e-04	k: 176	n:1160000
KS ci ratio: 3.640772e-02	ci left: 9.714646e-03	ci right 1.007574e-02	k: 11477	n:1160000
LRP1   1160000 perm   922 sec   (1258 perm/sec)   p_kst 9.893966e-03   p_cons 1.517241e-04   p_joint 2.931034e-05

Joint ci ratio: 6.533230e-01	ci left: 2.083665e-05	ci right 4.160363e-05	k: 35	n:1170000
Cons ci ratio: 2.929720e-01	ci left: 1.306086e-04	ci right 1.762000e-04	k: 178	n:1170000
KS ci ratio: 3.623117e-02	ci left: 9.726473e-03	ci right 1.008622e-02	k: 11589	n:1170000
LRP1   1170000 perm   934 sec   (1252 perm/sec)   p_kst 9.905128e-03   p_cons 1.521368e-04   p_joint 2.991453e-05

Joint ci ratio: 6.533231e-01	ci left: 2.066007e-05	ci right 4.125106e-05	k: 35	n:1180000
Cons ci ratio: 2.913488e-01	ci left: 1.310725e-04	ci right 1.765255e-04	k: 180	n:1180000
KS ci ratio: 3.604939e-02	ci left: 9.742303e-03	ci right 1.010079e-02	k: 11706	n:1180000
LRP1   1180000 perm   947 sec   (1246 perm/sec)   p_kst 9.920339e-03   p_cons 1.525424e-04   p_joint 2.966102e-05

Joint ci ratio: 6.533232e-01	ci left: 2.048645e-05	ci right 4.090441e-05	k: 35	n:1190000
Cons ci ratio: 2.905474e-01	ci left: 1.307500e-04	ci right 1.759436e-04	k: 181	n:1190000
KS ci ratio: 3.589640e-02	ci left: 9.743713e-03	ci right 1.010070e-02	k: 11806	n:1190000
LRP1   1190000 perm   959 sec   (1240 perm/sec)   p_kst 9.921008e-03   p_cons 1.521008e-04   p_joint 2.941176e-05

Joint ci ratio: 6.444338e-01	ci left: 2.101172e-05	ci right 4.153241e-05	k: 36	n:1200000
Cons ci ratio: 2.905476e-01	ci left: 1.296604e-04	ci right 1.744774e-04	k: 181	n:1200000
KS ci ratio: 3.575595e-02	ci left: 9.739321e-03	ci right 1.009472e-02	k: 11899	n:1200000
LRP1   1200000 perm   972 sec   (1235 perm/sec)   p_kst 9.915833e-03   p_cons 1.508333e-04   p_joint 3.000000e-05

Joint ci ratio: 6.444339e-01	ci left: 2.083807e-05	ci right 4.118916e-05	k: 36	n:1210000
Cons ci ratio: 2.881820e-01	ci left: 1.308883e-04	ci right 1.756942e-04	k: 184	n:1210000
KS ci ratio: 3.559017e-02	ci left: 9.749749e-03	ci right 1.010384e-02	k: 12010	n:1210000
LRP1   1210000 perm   985 sec   (1229 perm/sec)   p_kst 9.925620e-03   p_cons 1.520661e-04   p_joint 2.975207e-05

Joint ci ratio: 6.444340e-01	ci left: 2.066726e-05	ci right 4.085155e-05	k: 36	n:1220000
Cons ci ratio: 2.866367e-01	ci left: 1.313366e-04	ci right 1.760113e-04	k: 186	n:1220000
KS ci ratio: 3.543553e-02	ci left: 9.755135e-03	ci right 1.010785e-02	k: 12115	n:1220000
LRP1   1220000 perm   998 sec   (1223 perm/sec)   p_kst 9.930328e-03   p_cons 1.524590e-04   p_joint 2.950820e-05

Joint ci ratio: 6.444341e-01	ci left: 2.049923e-05	ci right 4.051943e-05	k: 36	n:1230000
Cons ci ratio: 2.866369e-01	ci left: 1.302688e-04	ci right 1.745803e-04	k: 186	n:1230000
KS ci ratio: 3.528144e-02	ci left: 9.761242e-03	ci right 1.011262e-02	k: 12221	n:1230000
LRP1   1230000 perm   1010 sec   (1217 perm/sec)   p_kst 9.935772e-03   p_cons 1.512195e-04   p_joint 2.926829e-05

Joint ci ratio: 6.358980e-01	ci left: 2.100929e-05	ci right 4.112850e-05	k: 37	n:1240000
Cons ci ratio: 2.851162e-01	ci left: 1.307155e-04	ci right 1.749007e-04	k: 188	n:1240000
KS ci ratio: 3.516681e-02	ci left: 9.746469e-03	ci right 1.009615e-02	k: 12301	n:1240000
LRP1   1240000 perm   1023 sec   (1212 perm/sec)   p_kst 9.920161e-03   p_cons 1.516129e-04   p_joint 2.983871e-05

Joint ci ratio: 6.358981e-01	ci left: 2.084121e-05	ci right 4.079947e-05	k: 37	n:1250000
Cons ci ratio: 2.843650e-01	ci left: 1.304127e-04	ci right 1.743584e-04	k: 189	n:1250000
KS ci ratio: 3.503472e-02	ci left: 9.742244e-03	ci right 1.009043e-02	k: 12394	n:1250000
LRP1   1250000 perm   1036 sec   (1206 perm/sec)   p_kst 9.915200e-03   p_cons 1.512000e-04   p_joint 2.960000e-05

Joint ci ratio: 6.276924e-01	ci left: 2.134220e-05	ci right 4.139498e-05	k: 38	n:1260000
Cons ci ratio: 2.836196e-01	ci left: 1.301148e-04	ci right 1.738247e-04	k: 190	n:1260000
KS ci ratio: 3.490411e-02	ci left: 9.738089e-03	ci right 1.008480e-02	k: 12487	n:1260000
LRP1   1260000 perm   1049 sec   (1201 perm/sec)   p_kst 9.910317e-03   p_cons 1.507937e-04   p_joint 3.015873e-05

Joint ci ratio: 6.276925e-01	ci left: 2.117415e-05	ci right 4.106904e-05	k: 38	n:1270000
Cons ci ratio: 2.828801e-01	ci left: 1.298217e-04	ci right 1.732992e-04	k: 191	n:1270000
KS ci ratio: 3.475960e-02	ci left: 9.742588e-03	ci right 1.008800e-02	k: 12591	n:1270000
LRP1   1270000 perm   1063 sec   (1195 perm/sec)   p_kst 9.914173e-03   p_cons 1.503937e-04   p_joint 2.992126e-05

Joint ci ratio: 6.276926e-01	ci left: 2.100872e-05	ci right 4.074819e-05	k: 38	n:1280000
Cons ci ratio: 2.828803e-01	ci left: 1.288075e-04	ci right 1.719453e-04	k: 191	n:1280000
KS ci ratio: 3.459761e-02	ci left: 9.757863e-03	ci right 1.010217e-02	k: 12709	n:1280000
LRP1   1280000 perm   1076 sec   (1189 perm/sec)   p_kst 9.928906e-03   p_cons 1.492187e-04   p_joint 2.968750e-05

Joint ci ratio: 6.276926e-01	ci left: 2.084587e-05	ci right 4.043231e-05	k: 38	n:1290000
Cons ci ratio: 2.828805e-01	ci left: 1.278090e-04	ci right 1.706124e-04	k: 191	n:1290000
KS ci ratio: 3.447181e-02	ci left: 9.753691e-03	ci right 1.009658e-02	k: 12802	n:1290000
LRP1   1290000 perm   1090 sec   (1184 perm/sec)   p_kst 9.924031e-03   p_cons 1.480620e-04   p_joint 2.945736e-05

Joint ci ratio: 5.843488e-01	ci left: 2.459277e-05	ci right 4.543662e-05	k: 44	n:1300000
Cons ci ratio: 2.806959e-01	ci left: 1.289705e-04	ci right 1.717703e-04	k: 194	n:1300000
KS ci ratio: 3.437026e-02	ci left: 9.736620e-03	ci right 1.007788e-02	k: 12878	n:1300000
LRP1   1300000 perm   1103 sec   (1178 perm/sec)   p_kst 9.906154e-03   p_cons 1.492308e-04   p_joint 3.384615e-05

Joint ci ratio: 5.843488e-01	ci left: 2.440504e-05	ci right 4.508978e-05	k: 44	n:1310000
Cons ci ratio: 2.806960e-01	ci left: 1.279860e-04	ci right 1.704591e-04	k: 194	n:1310000
KS ci ratio: 3.424425e-02	ci left: 9.734191e-03	ci right 1.007409e-02	k: 12973	n:1310000
LRP1   1310000 perm   1117 sec   (1172 perm/sec)   p_kst 9.903053e-03   p_cons 1.480916e-04   p_joint 3.358779e-05

Joint ci ratio: 5.779622e-01	ci left: 2.486625e-05	ci right 4.561606e-05	k: 45	n:1320000
Cons ci ratio: 2.792675e-01	ci left: 1.284252e-04	ci right 1.707890e-04	k: 196	n:1320000
KS ci ratio: 3.413412e-02	ci left: 9.723539e-03	ci right 1.006195e-02	k: 13057	n:1320000
LRP1   1320000 perm   1131 sec   (1167 perm/sec)   p_kst 9.891667e-03   p_cons 1.484848e-04   p_joint 3.409091e-05

Joint ci ratio: 5.779623e-01	ci left: 2.467928e-05	ci right 4.527308e-05	k: 45	n:1330000
Cons ci ratio: 2.785614e-01	ci left: 1.281589e-04	ci right 1.703092e-04	k: 197	n:1330000
KS ci ratio: 3.401460e-02	ci left: 9.719013e-03	ci right 1.005606e-02	k: 13149	n:1330000
LRP1   1330000 perm   1145 sec   (1162 perm/sec)   p_kst 9.886466e-03   p_cons 1.481203e-04   p_joint 3.383459e-05

Joint ci ratio: 5.717805e-01	ci left: 2.513278e-05	ci right 4.578896e-05	k: 46	n:1340000
Cons ci ratio: 2.771651e-01	ci left: 1.285910e-04	ci right 1.706345e-04	k: 199	n:1340000
KS ci ratio: 3.388986e-02	ci left: 9.718256e-03	ci right 1.005402e-02	k: 13246	n:1340000
LRP1   1340000 perm   1159 sec   (1157 perm/sec)   p_kst 9.885075e-03   p_cons 1.485075e-04   p_joint 3.432836e-05

Joint ci ratio: 5.657930e-01	ci left: 2.558073e-05	ci right 4.629606e-05	k: 47	n:1350000
Cons ci ratio: 2.764748e-01	ci left: 1.283278e-04	ci right 1.701626e-04	k: 200	n:1350000
KS ci ratio: 3.376521e-02	ci left: 9.718248e-03	ci right 1.005275e-02	k: 13344	n:1350000
LRP1   1350000 perm   1173 sec   (1151 perm/sec)   p_kst 9.884444e-03   p_cons 1.481481e-04   p_joint 3.481481e-05

Joint ci ratio: 5.657931e-01	ci left: 2.539263e-05	ci right 4.595565e-05	k: 47	n:1360000
Cons ci ratio: 2.757897e-01	ci left: 1.280686e-04	ci right 1.696974e-04	k: 201	n:1360000
KS ci ratio: 3.364192e-02	ci left: 9.718242e-03	ci right 1.005150e-02	k: 13442	n:1360000
LRP1   1360000 perm   1187 sec   (1146 perm/sec)   p_kst 9.883824e-03   p_cons 1.477941e-04   p_joint 3.455882e-05

Joint ci ratio: 5.599898e-01	ci left: 2.583326e-05	ci right 4.645305e-05	k: 48	n:1370000
Cons ci ratio: 2.737641e-01	ci left: 1.291727e-04	ci right 1.707990e-04	k: 204	n:1370000
KS ci ratio: 3.352122e-02	ci left: 9.717514e-03	ci right 1.004953e-02	k: 13539	n:1370000
LRP1   1370000 perm   1201 sec   (1141 perm/sec)   p_kst 9.882482e-03   p_cons 1.489051e-04   p_joint 3.503650e-05

Joint ci ratio: 5.599899e-01	ci left: 2.564606e-05	ci right 4.611643e-05	k: 48	n:1380000
Cons ci ratio: 2.730989e-01	ci left: 1.289117e-04	ci right 1.703356e-04	k: 205	n:1380000
KS ci ratio: 3.338945e-02	ci left: 9.723985e-03	ci right 1.005489e-02	k: 13646	n:1380000
LRP1   1380000 perm   1215 sec   (1136 perm/sec)   p_kst 9.888406e-03   p_cons 1.485507e-04   p_joint 3.478261e-05

Joint ci ratio: 5.843494e-01	ci left: 2.300043e-05	ci right 4.249470e-05	k: 44	n:1390000
Cons ci ratio: 2.704852e-01	ci left: 1.306659e-04	ci right 1.721834e-04	k: 209	n:1390000
KS ci ratio: 3.328367e-02	ci left: 9.716096e-03	ci right 1.004566e-02	k: 13733	n:1390000
LRP1   1390000 perm   1229 sec   (1131 perm/sec)   p_kst 9.879856e-03   p_cons 1.503597e-04   p_joint 3.165468e-05

Joint ci ratio: 5.779628e-01	ci left: 2.344531e-05	ci right 4.300944e-05	k: 45	n:1400000
Cons ci ratio: 2.698435e-01	ci left: 1.303985e-04	ci right 1.717161e-04	k: 210	n:1400000
KS ci ratio: 3.315951e-02	ci left: 9.719656e-03	ci right 1.004809e-02	k: 13836	n:1400000
LRP1   1400000 perm   1243 sec   (1126 perm/sec)   p_kst 9.882857e-03   p_cons 1.500000e-04   p_joint 3.214286e-05

Joint ci ratio: 5.779628e-01	ci left: 2.327903e-05	ci right 4.270441e-05	k: 45	n:1410000
Cons ci ratio: 2.692064e-01	ci left: 1.301349e-04	ci right 1.712553e-04	k: 211	n:1410000
KS ci ratio: 3.305469e-02	ci left: 9.712617e-03	ci right 1.003976e-02	k: 13924	n:1410000
LRP1   1410000 perm   1257 sec   (1121 perm/sec)   p_kst 9.875177e-03   p_cons 1.496454e-04   p_joint 3.191489e-05

Joint ci ratio: 5.717811e-01	ci left: 2.371684e-05	ci right 4.320931e-05	k: 46	n:1420000
Cons ci ratio: 2.685737e-01	ci left: 1.298752e-04	ci right 1.708008e-04	k: 212	n:1420000
KS ci ratio: 3.294968e-02	ci left: 9.706376e-03	ci right 1.003225e-02	k: 14013	n:1420000
LRP1   1420000 perm   1272 sec   (1116 perm/sec)   p_kst 9.868310e-03   p_cons 1.492958e-04   p_joint 3.239437e-05

Joint ci ratio: 5.657936e-01	ci left: 2.414963e-05	ci right 4.370608e-05	k: 47	n:1430000
Cons ci ratio: 2.679455e-01	ci left: 1.296193e-04	ci right 1.703526e-04	k: 213	n:1430000
KS ci ratio: 3.282216e-02	ci left: 9.714097e-03	ci right 1.003894e-02	k: 14122	n:1430000
LRP1   1430000 perm   1286 sec   (1112 perm/sec)   p_kst 9.875524e-03   p_cons 1.489510e-04   p_joint 3.286713e-05

Joint ci ratio: 5.657936e-01	ci left: 2.398192e-05	ci right 4.340257e-05	k: 47	n:1440000
Cons ci ratio: 2.648688e-01	ci left: 1.319595e-04	ci right 1.728732e-04	k: 218	n:1440000
KS ci ratio: 3.269727e-02	ci left: 9.721024e-03	ci right 1.004484e-02	k: 14230	n:1440000
LRP1   1440000 perm   1301 sec   (1107 perm/sec)   p_kst 9.881944e-03   p_cons 1.513889e-04   p_joint 3.263889e-05

Joint ci ratio: 5.599903e-01	ci left: 2.440797e-05	ci right 4.389013e-05	k: 48	n:1450000
Cons ci ratio: 2.636675e-01	ci left: 1.323374e-04	ci right 1.731514e-04	k: 220	n:1450000
KS ci ratio: 3.259102e-02	ci left: 9.717597e-03	ci right 1.004023e-02	k: 14323	n:1450000
LRP1   1450000 perm   1316 sec   (1102 perm/sec)   p_kst 9.877931e-03   p_cons 1.517241e-04   p_joint 3.310345e-05

Joint ci ratio: 5.489000e-01	ci left: 2.541857e-05	ci right 4.514959e-05	k: 50	n:1460000
Cons ci ratio: 2.618958e-01	ci left: 1.333505e-04	ci right 1.741553e-04	k: 223	n:1460000
KS ci ratio: 3.248580e-02	ci left: 9.714218e-03	ci right 1.003568e-02	k: 14416	n:1460000
LRP1   1460000 perm   1331 sec   (1097 perm/sec)   p_kst 9.873973e-03   p_cons 1.527397e-04   p_joint 3.424658e-05

Joint ci ratio: 5.435964e-01	ci left: 2.583198e-05	ci right 4.561579e-05	k: 51	n:1470000
Cons ci ratio: 2.601594e-01	ci left: 1.343506e-04	ci right 1.751446e-04	k: 226	n:1470000
KS ci ratio: 3.237821e-02	ci left: 9.712912e-03	ci right 1.003324e-02	k: 14512	n:1470000
LRP1   1470000 perm   1345 sec   (1093 perm/sec)   p_kst 9.872109e-03   p_cons 1.537415e-04   p_joint 3.469388e-05

Joint ci ratio: 4.652071e-01	ci left: 3.687074e-05	ci right 5.975692e-05	k: 70	n:1480000
Cons ci ratio: 2.590208e-01	ci left: 1.347063e-04	ci right 1.754002e-04	k: 228	n:1480000
KS ci ratio: 3.227614e-02	ci left: 9.708943e-03	ci right 1.002811e-02	k: 14604	n:1480000
LRP1   1480000 perm   1360 sec   (1088 perm/sec)   p_kst 9.867568e-03   p_cons 1.540541e-04   p_joint 4.729730e-05

Joint ci ratio: 4.619651e-01	ci left: 3.721601e-05	ci right 6.010489e-05	k: 71	n:1490000
Cons ci ratio: 2.578970e-01	ci left: 1.350575e-04	ci right 1.756521e-04	k: 230	n:1490000
KS ci ratio: 3.215516e-02	ci left: 9.717014e-03	ci right 1.003523e-02	k: 14714	n:1490000
LRP1   1490000 perm   1375 sec   (1084 perm/sec)   p_kst 9.875168e-03   p_cons 1.543624e-04   p_joint 4.765101e-05

Joint ci ratio: 4.619652e-01	ci left: 3.696791e-05	ci right 5.970419e-05	k: 71	n:1500000
Cons ci ratio: 2.567877e-01	ci left: 1.354045e-04	ci right 1.759002e-04	k: 232	n:1500000
KS ci ratio: 3.205737e-02	ci left: 9.711752e-03	ci right 1.002881e-02	k: 14804	n:1500000
LRP1   1500000 perm   1390 sec   (1079 perm/sec)   p_kst 9.869333e-03   p_cons 1.546667e-04   p_joint 4.733333e-05

Joint ci ratio: 4.587901e-01	ci left: 3.730850e-05	ci right 6.004737e-05	k: 72	n:1510000
Cons ci ratio: 2.556926e-01	ci left: 1.357472e-04	ci right 1.761447e-04	k: 234	n:1510000
KS ci ratio: 3.196371e-02	ci left: 9.704590e-03	ci right 1.002047e-02	k: 14891	n:1510000
LRP1   1510000 perm   1405 sec   (1075 perm/sec)   p_kst 9.861589e-03   p_cons 1.549669e-04   p_joint 4.768212e-05

Joint ci ratio: 4.587901e-01	ci left: 3.706305e-05	ci right 5.965232e-05	k: 72	n:1520000
Cons ci ratio: 2.546114e-01	ci left: 1.360858e-04	ci right 1.763856e-04	k: 236	n:1520000
KS ci ratio: 3.184298e-02	ci left: 9.714494e-03	ci right 1.002948e-02	k: 15004	n:1520000
LRP1   1520000 perm   1420 sec   (1070 perm/sec)   p_kst 9.871053e-03   p_cons 1.552632e-04   p_joint 4.736842e-05

Joint ci ratio: 4.587902e-01	ci left: 3.682081e-05	ci right 5.926244e-05	k: 72	n:1530000
Cons ci ratio: 2.535438e-01	ci left: 1.364203e-04	ci right 1.766230e-04	k: 238	n:1530000
KS ci ratio: 3.175331e-02	ci left: 9.706114e-03	ci right 1.001993e-02	k: 15089	n:1530000
LRP1   1530000 perm   1435 sec   (1066 perm/sec)   p_kst 9.862092e-03   p_cons 1.555556e-04   p_joint 4.705882e-05

Joint ci ratio: 6.444361e-01	ci left: 1.637275e-05	ci right 3.236295e-05	k: 36	n:1540000
Cons ci ratio: 2.530151e-01	ci left: 1.361426e-04	ci right 1.761666e-04	k: 239	n:1540000
KS ci ratio: 3.166545e-02	ci left: 9.697199e-03	ci right 1.000984e-02	k: 15173	n:1540000
LRP1   1540000 perm   1451 sec   (1061 perm/sec)   p_kst 9.852597e-03   p_cons 1.551948e-04   p_joint 2.337662e-05

Joint ci ratio: 6.359000e-01	ci left: 1.680742e-05	ci right 3.290284e-05	k: 37	n:1550000
Cons ci ratio: 2.519674e-01	ci left: 1.364729e-04	ci right 1.764018e-04	k: 241	n:1550000
KS ci ratio: 3.155639e-02	ci left: 9.701843e-03	ci right 1.001354e-02	k: 15278	n:1550000
LRP1   1550000 perm   1466 sec   (1057 perm/sec)   p_kst 9.856774e-03   p_cons 1.554839e-04   p_joint 2.387097e-05

Joint ci ratio: 6.359000e-01	ci left: 1.669968e-05	ci right 3.269192e-05	k: 37	n:1560000
Cons ci ratio: 2.499103e-01	ci left: 1.380010e-04	ci right 1.779961e-04	k: 245	n:1560000
KS ci ratio: 3.142268e-02	ci left: 9.722331e-03	ci right 1.003334e-02	k: 15408	n:1560000
LRP1   1560000 perm   1482 sec   (1053 perm/sec)   p_kst 9.876923e-03   p_cons 1.570513e-04   p_joint 2.371795e-05

Joint ci ratio: 6.359001e-01	ci left: 1.659331e-05	ci right 3.248369e-05	k: 37	n:1570000
Cons ci ratio: 2.484001e-01	ci left: 1.389135e-04	ci right 1.788922e-04	k: 248	n:1570000
KS ci ratio: 3.132017e-02	ci left: 9.724232e-03	ci right 1.003427e-02	k: 15509	n:1570000
LRP1   1570000 perm   1498 sec   (1048 perm/sec)   p_kst 9.878344e-03   p_cons 1.579618e-04   p_joint 2.356688e-05

Joint ci ratio: 6.359001e-01	ci left: 1.648829e-05	ci right 3.227810e-05	k: 37	n:1580000
Cons ci ratio: 2.484003e-01	ci left: 1.380343e-04	ci right 1.777600e-04	k: 248	n:1580000
KS ci ratio: 3.122877e-02	ci left: 9.719831e-03	ci right 1.002881e-02	k: 15600	n:1580000
LRP1   1580000 perm   1513 sec   (1044 perm/sec)   p_kst 9.873418e-03   p_cons 1.569620e-04   p_joint 2.341772e-05

Joint ci ratio: 4.438416e-01	ci left: 3.821855e-05	ci right 6.052592e-05	k: 77	n:1590000
Cons ci ratio: 2.469171e-01	ci left: 1.389359e-04	ci right 1.786456e-04	k: 251	n:1590000
KS ci ratio: 3.112915e-02	ci left: 9.721102e-03	ci right 1.002911e-02	k: 15700	n:1590000
LRP1   1590000 perm   1529 sec   (1040 perm/sec)   p_kst 9.874214e-03   p_cons 1.578616e-04   p_joint 4.842767e-05

Joint ci ratio: 4.438416e-01	ci left: 3.797968e-05	ci right 6.014763e-05	k: 77	n:1600000
Cons ci ratio: 2.469173e-01	ci left: 1.380675e-04	ci right 1.775291e-04	k: 251	n:1600000
KS ci ratio: 3.101958e-02	ci left: 9.729182e-03	ci right 1.003635e-02	k: 15811	n:1600000
LRP1   1600000 perm   1545 sec   (1036 perm/sec)   p_kst 9.881875e-03   p_cons 1.568750e-04   p_joint 4.812500e-05

Joint ci ratio: 4.438417e-01	ci left: 3.774378e-05	ci right 5.977405e-05	k: 77	n:1610000
Cons ci ratio: 2.459432e-01	ci left: 1.383755e-04	ci right 1.777452e-04	k: 253	n:1610000
KS ci ratio: 3.091017e-02	ci left: 9.737780e-03	ci right 1.004411e-02	k: 15923	n:1610000
LRP1   1610000 perm   1561 sec   (1031 perm/sec)   p_kst 9.890062e-03   p_cons 1.571429e-04   p_joint 4.782609e-05

Joint ci ratio: 4.410236e-01	ci left: 3.805929e-05	ci right 6.009071e-05	k: 78	n:1620000
Cons ci ratio: 2.454605e-01	ci left: 1.381006e-04	ci right 1.773033e-04	k: 254	n:1620000
KS ci ratio: 3.081647e-02	ci left: 9.737084e-03	ci right 1.004245e-02	k: 16020	n:1620000
LRP1   1620000 perm   1577 sec   (1027 perm/sec)   p_kst 9.888889e-03   p_cons 1.567901e-04   p_joint 4.814815e-05

Joint ci ratio: 4.202568e-01	ci left: 4.220199e-05	ci right 6.515868e-05	k: 86	n:1630000
Cons ci ratio: 2.445035e-01	ci left: 1.384051e-04	ci right 1.775177e-04	k: 256	n:1630000
KS ci ratio: 3.070823e-02	ci left: 9.746140e-03	ci right 1.005070e-02	k: 16133	n:1630000
LRP1   1630000 perm   1593 sec   (1023 perm/sec)   p_kst 9.897546e-03   p_cons 1.570552e-04   p_joint 5.276074e-05

Joint ci ratio: 4.202568e-01	ci left: 4.194466e-05	ci right 6.476137e-05	k: 86	n:1640000
Cons ci ratio: 2.426225e-01	ci left: 1.398513e-04	ci right 1.790228e-04	k: 260	n:1640000
KS ci ratio: 3.060588e-02	ci left: 9.752062e-03	ci right 1.005577e-02	k: 16241	n:1640000
LRP1   1640000 perm   1609 sec   (1019 perm/sec)   p_kst 9.903049e-03   p_cons 1.585366e-04   p_joint 5.243902e-05

Joint ci ratio: 4.202569e-01	ci left: 4.169045e-05	ci right 6.436888e-05	k: 86	n:1650000
Cons ci ratio: 2.416982e-01	ci left: 1.401423e-04	ci right 1.792234e-04	k: 262	n:1650000
KS ci ratio: 3.049607e-02	ci left: 9.763327e-03	ci right 1.006628e-02	k: 16358	n:1650000
LRP1   1650000 perm   1625 sec   (1015 perm/sec)   p_kst 9.913939e-03   p_cons 1.587879e-04   p_joint 5.212121e-05

Joint ci ratio: 4.202570e-01	ci left: 4.143930e-05	ci right 6.398112e-05	k: 86	n:1660000
Cons ci ratio: 2.416983e-01	ci left: 1.392981e-04	ci right 1.781437e-04	k: 262	n:1660000
KS ci ratio: 3.039582e-02	ci left: 9.769077e-03	ci right 1.007119e-02	k: 16466	n:1660000
LRP1   1660000 perm   1641 sec   (1011 perm/sec)   p_kst 9.919277e-03   p_cons 1.578313e-04   p_joint 5.180723e-05

Joint ci ratio: 4.178623e-01	ci left: 4.172681e-05	ci right 6.425960e-05	k: 87	n:1670000
Cons ci ratio: 2.403314e-01	ci left: 1.401519e-04	ci right 1.789817e-04	k: 265	n:1670000
KS ci ratio: 3.030671e-02	ci left: 9.768223e-03	ci right 1.006941e-02	k: 16563	n:1670000
LRP1   1670000 perm   1658 sec   (1007 perm/sec)   p_kst 9.917964e-03   p_cons 1.586826e-04   p_joint 5.209581e-05

Joint ci ratio: 4.178623e-01	ci left: 4.147844e-05	ci right 6.387710e-05	k: 87	n:1680000
Cons ci ratio: 2.385444e-01	ci left: 1.415558e-04	ci right 1.804398e-04	k: 269	n:1680000
KS ci ratio: 3.021472e-02	ci left: 9.769743e-03	ci right 1.007005e-02	k: 16664	n:1680000
LRP1   1680000 perm   1674 sec   (1003 perm/sec)   p_kst 9.919048e-03   p_cons 1.601190e-04   p_joint 5.178571e-05

Joint ci ratio: 4.178624e-01	ci left: 4.123300e-05	ci right 6.349913e-05	k: 87	n:1690000
Cons ci ratio: 2.385445e-01	ci left: 1.407182e-04	ci right 1.793721e-04	k: 269	n:1690000
KS ci ratio: 3.012446e-02	ci left: 9.770659e-03	ci right 1.007008e-02	k: 16764	n:1690000
LRP1   1690000 perm   1691 sec   (999 perm/sec)   p_kst 9.919527e-03   p_cons 1.591716e-04   p_joint 5.147929e-05

Joint ci ratio: 4.178625e-01	ci left: 4.099045e-05	ci right 6.312561e-05	k: 87	n:1700000
Cons ci ratio: 2.385446e-01	ci left: 1.398904e-04	ci right 1.783170e-04	k: 269	n:1700000
KS ci ratio: 3.003141e-02	ci left: 9.773901e-03	ci right 1.007248e-02	k: 16868	n:1700000
LRP1   1700000 perm   1708 sec   (995 perm/sec)   p_kst 9.922353e-03   p_cons 1.582353e-04   p_joint 5.117647e-05

Joint ci ratio: 4.155082e-01	ci left: 4.127422e-05	ci right 6.340223e-05	k: 88	n:1710000
Cons ci ratio: 2.385447e-01	ci left: 1.390723e-04	ci right 1.772742e-04	k: 269	n:1710000
KS ci ratio: 2.995616e-02	ci left: 9.766078e-03	ci right 1.006366e-02	k: 16953	n:1710000
LRP1   1710000 perm   1725 sec   (992 perm/sec)   p_kst 9.914035e-03   p_cons 1.573099e-04   p_joint 5.146199e-05

Joint ci ratio: 4.302654e-01	ci left: 3.791705e-05	ci right 5.917618e-05	k: 82	n:1720000
Cons ci ratio: 2.372303e-01	ci left: 1.399040e-04	ci right 1.780915e-04	k: 272	n:1720000
KS ci ratio: 2.985052e-02	ci left: 9.778545e-03	ci right 1.007543e-02	k: 17073	n:1720000
LRP1   1720000 perm   1741 sec   (988 perm/sec)   p_kst 9.926163e-03   p_cons 1.581395e-04   p_joint 4.767442e-05

Joint ci ratio: 4.251731e-01	ci left: 3.872948e-05	ci right 6.011394e-05	k: 84	n:1730000
Cons ci ratio: 2.372304e-01	ci left: 1.390953e-04	ci right 1.770621e-04	k: 272	n:1730000
KS ci ratio: 2.976436e-02	ci left: 9.778821e-03	ci right 1.007485e-02	k: 17172	n:1730000
LRP1   1730000 perm   1758 sec   (984 perm/sec)   p_kst 9.926012e-03   p_cons 1.572254e-04   p_joint 4.855491e-05

Joint ci ratio: 4.251732e-01	ci left: 3.850690e-05	ci right 5.976846e-05	k: 84	n:1740000
Cons ci ratio: 2.346654e-01	ci left: 1.415404e-04	ci right 1.796962e-04	k: 278	n:1740000
KS ci ratio: 2.967373e-02	ci left: 9.782518e-03	ci right 1.007774e-02	k: 17277	n:1740000
LRP1   1740000 perm   1776 sec   (980 perm/sec)   p_kst 9.929310e-03   p_cons 1.597701e-04   p_joint 4.827586e-05

Joint ci ratio: 4.251732e-01	ci left: 3.828685e-05	ci right 5.942693e-05	k: 84	n:1750000
Cons ci ratio: 2.342460e-01	ci left: 1.412694e-04	ci right 1.792743e-04	k: 279	n:1750000
KS ci ratio: 2.959769e-02	ci left: 9.777097e-03	ci right 1.007139e-02	k: 17366	n:1750000
LRP1   1750000 perm   1793 sec   (976 perm/sec)   p_kst 9.923429e-03   p_cons 1.594286e-04   p_joint 4.800000e-05

Joint ci ratio: 4.178628e-01	ci left: 3.959304e-05	ci right 6.097361e-05	k: 87	n:1760000
Cons ci ratio: 2.338289e-01	ci left: 1.410016e-04	ci right 1.788571e-04	k: 280	n:1760000
KS ci ratio: 2.952052e-02	ci left: 9.772868e-03	ci right 1.006625e-02	k: 17457	n:1760000
LRP1   1760000 perm   1810 sec   (973 perm/sec)   p_kst 9.918750e-03   p_cons 1.590909e-04   p_joint 4.943182e-05

Joint ci ratio: 4.155086e-01	ci left: 3.987509e-05	ci right 6.125301e-05	k: 88	n:1770000
Cons ci ratio: 2.334139e-01	ci left: 1.407369e-04	ci right 1.784446e-04	k: 281	n:1770000
KS ci ratio: 2.943971e-02	ci left: 9.771491e-03	ci right 1.006401e-02	k: 17553	n:1770000
LRP1   1770000 perm   1827 sec   (969 perm/sec)   p_kst 9.916949e-03   p_cons 1.587571e-04   p_joint 4.971751e-05

Joint ci ratio: 4.155087e-01	ci left: 3.965107e-05	ci right 6.090890e-05	k: 88	n:1780000
Cons ci ratio: 2.334140e-01	ci left: 1.399463e-04	ci right 1.774421e-04	k: 281	n:1780000
KS ci ratio: 2.935537e-02	ci left: 9.772920e-03	ci right 1.006463e-02	k: 17654	n:1780000
LRP1   1780000 perm   1844 sec   (966 perm/sec)   p_kst 9.917978e-03   p_cons 1.578652e-04   p_joint 4.943820e-05

Joint ci ratio: 4.155087e-01	ci left: 3.942955e-05	ci right 6.056863e-05	k: 88	n:1790000
Cons ci ratio: 2.325907e-01	ci left: 1.402165e-04	ci right 1.776332e-04	k: 283	n:1790000
KS ci ratio: 2.926842e-02	ci left: 9.776552e-03	ci right 1.006749e-02	k: 17759	n:1790000
LRP1   1790000 perm   1861 sec   (962 perm/sec)   p_kst 9.921229e-03   p_cons 1.581006e-04   p_joint 4.916201e-05

Joint ci ratio: 4.155088e-01	ci left: 3.921050e-05	ci right 6.023214e-05	k: 88	n:1800000
Cons ci ratio: 2.321823e-01	ci left: 1.399608e-04	ci right 1.772342e-04	k: 284	n:1800000
KS ci ratio: 2.917481e-02	ci left: 9.785109e-03	ci right 1.007536e-02	k: 17873	n:1800000
LRP1   1800000 perm   1878 sec   (959 perm/sec)   p_kst 9.929444e-03   p_cons 1.577778e-04   p_joint 4.888889e-05

Joint ci ratio: 4.155088e-01	ci left: 3.899386e-05	ci right 5.989936e-05	k: 88	n:1810000
Cons ci ratio: 2.309698e-01	ci left: 1.407488e-04	ci right 1.780085e-04	k: 287	n:1810000
KS ci ratio: 2.909435e-02	ci left: 9.785346e-03	ci right 1.007479e-02	k: 17972	n:1810000
LRP1   1810000 perm   1895 sec   (955 perm/sec)   p_kst 9.929282e-03   p_cons 1.585635e-04   p_joint 4.861878e-05

Joint ci ratio: 4.155089e-01	ci left: 3.877961e-05	ci right 5.957025e-05	k: 88	n:1820000
Cons ci ratio: 2.305699e-01	ci left: 1.404932e-04	ci right 1.776116e-04	k: 288	n:1820000
KS ci ratio: 2.899997e-02	ci left: 9.795399e-03	ci right 1.008419e-02	k: 18089	n:1820000
LRP1   1820000 perm   1913 sec   (952 perm/sec)   p_kst 9.939011e-03   p_cons 1.582418e-04   p_joint 4.835165e-05

Joint ci ratio: 4.131940e-01	ci left: 3.905718e-05	ci right 5.984784e-05	k: 89	n:1830000
Cons ci ratio: 2.301720e-01	ci left: 1.402403e-04	ci right 1.772190e-04	k: 289	n:1830000
KS ci ratio: 2.890169e-02	ci left: 9.808600e-03	ci right 1.009678e-02	k: 18212	n:1830000
LRP1   1830000 perm   1930 sec   (948 perm/sec)   p_kst 9.951913e-03   p_cons 1.579235e-04   p_joint 4.863388e-05

Joint ci ratio: 4.086779e-01	ci left: 3.981949e-05	ci right 6.072131e-05	k: 91	n:1840000
Cons ci ratio: 2.282129e-01	ci left: 1.420396e-04	ci right 1.791289e-04	k: 294	n:1840000
KS ci ratio: 2.882108e-02	ci left: 9.810328e-03	ci right 1.009774e-02	k: 18314	n:1840000
LRP1   1840000 perm   1948 sec   (945 perm/sec)   p_kst 9.953261e-03   p_cons 1.597826e-04   p_joint 4.945652e-05

Joint ci ratio: 4.086780e-01	ci left: 3.960425e-05	ci right 6.039309e-05	k: 91	n:1850000
Cons ci ratio: 2.274431e-01	ci left: 1.422912e-04	ci right 1.793033e-04	k: 296	n:1850000
KS ci ratio: 2.873090e-02	ci left: 9.819014e-03	ci right 1.010577e-02	k: 18429	n:1850000
LRP1   1850000 perm   1965 sec   (941 perm/sec)   p_kst 9.961622e-03   p_cons 1.600000e-04   p_joint 4.918919e-05

Joint ci ratio: 4.086780e-01	ci left: 3.939132e-05	ci right 6.006839e-05	k: 91	n:1860000
Cons ci ratio: 2.259267e-01	ci left: 1.435546e-04	ci right 1.806118e-04	k: 300	n:1860000
KS ci ratio: 2.865092e-02	ci left: 9.821203e-03	ci right 1.010721e-02	k: 18532	n:1860000
LRP1   1860000 perm   1983 sec   (938 perm/sec)   p_kst 9.963441e-03   p_cons 1.612903e-04   p_joint 4.892473e-05

Joint ci ratio: 4.064748e-01	ci left: 3.966060e-05	ci right 6.033647e-05	k: 92	n:1870000
Cons ci ratio: 2.251798e-01	ci left: 1.437960e-04	ci right 1.807758e-04	k: 302	n:1870000
KS ci ratio: 2.858556e-02	ci left: 9.813812e-03	ci right 1.009894e-02	k: 18617	n:1870000
LRP1   1870000 perm   2001 sec   (935 perm/sec)   p_kst 9.955615e-03   p_cons 1.614973e-04   p_joint 4.919786e-05

Joint ci ratio: 4.064749e-01	ci left: 3.944964e-05	ci right 6.001554e-05	k: 92	n:1880000
Cons ci ratio: 2.244403e-01	ci left: 1.440351e-04	ci right 1.809378e-04	k: 304	n:1880000
KS ci ratio: 2.852372e-02	ci left: 9.804388e-03	ci right 1.008861e-02	k: 18698	n:1880000
LRP1   1880000 perm   2018 sec   (932 perm/sec)   p_kst 9.945745e-03   p_cons 1.617021e-04   p_joint 4.893617e-05

Joint ci ratio: 4.064750e-01	ci left: 3.924091e-05	ci right 5.969800e-05	k: 92	n:1890000
Cons ci ratio: 2.237080e-01	ci left: 1.442718e-04	ci right 1.810980e-04	k: 306	n:1890000
KS ci ratio: 2.845310e-02	ci left: 9.801368e-03	ci right 1.008479e-02	k: 18791	n:1890000
LRP1   1890000 perm   2036 sec   (928 perm/sec)   p_kst 9.942328e-03   p_cons 1.619048e-04   p_joint 4.867725e-05

Joint ci ratio: 4.043070e-01	ci left: 3.950702e-05	ci right 5.996350e-05	k: 93	n:1900000
Cons ci ratio: 2.226228e-01	ci left: 1.450032e-04	ci right 1.818119e-04	k: 309	n:1900000
KS ci ratio: 2.838528e-02	ci left: 9.796814e-03	ci right 1.007942e-02	k: 18881	n:1900000
LRP1   1900000 perm   2054 sec   (925 perm/sec)   p_kst 9.937368e-03   p_cons 1.626316e-04   p_joint 4.894737e-05

Joint ci ratio: 4.043071e-01	ci left: 3.930018e-05	ci right 5.964956e-05	k: 93	n:1910000
Cons ci ratio: 2.219081e-01	ci left: 1.452328e-04	ci right 1.819653e-04	k: 311	n:1910000
KS ci ratio: 2.831870e-02	ci left: 9.791788e-03	ci right 1.007358e-02	k: 18970	n:1910000
LRP1   1910000 perm   2073 sec   (921 perm/sec)   p_kst 9.931937e-03   p_cons 1.628272e-04   p_joint 4.869110e-05

Joint ci ratio: 4.043071e-01	ci left: 3.909549e-05	ci right 5.933889e-05	k: 93	n:1920000
Cons ci ratio: 2.219082e-01	ci left: 1.444764e-04	ci right 1.810176e-04	k: 311	n:1920000
KS ci ratio: 2.825782e-02	ci left: 9.783195e-03	ci right 1.006412e-02	k: 19052	n:1920000
LRP1   1920000 perm   2091 sec   (918 perm/sec)   p_kst 9.922917e-03   p_cons 1.619792e-04   p_joint 4.843750e-05

Joint ci ratio: 4.043072e-01	ci left: 3.889292e-05	ci right 5.903143e-05	k: 93	n:1930000
Cons ci ratio: 2.208489e-01	ci left: 1.451960e-04	ci right 1.817201e-04	k: 314	n:1930000
KS ci ratio: 2.818469e-02	ci left: 9.783438e-03	ci right 1.006363e-02	k: 19151	n:1930000
LRP1   1930000 perm   2109 sec   (915 perm/sec)   p_kst 9.922798e-03   p_cons 1.626943e-04   p_joint 4.818653e-05

Joint ci ratio: 4.043072e-01	ci left: 3.869244e-05	ci right 5.872715e-05	k: 93	n:1940000
Cons ci ratio: 2.204992e-01	ci left: 1.449346e-04	ci right 1.813273e-04	k: 315	n:1940000
KS ci ratio: 2.810328e-02	ci left: 9.789822e-03	ci right 1.006938e-02	k: 19262	n:1940000
LRP1   1940000 perm   2127 sec   (912 perm/sec)   p_kst 9.928866e-03   p_cons 1.623711e-04   p_joint 4.793814e-05

Joint ci ratio: 4.043073e-01	ci left: 3.849401e-05	ci right 5.842599e-05	k: 93	n:1950000
Cons ci ratio: 2.204993e-01	ci left: 1.441913e-04	ci right 1.803975e-04	k: 315	n:1950000
KS ci ratio: 2.803866e-02	ci left: 9.784938e-03	ci right 1.006370e-02	k: 19351	n:1950000
LRP1   1950000 perm   2145 sec   (909 perm/sec)   p_kst 9.923590e-03   p_cons 1.615385e-04   p_joint 4.769231e-05

Joint ci ratio: 4.000734e-01	ci left: 3.921480e-05	ci right 5.925099e-05	k: 95	n:1960000
Cons ci ratio: 2.191167e-01	ci left: 1.453841e-04	ci right 1.816300e-04	k: 319	n:1960000
KS ci ratio: 2.795633e-02	ci left: 9.792772e-03	ci right 1.007092e-02	k: 19465	n:1960000
LRP1   1960000 perm   2164 sec   (906 perm/sec)   p_kst 9.931122e-03   p_cons 1.627551e-04   p_joint 4.846939e-05

Joint ci ratio: 4.000735e-01	ci left: 3.901574e-05	ci right 5.895023e-05	k: 95	n:1970000
Cons ci ratio: 2.184351e-01	ci left: 1.456057e-04	ci right 1.817788e-04	k: 321	n:1970000
KS ci ratio: 2.788048e-02	ci left: 9.796494e-03	ci right 1.007398e-02	k: 19571	n:1970000
LRP1   1970000 perm   2182 sec   (903 perm/sec)   p_kst 9.934518e-03   p_cons 1.629442e-04   p_joint 4.822335e-05

Joint ci ratio: 3.980058e-01	ci left: 3.927305e-05	ci right 5.920798e-05	k: 96	n:1980000
Cons ci ratio: 2.184352e-01	ci left: 1.448703e-04	ci right 1.808608e-04	k: 321	n:1980000
KS ci ratio: 2.781380e-02	ci left: 9.794161e-03	ci right 1.007091e-02	k: 19665	n:1980000
LRP1   1980000 perm   2200 sec   (900 perm/sec)   p_kst 9.931818e-03   p_cons 1.621212e-04   p_joint 4.848485e-05

Joint ci ratio: 3.980059e-01	ci left: 3.907570e-05	ci right 5.891046e-05	k: 96	n:1990000
Cons ci ratio: 2.180969e-01	ci left: 1.446174e-04	ci right 1.804819e-04	k: 322	n:1990000
KS ci ratio: 2.773768e-02	ci left: 9.798839e-03	ci right 1.007495e-02	k: 19773	n:1990000
LRP1   1990000 perm   2219 sec   (897 perm/sec)   p_kst 9.936181e-03   p_cons 1.618090e-04   p_joint 4.824121e-05

Joint ci ratio: 3.980059e-01	ci left: 3.888032e-05	ci right 5.861590e-05	k: 96	n:2000000
Cons ci ratio: 2.180970e-01	ci left: 1.438943e-04	ci right 1.795795e-04	k: 322	n:2000000
KS ci ratio: 2.766359e-02	ci left: 9.802478e-03	ci right 1.007794e-02	k: 19879	n:2000000
LRP1   2000000 perm   2237 sec   (894 perm/sec)   p_kst 9.939500e-03   p_cons 1.610000e-04   p_joint 4.800000e-05

Joint ci ratio: 3.980060e-01	ci left: 3.868689e-05	ci right 5.832428e-05	k: 96	n:2010000
Cons ci ratio: 2.174248e-01	ci left: 1.441192e-04	ci right 1.797352e-04	k: 324	n:2010000
KS ci ratio: 2.760125e-02	ci left: 9.798176e-03	ci right 1.007289e-02	k: 19969	n:2010000
LRP1   2010000 perm   2255 sec   (891 perm/sec)   p_kst 9.934826e-03   p_cons 1.611940e-04   p_joint 4.776119e-05

Joint ci ratio: 3.980060e-01	ci left: 3.849537e-05	ci right 5.803555e-05	k: 96	n:2020000
Cons ci ratio: 2.170911e-01	ci left: 1.438738e-04	ci right 1.793674e-04	k: 325	n:2020000
KS ci ratio: 2.752962e-02	ci left: 9.800800e-03	ci right 1.007486e-02	k: 20073	n:2020000
LRP1   2020000 perm   2274 sec   (888 perm/sec)   p_kst 9.937129e-03   p_cons 1.608911e-04   p_joint 4.752475e-05

Joint ci ratio: 3.939651e-01	ci left: 3.919285e-05	ci right 5.883250e-05	k: 98	n:2030000
Cons ci ratio: 2.164283e-01	ci left: 1.440968e-04	ci right 1.795224e-04	k: 327	n:2030000
KS ci ratio: 2.745787e-02	ci left: 9.803889e-03	ci right 1.007731e-02	k: 20178	n:2030000
LRP1   2030000 perm   2293 sec   (885 perm/sec)   p_kst 9.939901e-03   p_cons 1.610837e-04   p_joint 4.827586e-05

Joint ci ratio: 3.939652e-01	ci left: 3.900072e-05	ci right 5.854411e-05	k: 98	n:2040000
Cons ci ratio: 2.151204e-01	ci left: 1.452453e-04	ci right 1.807090e-04	k: 331	n:2040000
KS ci ratio: 2.739008e-02	ci left: 9.804515e-03	ci right 1.007727e-02	k: 20278	n:2040000
LRP1   2040000 perm   2312 sec   (882 perm/sec)   p_kst 9.940196e-03   p_cons 1.622549e-04   p_joint 4.803922e-05

Joint ci ratio: 3.919903e-01	ci left: 3.925008e-05	ci right 5.879430e-05	k: 99	n:2050000
Cons ci ratio: 2.151205e-01	ci left: 1.445368e-04	ci right 1.798275e-04	k: 331	n:2050000
KS ci ratio: 2.732482e-02	ci left: 9.803681e-03	ci right 1.007575e-02	k: 20375	n:2050000
LRP1   2050000 perm   2331 sec   (880 perm/sec)   p_kst 9.939024e-03   p_cons 1.614634e-04   p_joint 4.829268e-05

Joint ci ratio: 3.900449e-01	ci left: 3.949725e-05	ci right 5.904182e-05	k: 100	n:2060000
Cons ci ratio: 2.144754e-01	ci left: 1.447538e-04	ci right 1.799776e-04	k: 333	n:2060000
KS ci ratio: 2.726138e-02	ci left: 9.801892e-03	ci right 1.007327e-02	k: 20470	n:2060000
LRP1   2060000 perm   2350 sec   (877 perm/sec)   p_kst 9.936893e-03   p_cons 1.616505e-04   p_joint 4.854369e-05

Joint ci ratio: 3.900450e-01	ci left: 3.930644e-05	ci right 5.875660e-05	k: 100	n:2070000
Cons ci ratio: 2.138361e-01	ci left: 1.449689e-04	ci right 1.801260e-04	k: 335	n:2070000
KS ci ratio: 2.720505e-02	ci left: 9.795323e-03	ci right 1.006595e-02	k: 20555	n:2070000
LRP1   2070000 perm   2369 sec   (874 perm/sec)   p_kst 9.929952e-03   p_cons 1.618357e-04   p_joint 4.830918e-05

Joint ci ratio: 3.881282e-01	ci left: 3.955121e-05	ci right 5.900169e-05	k: 101	n:2080000
Cons ci ratio: 2.138362e-01	ci left: 1.442719e-04	ci right 1.792601e-04	k: 335	n:2080000
KS ci ratio: 2.714774e-02	ci left: 9.789772e-03	ci right 1.005967e-02	k: 20642	n:2080000
LRP1   2080000 perm   2388 sec   (871 perm/sec)   p_kst 9.924038e-03   p_cons 1.610577e-04   p_joint 4.855769e-05

Joint ci ratio: 3.881283e-01	ci left: 3.936197e-05	ci right 5.871939e-05	k: 101	n:2090000
Cons ci ratio: 2.135187e-01	ci left: 1.440345e-04	ci right 1.789064e-04	k: 336	n:2090000
KS ci ratio: 2.708420e-02	ci left: 9.789028e-03	ci right 1.005827e-02	k: 20739	n:2090000
LRP1   2090000 perm   2408 sec   (868 perm/sec)   p_kst 9.922967e-03   p_cons 1.607656e-04   p_joint 4.832536e-05

Joint ci ratio: 3.862395e-01	ci left: 3.960436e-05	ci right 5.896209e-05	k: 102	n:2100000
Cons ci ratio: 2.132027e-01	ci left: 1.437993e-04	ci right 1.785561e-04	k: 337	n:2100000
KS ci ratio: 2.702110e-02	ci left: 9.788292e-03	ci right 1.005687e-02	k: 20836	n:2100000
LRP1   2100000 perm   2427 sec   (865 perm/sec)   p_kst 9.921905e-03   p_cons 1.604762e-04   p_joint 4.857143e-05

Joint ci ratio: 3.843781e-01	ci left: 3.984469e-05	ci right 5.920228e-05	k: 103	n:2110000
Cons ci ratio: 2.128880e-01	ci left: 1.435665e-04	ci right 1.782090e-04	k: 338	n:2110000
KS ci ratio: 2.694349e-02	ci left: 9.798391e-03	ci right 1.006646e-02	k: 20956	n:2110000
LRP1   2110000 perm   2447 sec   (862 perm/sec)   p_kst 9.931754e-03   p_cons 1.601896e-04   p_joint 4.881517e-05

Joint ci ratio: 3.825433e-01	ci left: 4.008297e-05	ci right 5.943998e-05	k: 104	n:2120000
Cons ci ratio: 2.119522e-01	ci left: 1.442291e-04	ci right 1.788586e-04	k: 341	n:2120000
KS ci ratio: 2.687234e-02	ci left: 9.804178e-03	ci right 1.007169e-02	k: 21067	n:2120000
LRP1   2120000 perm   2467 sec   (859 perm/sec)   p_kst 9.937264e-03   p_cons 1.608491e-04   p_joint 4.905660e-05

Joint ci ratio: 3.825433e-01	ci left: 3.989479e-05	ci right 5.916092e-05	k: 104	n:2130000
Cons ci ratio: 2.110286e-01	ci left: 1.448858e-04	ci right 1.795019e-04	k: 344	n:2130000
KS ci ratio: 2.680048e-02	ci left: 9.810846e-03	ci right 1.007781e-02	k: 21180	n:2130000
LRP1   2130000 perm   2486 sec   (857 perm/sec)   p_kst 9.943662e-03   p_cons 1.615023e-04   p_joint 4.882629e-05

Joint ci ratio: 3.825434e-01	ci left: 3.970836e-05	ci right 5.888447e-05	k: 104	n:2140000
Cons ci ratio: 2.107234e-01	ci left: 1.446514e-04	ci right 1.791550e-04	k: 345	n:2140000
KS ci ratio: 2.673173e-02	ci left: 9.815595e-03	ci right 1.008200e-02	k: 21289	n:2140000
LRP1   2140000 perm   2506 sec   (854 perm/sec)   p_kst 9.948131e-03   p_cons 1.612150e-04   p_joint 4.859813e-05

Joint ci ratio: 3.825434e-01	ci left: 3.952367e-05	ci right 5.861059e-05	k: 104	n:2150000
Cons ci ratio: 2.104196e-01	ci left: 1.444192e-04	ci right 1.788113e-04	k: 346	n:2150000
KS ci ratio: 2.665972e-02	ci left: 9.823072e-03	ci right 1.008895e-02	k: 21404	n:2150000
LRP1   2150000 perm   2526 sec   (851 perm/sec)   p_kst 9.955349e-03   p_cons 1.609302e-04   p_joint 4.837209e-05

Joint ci ratio: 3.825434e-01	ci left: 3.934069e-05	ci right 5.833924e-05	k: 104	n:2160000
Cons ci ratio: 2.092171e-01	ci left: 1.455051e-04	ci right 1.799325e-04	k: 350	n:2160000
KS ci ratio: 2.658705e-02	ci left: 9.831402e-03	ci right 1.009677e-02	k: 21521	n:2160000
LRP1   2160000 perm   2546 sec   (848 perm/sec)   p_kst 9.963426e-03   p_cons 1.620370e-04   p_joint 4.814815e-05

Joint ci ratio: 3.807347e-01	ci left: 3.957602e-05	ci right 5.857523e-05	k: 105	n:2170000
Cons ci ratio: 2.089197e-01	ci left: 1.452713e-04	ci right 1.795883e-04	k: 351	n:2170000
KS ci ratio: 2.652364e-02	ci left: 9.833246e-03	ci right 1.009802e-02	k: 21624	n:2170000
LRP1   2170000 perm   2566 sec   (846 perm/sec)   p_kst 9.964977e-03   p_cons 1.617512e-04   p_joint 4.838710e-05

Joint ci ratio: 3.807347e-01	ci left: 3.939447e-05	ci right 5.830654e-05	k: 105	n:2180000
Cons ci ratio: 2.086236e-01	ci left: 1.450397e-04	ci right 1.792471e-04	k: 352	n:2180000
KS ci ratio: 2.645514e-02	ci left: 9.839176e-03	ci right 1.010341e-02	k: 21736	n:2180000
LRP1   2180000 perm   2586 sec   (843 perm/sec)   p_kst 9.970642e-03   p_cons 1.614679e-04   p_joint 4.816514e-05

Joint ci ratio: 3.807348e-01	ci left: 3.921459e-05	ci right 5.804030e-05	k: 105	n:2190000
Cons ci ratio: 2.080351e-01	ci left: 1.452430e-04	ci right 1.793895e-04	k: 354	n:2190000
KS ci ratio: 2.641038e-02	ci left: 9.827814e-03	ci right 1.009129e-02	k: 21810	n:2190000
LRP1   2190000 perm   2607 sec   (840 perm/sec)   p_kst 9.958904e-03   p_cons 1.616438e-04   p_joint 4.794521e-05

Joint ci ratio: 3.771928e-01	ci left: 3.985884e-05	ci right 5.877177e-05	k: 107	n:2200000
Cons ci ratio: 2.080352e-01	ci left: 1.445828e-04	ci right 1.785741e-04	k: 354	n:2200000
KS ci ratio: 2.635916e-02	ci left: 9.821523e-03	ci right 1.008431e-02	k: 21895	n:2200000
LRP1   2200000 perm   2627 sec   (837 perm/sec)   p_kst 9.952273e-03   p_cons 1.609091e-04   p_joint 4.863636e-05

Joint ci ratio: 3.771929e-01	ci left: 3.967848e-05	ci right 5.850583e-05	k: 107	n:2210000
Cons ci ratio: 2.080352e-01	ci left: 1.439286e-04	ci right 1.777660e-04	k: 354	n:2210000
KS ci ratio: 2.630159e-02	ci left: 9.820235e-03	ci right 1.008241e-02	k: 21991	n:2210000
LRP1   2210000 perm   2647 sec   (835 perm/sec)   p_kst 9.950679e-03   p_cons 1.601810e-04   p_joint 4.841629e-05

Joint ci ratio: 3.754586e-01	ci left: 3.990759e-05	ci right 5.873516e-05	k: 108	n:2220000
Cons ci ratio: 2.080353e-01	ci left: 1.432802e-04	ci right 1.769653e-04	k: 354	n:2220000
KS ci ratio: 2.624379e-02	ci left: 9.819406e-03	ci right 1.008097e-02	k: 22088	n:2220000
LRP1   2220000 perm   2668 sec   (832 perm/sec)   p_kst 9.949550e-03   p_cons 1.594595e-04   p_joint 4.864865e-05

Joint ci ratio: 3.737480e-01	ci left: 4.013485e-05	ci right 5.896223e-05	k: 109	n:2230000
Cons ci ratio: 2.068730e-01	ci left: 1.443383e-04	ci right 1.780585e-04	k: 358	n:2230000
KS ci ratio: 2.618816e-02	ci left: 9.817249e-03	ci right 1.007820e-02	k: 22182	n:2230000
LRP1   2230000 perm   2689 sec   (829 perm/sec)   p_kst 9.947085e-03   p_cons 1.605381e-04   p_joint 4.887892e-05

Joint ci ratio: 3.737481e-01	ci left: 3.995567e-05	ci right 5.869901e-05	k: 109	n:2240000
Cons ci ratio: 2.068731e-01	ci left: 1.436939e-04	ci right 1.772636e-04	k: 358	n:2240000
KS ci ratio: 2.613406e-02	ci left: 9.814225e-03	ci right 1.007454e-02	k: 22274	n:2240000
LRP1   2240000 perm   2709 sec   (827 perm/sec)   p_kst 9.943750e-03   p_cons 1.598214e-04   p_joint 4.866071e-05

Joint ci ratio: 3.737481e-01	ci left: 3.977809e-05	ci right 5.843813e-05	k: 109	n:2250000
Cons ci ratio: 2.057300e-01	ci left: 1.447412e-04	ci right 1.783452e-04	k: 362	n:2250000
KS ci ratio: 2.606971e-02	ci left: 9.819176e-03	ci right 1.007898e-02	k: 22384	n:2250000
LRP1   2250000 perm   2731 sec   (824 perm/sec)   p_kst 9.948444e-03   p_cons 1.608889e-04   p_joint 4.844444e-05

Joint ci ratio: 3.737482e-01	ci left: 3.960208e-05	ci right 5.817955e-05	k: 109	n:2260000
Cons ci ratio: 2.051656e-01	ci left: 1.449402e-04	ci right 1.784865e-04	k: 364	n:2260000
KS ci ratio: 2.601518e-02	ci left: 9.817050e-03	ci right 1.007624e-02	k: 22478	n:2260000
LRP1   2260000 perm   2751 sec   (821 perm/sec)   p_kst 9.946018e-03   p_cons 1.610619e-04   p_joint 4.823009e-05

Joint ci ratio: 3.720608e-01	ci left: 3.982687e-05	ci right 5.840488e-05	k: 110	n:2270000
Cons ci ratio: 2.051656e-01	ci left: 1.443017e-04	ci right 1.777002e-04	k: 364	n:2270000
KS ci ratio: 2.595983e-02	ci left: 9.815819e-03	ci right 1.007442e-02	k: 22574	n:2270000
LRP1   2270000 perm   2772 sec   (819 perm/sec)   p_kst 9.944493e-03   p_cons 1.603524e-04   p_joint 4.845815e-05

Joint ci ratio: 3.703960e-01	ci left: 4.004987e-05	ci right 5.862806e-05	k: 111	n:2280000
Cons ci ratio: 2.046058e-01	ci left: 1.445010e-04	ci right 1.778430e-04	k: 366	n:2280000
KS ci ratio: 2.590482e-02	ci left: 9.814600e-03	ci right 1.007261e-02	k: 22670	n:2280000
LRP1   2280000 perm   2793 sec   (816 perm/sec)   p_kst 9.942982e-03   p_cons 1.605263e-04   p_joint 4.868421e-05

Joint ci ratio: 3.703960e-01	ci left: 3.987498e-05	ci right 5.837204e-05	k: 111	n:2290000
Cons ci ratio: 2.040506e-01	ci left: 1.446986e-04	ci right 1.779844e-04	k: 368	n:2290000
KS ci ratio: 2.584788e-02	ci left: 9.815127e-03	ci right 1.007258e-02	k: 22770	n:2290000
LRP1   2290000 perm   2814 sec   (814 perm/sec)   p_kst 9.943231e-03   p_cons 1.606987e-04   p_joint 4.847162e-05

Joint ci ratio: 3.703961e-01	ci left: 3.970161e-05	ci right 5.811825e-05	k: 111	n:2300000
Cons ci ratio: 2.037747e-01	ci left: 1.444821e-04	ci right 1.776675e-04	k: 369	n:2300000
KS ci ratio: 2.579757e-02	ci left: 9.810898e-03	ci right 1.006773e-02	k: 22859	n:2300000
LRP1   2300000 perm   2835 sec   (811 perm/sec)   p_kst 9.938696e-03   p_cons 1.604348e-04   p_joint 4.826087e-05

Joint ci ratio: 3.671325e-01	ci left: 4.031531e-05	ci right 5.881233e-05	k: 113	n:2310000
Cons ci ratio: 2.032261e-01	ci left: 1.446783e-04	ci right 1.778082e-04	k: 371	n:2310000
KS ci ratio: 2.574642e-02	ci left: 9.807566e-03	ci right 1.006379e-02	k: 22950	n:2310000
LRP1   2310000 perm   2856 sec   (809 perm/sec)   p_kst 9.935065e-03   p_cons 1.606061e-04   p_joint 4.891775e-05

Joint ci ratio: 3.639537e-01	ci left: 4.092443e-05	ci right 5.949974e-05	k: 115	n:2320000
Cons ci ratio: 2.032262e-01	ci left: 1.440547e-04	ci right 1.770418e-04	k: 371	n:2320000
KS ci ratio: 2.568657e-02	ci left: 9.811117e-03	ci right 1.006683e-02	k: 23057	n:2320000
LRP1   2320000 perm   2878 sec   (806 perm/sec)   p_kst 9.938362e-03   p_cons 1.599138e-04   p_joint 4.956897e-05

Joint ci ratio: 3.639537e-01	ci left: 4.074879e-05	ci right 5.924438e-05	k: 115	n:2330000
Cons ci ratio: 2.029536e-01	ci left: 1.438438e-04	ci right 1.767329e-04	k: 372	n:2330000
KS ci ratio: 2.563217e-02	ci left: 9.810799e-03	ci right 1.006596e-02	k: 23155	n:2330000
LRP1   2330000 perm   2899 sec   (804 perm/sec)   p_kst 9.937768e-03   p_cons 1.596567e-04   p_joint 4.935622e-05

Joint ci ratio: 3.623950e-01	ci left: 4.096301e-05	ci right 5.945738e-05	k: 116	n:2340000
Cons ci ratio: 2.024117e-01	ci left: 1.440404e-04	ci right 1.768757e-04	k: 374	n:2340000
KS ci ratio: 2.557145e-02	ci left: 9.815581e-03	ci right 1.007025e-02	k: 23265	n:2340000
LRP1   2340000 perm   2920 sec   (801 perm/sec)   p_kst 9.942308e-03   p_cons 1.598291e-04   p_joint 4.957265e-05

Joint ci ratio: 3.608561e-01	ci left: 4.117557e-05	ci right 5.966840e-05	k: 117	n:2350000
Cons ci ratio: 2.016068e-01	ci left: 1.446395e-04	ci right 1.774641e-04	k: 377	n:2350000
KS ci ratio: 2.551777e-02	ci left: 9.815248e-03	ci right 1.006937e-02	k: 23363	n:2350000
LRP1   2350000 perm   2941 sec   (799 perm/sec)   p_kst 9.941702e-03   p_cons 1.604255e-04   p_joint 4.978723e-05

Joint ci ratio: 3.608562e-01	ci left: 4.100109e-05	ci right 5.941557e-05	k: 117	n:2360000
Cons ci ratio: 2.008114e-01	ci left: 1.452338e-04	ci right 1.780473e-04	k: 380	n:2360000
KS ci ratio: 2.545402e-02	ci left: 9.822919e-03	ci right 1.007659e-02	k: 23480	n:2360000
LRP1   2360000 perm   2963 sec   (796 perm/sec)   p_kst 9.949153e-03   p_cons 1.610169e-04   p_joint 4.957627e-05

Joint ci ratio: 3.608562e-01	ci left: 4.082809e-05	ci right 5.916487e-05	k: 117	n:2370000
Cons ci ratio: 2.002864e-01	ci left: 1.454225e-04	ci right 1.781822e-04	k: 382	n:2370000
KS ci ratio: 2.539020e-02	ci left: 9.830945e-03	ci right 1.008418e-02	k: 23598	n:2370000
LRP1   2370000 perm   2985 sec   (794 perm/sec)   p_kst 9.956962e-03   p_cons 1.611814e-04   p_joint 4.936709e-05

Joint ci ratio: 3.608562e-01	ci left: 4.065655e-05	ci right 5.891628e-05	k: 117	n:2380000
Cons ci ratio: 1.995065e-01	ci left: 1.460089e-04	ci right 1.787571e-04	k: 385	n:2380000
KS ci ratio: 2.533657e-02	ci left: 9.831389e-03	ci right 1.008409e-02	k: 23698	n:2380000
LRP1   2380000 perm   3007 sec   (792 perm/sec)   p_kst 9.957143e-03   p_cons 1.617647e-04   p_joint 4.915966e-05

Joint ci ratio: 3.608563e-01	ci left: 4.048643e-05	ci right 5.866977e-05	k: 117	n:2390000
Cons ci ratio: 1.992486e-01	ci left: 1.457955e-04	ci right 1.784484e-04	k: 386	n:2390000
KS ci ratio: 2.527524e-02	ci left: 9.838067e-03	ci right 1.009032e-02	k: 23813	n:2390000
LRP1   2390000 perm   3029 sec   (789 perm/sec)   p_kst 9.963598e-03   p_cons 1.615063e-04   p_joint 4.895397e-05

Joint ci ratio: 3.593368e-01	ci left: 4.069671e-05	ci right 5.887952e-05	k: 118	n:2400000
Cons ci ratio: 1.987357e-01	ci left: 1.459798e-04	ci right 1.785797e-04	k: 388	n:2400000
KS ci ratio: 2.522394e-02	ci left: 9.837236e-03	ci right 1.008895e-02	k: 23910	n:2400000
LRP1   2400000 perm   3051 sec   (787 perm/sec)   p_kst 9.962500e-03   p_cons 1.616667e-04   p_joint 4.916667e-05

Joint ci ratio: 3.593369e-01	ci left: 4.052785e-05	ci right 5.863520e-05	k: 118	n:2410000
Cons ci ratio: 1.984808e-01	ci left: 1.457684e-04	ci right 1.782742e-04	k: 389	n:2410000
KS ci ratio: 2.517294e-02	ci left: 9.836413e-03	ci right 1.008759e-02	k: 24007	n:2410000
LRP1   2410000 perm   3073 sec   (784 perm/sec)   p_kst 9.961411e-03   p_cons 1.614108e-04   p_joint 4.896266e-05

Joint ci ratio: 3.578365e-01	ci left: 4.073638e-05	ci right 5.884320e-05	k: 119	n:2420000
Cons ci ratio: 1.982269e-01	ci left: 1.455587e-04	ci right 1.779713e-04	k: 390	n:2420000
KS ci ratio: 2.512278e-02	ci left: 9.835187e-03	ci right 1.008582e-02	k: 24103	n:2420000
LRP1   2420000 perm   3095 sec   (782 perm/sec)   p_kst 9.959917e-03   p_cons 1.611570e-04   p_joint 4.917355e-05

Joint ci ratio: 3.578365e-01	ci left: 4.056874e-05	ci right 5.860105e-05	k: 119	n:2430000
Cons ci ratio: 1.979739e-01	ci left: 1.453509e-04	ci right 1.776708e-04	k: 391	n:2430000
KS ci ratio: 2.507554e-02	ci left: 9.831926e-03	ci right 1.008200e-02	k: 24194	n:2430000
LRP1   2430000 perm   3117 sec   (780 perm/sec)   p_kst 9.956379e-03   p_cons 1.609053e-04   p_joint 4.897119e-05

Joint ci ratio: 3.563547e-01	ci left: 4.077554e-05	ci right 5.880733e-05	k: 120	n:2440000
Cons ci ratio: 1.977219e-01	ci left: 1.451447e-04	ci right 1.773727e-04	k: 392	n:2440000
KS ci ratio: 2.502283e-02	ci left: 9.833173e-03	ci right 1.008275e-02	k: 24296	n:2440000
LRP1   2440000 perm   3139 sec   (777 perm/sec)   p_kst 9.957377e-03   p_cons 1.606557e-04   p_joint 4.918033e-05

Joint ci ratio: 3.563548e-01	ci left: 4.060911e-05	ci right 5.856731e-05	k: 120	n:2450000
Cons ci ratio: 1.974708e-01	ci left: 1.449402e-04	ci right 1.770771e-04	k: 393	n:2450000
KS ci ratio: 2.496220e-02	ci left: 9.840900e-03	ci right 1.009006e-02	k: 24414	n:2450000
LRP1   2450000 perm   3162 sec   (775 perm/sec)   p_kst 9.964898e-03   p_cons 1.604082e-04   p_joint 4.897959e-05

Joint ci ratio: 3.548913e-01	ci left: 4.081422e-05	ci right 5.877190e-05	k: 121	n:2460000
Cons ci ratio: 1.969715e-01	ci left: 1.451239e-04	ci right 1.772104e-04	k: 395	n:2460000
KS ci ratio: 2.492047e-02	ci left: 9.834021e-03	ci right 1.008258e-02	k: 24496	n:2460000
LRP1   2460000 perm   3184 sec   (773 perm/sec)   p_kst 9.957724e-03   p_cons 1.605691e-04   p_joint 4.918699e-05

Joint ci ratio: 3.548913e-01	ci left: 4.064898e-05	ci right 5.853396e-05	k: 121	n:2470000
Cons ci ratio: 1.969716e-01	ci left: 1.445364e-04	ci right 1.764929e-04	k: 395	n:2470000
KS ci ratio: 2.487334e-02	ci left: 9.831625e-03	ci right 1.007965e-02	k: 24589	n:2470000
LRP1   2470000 perm   3207 sec   (770 perm/sec)   p_kst 9.955061e-03   p_cons 1.599190e-04   p_joint 4.898785e-05

Joint ci ratio: 3.548913e-01	ci left: 4.048508e-05	ci right 5.829793e-05	k: 121	n:2480000
Cons ci ratio: 1.967234e-01	ci left: 1.443369e-04	ci right 1.762043e-04	k: 396	n:2480000
KS ci ratio: 2.481429e-02	ci left: 9.838866e-03	ci right 1.008647e-02	k: 24706	n:2480000
LRP1   2480000 perm   3229 sec   (768 perm/sec)   p_kst 9.962097e-03   p_cons 1.596774e-04   p_joint 4.879032e-05

Joint ci ratio: 3.548914e-01	ci left: 4.032248e-05	ci right 5.806381e-05	k: 121	n:2490000
Cons ci ratio: 1.962297e-01	ci left: 1.445209e-04	ci right 1.763394e-04	k: 398	n:2490000
KS ci ratio: 2.476725e-02	ci left: 9.836870e-03	ci right 1.008395e-02	k: 24800	n:2490000
LRP1   2490000 perm   3252 sec   (766 perm/sec)   p_kst 9.959839e-03   p_cons 1.598394e-04   p_joint 4.859438e-05

Joint ci ratio: 3.398980e-01	ci left: 4.417751e-05	ci right 6.261376e-05	k: 132	n:2500000
Cons ci ratio: 1.952533e-01	ci left: 1.454644e-04	ci right 1.773123e-04	k: 402	n:2500000
KS ci ratio: 2.471195e-02	ci left: 9.841648e-03	ci right 1.008829e-02	k: 24911	n:2500000
LRP1   2500000 perm   3274 sec   (763 perm/sec)   p_kst 9.964400e-03   p_cons 1.608000e-04   p_joint 5.280000e-05

Joint ci ratio: 3.398980e-01	ci left: 4.400150e-05	ci right 6.236430e-05	k: 132	n:2510000
Cons ci ratio: 1.950116e-01	ci left: 1.452638e-04	ci right 1.770237e-04	k: 403	n:2510000
KS ci ratio: 2.465603e-02	ci left: 9.847180e-03	ci right 1.009339e-02	k: 25024	n:2510000
LRP1   2510000 perm   3297 sec   (761 perm/sec)   p_kst 9.969721e-03   p_cons 1.605578e-04   p_joint 5.258964e-05

Joint ci ratio: 3.386274e-01	ci left: 4.418991e-05	ci right 6.254733e-05	k: 133	n:2520000
Cons ci ratio: 1.947707e-01	ci left: 1.450649e-04	ci right 1.767374e-04	k: 404	n:2520000
KS ci ratio: 2.459801e-02	ci left: 9.854642e-03	ci right 1.010045e-02	k: 25142	n:2520000
LRP1   2520000 perm   3320 sec   (759 perm/sec)   p_kst 9.976984e-03   p_cons 1.603175e-04   p_joint 5.277778e-05

Joint ci ratio: 3.373708e-01	ci left: 4.437696e-05	ci right 6.272878e-05	k: 134	n:2530000
Cons ci ratio: 1.942915e-01	ci left: 1.452435e-04	ci right 1.768678e-04	k: 406	n:2530000
KS ci ratio: 2.455415e-02	ci left: 9.851045e-03	ci right 1.009632e-02	k: 25232	n:2530000
LRP1   2530000 perm   3343 sec   (757 perm/sec)   p_kst 9.973123e-03   p_cons 1.604743e-04   p_joint 5.296443e-05

Joint ci ratio: 3.373709e-01	ci left: 4.420225e-05	ci right 6.248182e-05	k: 134	n:2540000
Cons ci ratio: 1.933437e-01	ci left: 1.461701e-04	ci right 1.778226e-04	k: 410	n:2540000
KS ci ratio: 2.450076e-02	ci left: 9.855303e-03	ci right 1.010015e-02	k: 25342	n:2540000
LRP1   2540000 perm   3366 sec   (755 perm/sec)   p_kst 9.977165e-03   p_cons 1.614173e-04   p_joint 5.275591e-05

Joint ci ratio: 3.373709e-01	ci left: 4.402891e-05	ci right 6.223679e-05	k: 134	n:2550000
Cons ci ratio: 1.931089e-01	ci left: 1.459700e-04	ci right 1.775364e-04	k: 411	n:2550000
KS ci ratio: 2.445207e-02	ci left: 9.856020e-03	ci right 1.010039e-02	k: 25443	n:2550000
LRP1   2550000 perm   3389 sec   (752 perm/sec)   p_kst 9.977647e-03   p_cons 1.611765e-04   p_joint 5.254902e-05

Joint ci ratio: 3.348992e-01	ci left: 4.457224e-05	ci right 6.284062e-05	k: 136	n:2560000
Cons ci ratio: 1.931090e-01	ci left: 1.453998e-04	ci right 1.768429e-04	k: 411	n:2560000
KS ci ratio: 2.440513e-02	ci left: 9.855568e-03	ci right 1.009945e-02	k: 25541	n:2560000
LRP1   2560000 perm   3412 sec   (750 perm/sec)   p_kst 9.976953e-03   p_cons 1.605469e-04   p_joint 5.312500e-05

Joint ci ratio: 3.336835e-01	ci left: 4.475525e-05	ci right 6.301775e-05	k: 137	n:2570000
Cons ci ratio: 1.926419e-01	ci left: 1.455747e-04	ci right 1.769705e-04	k: 413	n:2570000
KS ci ratio: 2.435461e-02	ci left: 9.858213e-03	ci right 1.010165e-02	k: 25647	n:2570000
LRP1   2570000 perm   3436 sec   (748 perm/sec)   p_kst 9.979377e-03   p_cons 1.607004e-04   p_joint 5.330739e-05

Joint ci ratio: 3.336836e-01	ci left: 4.458178e-05	ci right 6.277350e-05	k: 137	n:2580000
Cons ci ratio: 1.921783e-01	ci left: 1.457483e-04	ci right 1.770971e-04	k: 415	n:2580000
KS ci ratio: 2.430966e-02	ci left: 9.856601e-03	ci right 1.009954e-02	k: 25742	n:2580000
LRP1   2580000 perm   3459 sec   (746 perm/sec)   p_kst 9.977519e-03   p_cons 1.608527e-04   p_joint 5.310078e-05

Joint ci ratio: 3.336836e-01	ci left: 4.440965e-05	ci right 6.253113e-05	k: 137	n:2590000
Cons ci ratio: 1.919477e-01	ci left: 1.455531e-04	ci right 1.768179e-04	k: 416	n:2590000
KS ci ratio: 2.426116e-02	ci left: 9.858071e-03	ci right 1.010056e-02	k: 25845	n:2590000
LRP1   2590000 perm   3483 sec   (744 perm/sec)   p_kst 9.978764e-03   p_cons 1.606178e-04   p_joint 5.289575e-05

Joint ci ratio: 3.336836e-01	ci left: 4.423885e-05	ci right 6.229063e-05	k: 137	n:2600000
Cons ci ratio: 1.919478e-01	ci left: 1.449933e-04	ci right 1.761379e-04	k: 416	n:2600000
KS ci ratio: 2.421389e-02	ci left: 9.858766e-03	ci right 1.010079e-02	k: 25946	n:2600000
LRP1   2600000 perm   3506 sec   (742 perm/sec)   p_kst 9.979231e-03   p_cons 1.600000e-04   p_joint 5.269231e-05

Joint ci ratio: 3.336837e-01	ci left: 4.406935e-05	ci right 6.205197e-05	k: 137	n:2610000
Cons ci ratio: 1.917181e-01	ci left: 1.448025e-04	ci right 1.758645e-04	k: 417	n:2610000
KS ci ratio: 2.417251e-02	ci left: 9.854886e-03	ci right 1.009639e-02	k: 26035	n:2610000
LRP1   2610000 perm   3529 sec   (739 perm/sec)   p_kst 9.975096e-03   p_cons 1.597701e-04   p_joint 5.249042e-05

Joint ci ratio: 3.312916e-01	ci left: 4.460079e-05	ci right 6.264197e-05	k: 139	n:2620000
Cons ci ratio: 1.912610e-01	ci left: 1.449766e-04	ci right 1.759932e-04	k: 419	n:2620000
KS ci ratio: 2.413042e-02	ci left: 9.851795e-03	ci right 1.009280e-02	k: 26126	n:2620000
LRP1   2620000 perm   3553 sec   (737 perm/sec)   p_kst 9.971756e-03   p_cons 1.599237e-04   p_joint 5.305344e-05

Joint ci ratio: 3.289501e-01	ci left: 4.512864e-05	ci right 6.322705e-05	k: 141	n:2630000
Cons ci ratio: 1.912611e-01	ci left: 1.444254e-04	ci right 1.753240e-04	k: 419	n:2630000
KS ci ratio: 2.408252e-02	ci left: 9.853641e-03	ci right 1.009421e-02	k: 26230	n:2630000
LRP1   2630000 perm   3576 sec   (735 perm/sec)   p_kst 9.973384e-03   p_cons 1.593156e-04   p_joint 5.361217e-05

Joint ci ratio: 3.277979e-01	ci left: 4.530527e-05	ci right 6.339745e-05	k: 142	n:2640000
Cons ci ratio: 1.908073e-01	ci left: 1.445996e-04	ci right 1.754537e-04	k: 421	n:2640000
KS ci ratio: 2.403582e-02	ci left: 9.854721e-03	ci right 1.009484e-02	k: 26332	n:2640000
LRP1   2640000 perm   3600 sec   (733 perm/sec)   p_kst 9.974242e-03   p_cons 1.594697e-04   p_joint 5.378788e-05

Joint ci ratio: 3.266577e-01	ci left: 4.548067e-05	ci right 6.356646e-05	k: 143	n:2650000
Cons ci ratio: 1.901326e-01	ci left: 1.451321e-04	ci right 1.759776e-04	k: 424	n:2650000
KS ci ratio: 2.399673e-02	ci left: 9.849791e-03	ci right 1.008939e-02	k: 26418	n:2650000
LRP1   2650000 perm   3624 sec   (731 perm/sec)   p_kst 9.969057e-03   p_cons 1.600000e-04   p_joint 5.396226e-05

Joint ci ratio: 3.255293e-01	ci left: 4.565485e-05	ci right 6.373410e-05	k: 144	n:2660000
Cons ci ratio: 1.894651e-01	ci left: 1.456607e-04	ci right 1.764974e-04	k: 427	n:2660000
KS ci ratio: 2.395327e-02	ci left: 9.848636e-03	ci right 1.008777e-02	k: 26514	n:2660000
LRP1   2660000 perm   3647 sec   (729 perm/sec)   p_kst 9.967669e-03   p_cons 1.605263e-04   p_joint 5.413534e-05

Joint ci ratio: 3.255294e-01	ci left: 4.548386e-05	ci right 6.349539e-05	k: 144	n:2670000
Cons ci ratio: 1.894651e-01	ci left: 1.451152e-04	ci right 1.758363e-04	k: 427	n:2670000
KS ci ratio: 2.391004e-02	ci left: 9.847489e-03	ci right 1.008616e-02	k: 26610	n:2670000
LRP1   2670000 perm   3671 sec   (727 perm/sec)   p_kst 9.966292e-03   p_cons 1.599251e-04   p_joint 5.393258e-05

Joint ci ratio: 3.244126e-01	ci left: 4.565685e-05	ci right 6.366194e-05	k: 145	n:2680000
Cons ci ratio: 1.888045e-01	ci left: 1.456401e-04	ci right 1.763526e-04	k: 430	n:2680000
KS ci ratio: 2.385892e-02	ci left: 9.853028e-03	ci right 1.009132e-02	k: 26724	n:2680000
LRP1   2680000 perm   3694 sec   (725 perm/sec)   p_kst 9.971642e-03   p_cons 1.604478e-04   p_joint 5.410448e-05

Joint ci ratio: 3.244126e-01	ci left: 4.548712e-05	ci right 6.342528e-05	k: 145	n:2690000
Cons ci ratio: 1.885859e-01	ci left: 1.454529e-04	ci right 1.760863e-04	k: 431	n:2690000
KS ci ratio: 2.380455e-02	ci left: 9.861484e-03	ci right 1.009942e-02	k: 26846	n:2690000
LRP1   2690000 perm   3718 sec   (724 perm/sec)   p_kst 9.979926e-03   p_cons 1.602230e-04   p_joint 5.390335e-05

Joint ci ratio: 3.244127e-01	ci left: 4.531865e-05	ci right 6.319037e-05	k: 145	n:2700000
Cons ci ratio: 1.883680e-01	ci left: 1.452670e-04	ci right 1.758219e-04	k: 432	n:2700000
KS ci ratio: 2.376613e-02	ci left: 9.856990e-03	ci right 1.009443e-02	k: 26933	n:2700000
LRP1   2700000 perm   3742 sec   (722 perm/sec)   p_kst 9.975185e-03   p_cons 1.600000e-04   p_joint 5.370370e-05

Joint ci ratio: 3.244127e-01	ci left: 4.515142e-05	ci right 6.295720e-05	k: 145	n:2710000
Cons ci ratio: 1.879345e-01	ci left: 1.454342e-04	ci right 1.759459e-04	k: 434	n:2710000
KS ci ratio: 2.371948e-02	ci left: 9.859500e-03	ci right 1.009653e-02	k: 27039	n:2710000
LRP1   2710000 perm   3765 sec   (720 perm/sec)   p_kst 9.977491e-03   p_cons 1.601476e-04   p_joint 5.350554e-05

Joint ci ratio: 3.233074e-01	ci left: 4.532318e-05	ci right 6.312317e-05	k: 146	n:2720000
Cons ci ratio: 1.875039e-01	ci left: 1.456003e-04	ci right 1.760688e-04	k: 436	n:2720000
KS ci ratio: 2.367221e-02	ci left: 9.862722e-03	ci right 1.009935e-02	k: 27147	n:2720000
LRP1   2720000 perm   3788 sec   (718 perm/sec)   p_kst 9.980515e-03   p_cons 1.602941e-04   p_joint 5.367647e-05

Joint ci ratio: 3.222132e-01	ci left: 4.549379e-05	ci right 6.328782e-05	k: 147	n:2730000
Cons ci ratio: 1.875040e-01	ci left: 1.450670e-04	ci right 1.754239e-04	k: 436	n:2730000
KS ci ratio: 2.363005e-02	ci left: 9.861916e-03	ci right 1.009810e-02	k: 27244	n:2730000
LRP1   2730000 perm   3812 sec   (716 perm/sec)   p_kst 9.979487e-03   p_cons 1.597070e-04   p_joint 5.384615e-05

Joint ci ratio: 3.222133e-01	ci left: 4.532775e-05	ci right 6.305684e-05	k: 147	n:2740000
Cons ci ratio: 1.875040e-01	ci left: 1.445375e-04	ci right 1.747836e-04	k: 436	n:2740000
KS ci ratio: 2.358854e-02	ci left: 9.860753e-03	ci right 1.009649e-02	k: 27340	n:2740000
LRP1   2740000 perm   3836 sec   (714 perm/sec)   p_kst 9.978102e-03   p_cons 1.591241e-04   p_joint 5.364964e-05

Joint ci ratio: 3.211302e-01	ci left: 4.549721e-05	ci right 6.322044e-05	k: 148	n:2750000
Cons ci ratio: 1.875041e-01	ci left: 1.440119e-04	ci right 1.741481e-04	k: 436	n:2750000
KS ci ratio: 2.354769e-02	ci left: 9.859238e-03	ci right 1.009452e-02	k: 27435	n:2750000
LRP1   2750000 perm   3860 sec   (712 perm/sec)   p_kst 9.976364e-03   p_cons 1.585455e-04   p_joint 5.381818e-05

Joint ci ratio: 3.211302e-01	ci left: 4.533236e-05	ci right 6.299138e-05	k: 148	n:2760000
Cons ci ratio: 1.870765e-01	ci left: 1.441808e-04	ci right 1.742757e-04	k: 438	n:2760000
KS ci ratio: 2.351309e-02	ci left: 9.852691e-03	ci right 1.008747e-02	k: 27516	n:2760000
LRP1   2760000 perm   3885 sec   (710 perm/sec)   p_kst 9.969565e-03   p_cons 1.586957e-04   p_joint 5.362319e-05

Joint ci ratio: 3.211302e-01	ci left: 4.516870e-05	ci right 6.276398e-05	k: 148	n:2770000
Cons ci ratio: 1.870765e-01	ci left: 1.436603e-04	ci right 1.736465e-04	k: 438	n:2770000
KS ci ratio: 2.347520e-02	ci left: 9.849062e-03	ci right 1.008337e-02	k: 27605	n:2770000
LRP1   2770000 perm   3909 sec   (709 perm/sec)   p_kst 9.965704e-03   p_cons 1.581227e-04   p_joint 5.342960e-05

Joint ci ratio: 3.189964e-01	ci left: 4.566786e-05	ci right 6.331523e-05	k: 150	n:2780000
Cons ci ratio: 1.864405e-01	ci left: 1.441722e-04	ci right 1.741514e-04	k: 441	n:2780000
KS ci ratio: 2.343151e-02	ci left: 9.850467e-03	ci right 1.008437e-02	k: 27708	n:2780000
LRP1   2780000 perm   3934 sec   (707 perm/sec)   p_kst 9.966906e-03   p_cons 1.586331e-04   p_joint 5.395683e-05

Joint ci ratio: 3.169045e-01	ci left: 4.616383e-05	ci right 6.386215e-05	k: 152	n:2790000
Cons ci ratio: 1.862300e-01	ci left: 1.439972e-04	ci right 1.739023e-04	k: 442	n:2790000
KS ci ratio: 2.338170e-02	ci left: 9.857208e-03	ci right 1.009076e-02	k: 27826	n:2790000
LRP1   2790000 perm   3959 sec   (705 perm/sec)   p_kst 9.973477e-03   p_cons 1.584229e-04   p_joint 5.448029e-05

Joint ci ratio: 3.169045e-01	ci left: 4.599896e-05	ci right 6.363407e-05	k: 152	n:2800000
Cons ci ratio: 1.860202e-01	ci left: 1.438234e-04	ci right 1.736550e-04	k: 443	n:2800000
KS ci ratio: 2.333896e-02	ci left: 9.858219e-03	ci right 1.009137e-02	k: 27928	n:2800000
LRP1   2800000 perm   3984 sec   (703 perm/sec)   p_kst 9.974286e-03   p_cons 1.582143e-04   p_joint 5.428571e-05

Joint ci ratio: 3.169045e-01	ci left: 4.583526e-05	ci right 6.340762e-05	k: 152	n:2810000
Cons ci ratio: 1.858111e-01	ci left: 1.436509e-04	ci right 1.734095e-04	k: 444	n:2810000
KS ci ratio: 2.330443e-02	ci left: 9.852502e-03	ci right 1.008516e-02	k: 28011	n:2810000
LRP1   2810000 perm   4008 sec   (701 perm/sec)   p_kst 9.968327e-03   p_cons 1.580071e-04   p_joint 5.409253e-05

Joint ci ratio: 3.158739e-01	ci left: 4.599918e-05	ci right 6.356544e-05	k: 153	n:2820000
Cons ci ratio: 1.851878e-01	ci left: 1.441559e-04	ci right 1.739077e-04	k: 447	n:2820000
KS ci ratio: 2.326586e-02	ci left: 9.850350e-03	ci right 1.008257e-02	k: 28104	n:2820000
LRP1   2820000 perm   4033 sec   (699 perm/sec)   p_kst 9.965957e-03   p_cons 1.585106e-04   p_joint 5.425532e-05

Joint ci ratio: 3.158740e-01	ci left: 4.583664e-05	ci right 6.334083e-05	k: 153	n:2830000
Cons ci ratio: 1.851879e-01	ci left: 1.436465e-04	ci right 1.732932e-04	k: 447	n:2830000
KS ci ratio: 2.322417e-02	ci left: 9.851025e-03	ci right 1.008284e-02	k: 28205	n:2830000
LRP1   2830000 perm   4058 sec   (697 perm/sec)   p_kst 9.966431e-03   p_cons 1.579505e-04   p_joint 5.406360e-05

Joint ci ratio: 3.148533e-01	ci left: 4.599949e-05	ci right 6.349769e-05	k: 154	n:2840000
Cons ci ratio: 1.849816e-01	ci left: 1.434765e-04	ci right 1.730514e-04	k: 448	n:2840000
KS ci ratio: 2.318724e-02	ci left: 9.847844e-03	ci right 1.007921e-02	k: 28295	n:2840000
LRP1   2840000 perm   4083 sec   (695 perm/sec)   p_kst 9.963028e-03   p_cons 1.577465e-04   p_joint 5.422535e-05

Joint ci ratio: 3.148534e-01	ci left: 4.583809e-05	ci right 6.327489e-05	k: 154	n:2850000
Cons ci ratio: 1.841630e-01	ci left: 1.443118e-04	ci right 1.739125e-04	k: 452	n:2850000
KS ci ratio: 2.314473e-02	ci left: 9.849571e-03	ci right 1.008055e-02	k: 28399	n:2850000
LRP1   2850000 perm   4109 sec   (694 perm/sec)   p_kst 9.964561e-03   p_cons 1.585965e-04   p_joint 5.403509e-05

Joint ci ratio: 3.138426e-01	ci left: 4.599988e-05	ci right 6.343079e-05	k: 155	n:2860000
Cons ci ratio: 1.839601e-01	ci left: 1.441407e-04	ci right 1.736702e-04	k: 453	n:2860000
KS ci ratio: 2.310614e-02	ci left: 9.848156e-03	ci right 1.007871e-02	k: 28494	n:2860000
LRP1   2860000 perm   4134 sec   (692 perm/sec)   p_kst 9.962937e-03   p_cons 1.583916e-04   p_joint 5.419580e-05

Joint ci ratio: 3.138426e-01	ci left: 4.583961e-05	ci right 6.320978e-05	k: 155	n:2870000
Cons ci ratio: 1.835562e-01	ci left: 1.443033e-04	ci right 1.737939e-04	k: 455	n:2870000
KS ci ratio: 2.306407e-02	ci left: 9.849870e-03	ci right 1.008004e-02	k: 28598	n:2870000
LRP1   2870000 perm   4159 sec   (690 perm/sec)   p_kst 9.964460e-03   p_cons 1.585366e-04   p_joint 5.400697e-05

Joint ci ratio: 3.138426e-01	ci left: 4.568044e-05	ci right 6.299030e-05	k: 155	n:2880000
Cons ci ratio: 1.829553e-01	ci left: 1.447961e-04	ci right 1.742799e-04	k: 458	n:2880000
KS ci ratio: 2.302061e-02	ci left: 9.852953e-03	ci right 1.008276e-02	k: 28706	n:2880000
LRP1   2880000 perm   4184 sec   (688 perm/sec)   p_kst 9.967361e-03   p_cons 1.590278e-04   p_joint 5.381944e-05

Joint ci ratio: 3.138427e-01	ci left: 4.552237e-05	ci right 6.277235e-05	k: 155	n:2890000
Cons ci ratio: 1.829554e-01	ci left: 1.442951e-04	ci right 1.736768e-04	k: 458	n:2890000
KS ci ratio: 2.297981e-02	ci left: 9.853951e-03	ci right 1.008336e-02	k: 28808	n:2890000
LRP1   2890000 perm   4210 sec   (687 perm/sec)   p_kst 9.968166e-03   p_cons 1.584775e-04   p_joint 5.363322e-05

Joint ci ratio: 3.128415e-01	ci left: 4.568312e-05	ci right 6.292774e-05	k: 156	n:2900000
Cons ci ratio: 1.827564e-01	ci left: 1.441266e-04	ci right 1.734385e-04	k: 459	n:2900000
KS ci ratio: 2.293963e-02	ci left: 9.854600e-03	ci right 1.008362e-02	k: 28909	n:2900000
LRP1   2900000 perm   4235 sec   (685 perm/sec)   p_kst 9.968621e-03   p_cons 1.582759e-04   p_joint 5.379310e-05

Joint ci ratio: 3.233079e-01	ci left: 4.236393e-05	ci right 5.900174e-05	k: 146	n:2910000
Cons ci ratio: 1.825581e-01	ci left: 1.439592e-04	ci right 1.732019e-04	k: 460	n:2910000
KS ci ratio: 2.289607e-02	ci left: 9.858319e-03	ci right 1.008699e-02	k: 29019	n:2910000
LRP1   2910000 perm   4261 sec   (683 perm/sec)   p_kst 9.972165e-03   p_cons 1.580756e-04   p_joint 5.017182e-05

Joint ci ratio: 3.222138e-01	ci left: 4.253357e-05	ci right 5.916980e-05	k: 147	n:2920000
Cons ci ratio: 1.823604e-01	ci left: 1.437930e-04	ci right 1.729668e-04	k: 461	n:2920000
KS ci ratio: 2.285196e-02	ci left: 9.862695e-03	ci right 1.009102e-02	k: 29131	n:2920000
LRP1   2920000 perm   4287 sec   (681 perm/sec)   p_kst 9.976370e-03   p_cons 1.578767e-04   p_joint 5.034247e-05

Joint ci ratio: 3.222138e-01	ci left: 4.238840e-05	ci right 5.896785e-05	k: 147	n:2930000
Cons ci ratio: 1.821634e-01	ci left: 1.436280e-04	ci right 1.727333e-04	k: 462	n:2930000
KS ci ratio: 2.281679e-02	ci left: 9.859575e-03	ci right 1.008747e-02	k: 29221	n:2930000
LRP1   2930000 perm   4313 sec   (679 perm/sec)   p_kst 9.973038e-03   p_cons 1.576792e-04   p_joint 5.017065e-05

Joint ci ratio: 3.222138e-01	ci left: 4.224422e-05	ci right 5.876728e-05	k: 147	n:2940000
Cons ci ratio: 1.821635e-01	ci left: 1.431395e-04	ci right 1.721458e-04	k: 462	n:2940000
KS ci ratio: 2.278020e-02	ci left: 9.857830e-03	ci right 1.008531e-02	k: 29315	n:2940000
LRP1   2940000 perm   4339 sec   (678 perm/sec)   p_kst 9.971088e-03   p_cons 1.571429e-04   p_joint 5.000000e-05

Joint ci ratio: 3.200585e-01	ci left: 4.272435e-05	ci right 5.930050e-05	k: 149	n:2950000
Cons ci ratio: 1.815761e-01	ci left: 1.436249e-04	ci right 1.726254e-04	k: 465	n:2950000
KS ci ratio: 2.274144e-02	ci left: 9.858119e-03	ci right 1.008522e-02	k: 29415	n:2950000
LRP1   2950000 perm   4365 sec   (676 perm/sec)   p_kst 9.971186e-03   p_cons 1.576271e-04   p_joint 5.050847e-05

Joint ci ratio: 3.200585e-01	ci left: 4.258001e-05	ci right 5.910016e-05	k: 149	n:2960000
Cons ci ratio: 1.813816e-01	ci left: 1.434622e-04	ci right 1.723954e-04	k: 466	n:2960000
KS ci ratio: 2.270405e-02	ci left: 9.857398e-03	ci right 1.008410e-02	k: 29512	n:2960000
LRP1   2960000 perm   4391 sec   (674 perm/sec)   p_kst 9.970270e-03   p_cons 1.574324e-04   p_joint 5.033784e-05

Joint ci ratio: 3.200585e-01	ci left: 4.243664e-05	ci right 5.890117e-05	k: 149	n:2970000
Cons ci ratio: 1.809945e-01	ci left: 1.436220e-04	ci right 1.725189e-04	k: 468	n:2970000
KS ci ratio: 2.266182e-02	ci left: 9.861036e-03	ci right 1.008740e-02	k: 29622	n:2970000
LRP1   2970000 perm   4418 sec   (672 perm/sec)   p_kst 9.973737e-03   p_cons 1.575758e-04   p_joint 5.016835e-05

Joint ci ratio: 3.189969e-01	ci left: 4.260290e-05	ci right 5.906591e-05	k: 150	n:2980000
Cons ci ratio: 1.808018e-01	ci left: 1.434604e-04	ci right 1.722907e-04	k: 469	n:2980000
KS ci ratio: 2.262174e-02	ci left: 9.862980e-03	ci right 1.008898e-02	k: 29727	n:2980000
LRP1   2980000 perm   4444 sec   (671 perm/sec)   p_kst 9.975503e-03   p_cons 1.573826e-04   p_joint 5.033557e-05

Joint ci ratio: 3.189970e-01	ci left: 4.246041e-05	ci right 5.886836e-05	k: 150	n:2990000
Cons ci ratio: 1.806098e-01	ci left: 1.432999e-04	ci right 1.720640e-04	k: 470	n:2990000
KS ci ratio: 2.258685e-02	ci left: 9.860589e-03	ci right 1.008618e-02	k: 29819	n:2990000
LRP1   2990000 perm   4471 sec   (669 perm/sec)   p_kst 9.972910e-03   p_cons 1.571906e-04   p_joint 5.016722e-05

Joint ci ratio: 3.189970e-01	ci left: 4.231888e-05	ci right 5.867213e-05	k: 150	n:3000000
Cons ci ratio: 1.798477e-01	ci left: 1.440955e-04	ci right 1.728839e-04	k: 474	n:3000000
KS ci ratio: 2.255250e-02	ci left: 9.857882e-03	ci right 1.008306e-02	k: 29910	n:3000000
LRP1   3000000 perm   4498 sec   (667 perm/sec)   p_kst 9.970000e-03   p_cons 1.580000e-04   p_joint 5.000000e-05

Joint ci ratio: 3.189970e-01	ci left: 4.217828e-05	ci right 5.847721e-05	k: 150	n:3010000
Cons ci ratio: 1.794702e-01	ci left: 1.442513e-04	ci right 1.730038e-04	k: 476	n:3010000
KS ci ratio: 2.251792e-02	ci left: 9.855524e-03	ci right 1.008030e-02	k: 30002	n:3010000
LRP1   3010000 perm   4524 sec   (665 perm/sec)   p_kst 9.967442e-03   p_cons 1.581395e-04   p_joint 4.983389e-05

Joint ci ratio: 3.179459e-01	ci left: 4.234328e-05	ci right 5.864108e-05	k: 151	n:3020000
Cons ci ratio: 1.787224e-01	ci left: 1.450388e-04	ci right 1.738148e-04	k: 480	n:3020000
KS ci ratio: 2.247898e-02	ci left: 9.857134e-03	ci right 1.008156e-02	k: 30106	n:3020000
LRP1   3020000 perm   4551 sec   (664 perm/sec)   p_kst 9.968874e-03   p_cons 1.589404e-04   p_joint 5.000000e-05

Joint ci ratio: 3.169052e-01	ci left: 4.250728e-05	ci right 5.880379e-05	k: 152	n:3030000
Cons ci ratio: 1.787224e-01	ci left: 1.445601e-04	ci right 1.732411e-04	k: 480	n:3030000
KS ci ratio: 2.243799e-02	ci left: 9.860702e-03	ci right 1.008479e-02	k: 30216	n:3030000
LRP1   3030000 perm   4578 sec   (662 perm/sec)   p_kst 9.972277e-03   p_cons 1.584158e-04   p_joint 5.016502e-05

Joint ci ratio: 3.158745e-01	ci left: 4.267028e-05	ci right 5.896533e-05	k: 153	n:3040000
Cons ci ratio: 1.787224e-01	ci left: 1.440846e-04	ci right 1.726713e-04	k: 480	n:3040000
KS ci ratio: 2.240356e-02	ci left: 9.858686e-03	ci right 1.008238e-02	k: 30309	n:3040000
LRP1   3040000 perm   4605 sec   (660 perm/sec)   p_kst 9.970066e-03   p_cons 1.578947e-04   p_joint 5.032895e-05

Joint ci ratio: 3.148539e-01	ci left: 4.283230e-05	ci right 5.912574e-05	k: 154	n:3050000
Cons ci ratio: 1.781677e-01	ci left: 1.445519e-04	ci right 1.731326e-04	k: 483	n:3050000
KS ci ratio: 2.236484e-02	ci left: 9.860596e-03	ci right 1.008394e-02	k: 30414	n:3050000
LRP1   3050000 perm   4632 sec   (658 perm/sec)   p_kst 9.971803e-03   p_cons 1.583607e-04   p_joint 5.049180e-05

Joint ci ratio: 3.148540e-01	ci left: 4.269232e-05	ci right 5.893252e-05	k: 154	n:3060000
Cons ci ratio: 1.779839e-01	ci left: 1.443917e-04	ci right 1.729082e-04	k: 484	n:3060000
KS ci ratio: 2.232632e-02	ci left: 9.862494e-03	ci right 1.008549e-02	k: 30519	n:3060000
LRP1   3060000 perm   4660 sec   (657 perm/sec)   p_kst 9.973529e-03   p_cons 1.581699e-04   p_joint 5.032680e-05

Joint ci ratio: 3.148540e-01	ci left: 4.255326e-05	ci right 5.874055e-05	k: 154	n:3070000
Cons ci ratio: 1.778007e-01	ci left: 1.442326e-04	ci right 1.726852e-04	k: 485	n:3070000
KS ci ratio: 2.228983e-02	ci left: 9.862760e-03	ci right 1.008540e-02	k: 30619	n:3070000
LRP1   3070000 perm   4687 sec   (655 perm/sec)   p_kst 9.973616e-03   p_cons 1.579805e-04   p_joint 5.016287e-05

Joint ci ratio: 3.138432e-01	ci left: 4.271417e-05	ci right 5.890004e-05	k: 155	n:3080000
Cons ci ratio: 1.776181e-01	ci left: 1.440745e-04	ci right 1.724636e-04	k: 486	n:3080000
KS ci ratio: 2.225352e-02	ci left: 9.863025e-03	ci right 1.008530e-02	k: 30719	n:3080000
LRP1   3080000 perm   4713 sec   (653 perm/sec)   p_kst 9.973701e-03   p_cons 1.577922e-04   p_joint 5.032468e-05

Joint ci ratio: 3.108682e-01	ci left: 4.347072e-05	ci right 5.975615e-05	k: 158	n:3090000
Cons ci ratio: 1.772545e-01	ci left: 1.442268e-04	ci right 1.725815e-04	k: 488	n:3090000
KS ci ratio: 2.222394e-02	ci left: 9.857495e-03	ci right 1.007935e-02	k: 30801	n:3090000
LRP1   3090000 perm   4741 sec   (652 perm/sec)   p_kst 9.967961e-03   p_cons 1.579288e-04   p_joint 5.113269e-05

Joint ci ratio: 3.108682e-01	ci left: 4.333049e-05	ci right 5.956339e-05	k: 158	n:3100000
Cons ci ratio: 1.772545e-01	ci left: 1.437615e-04	ci right 1.720247e-04	k: 488	n:3100000
KS ci ratio: 2.219013e-02	ci left: 9.855851e-03	ci right 1.007732e-02	k: 30895	n:3100000
LRP1   3100000 perm   4769 sec   (650 perm/sec)   p_kst 9.966129e-03   p_cons 1.574194e-04   p_joint 5.096774e-05

Joint ci ratio: 3.098952e-01	ci left: 4.348766e-05	ci right 5.971838e-05	k: 159	n:3110000
Cons ci ratio: 1.772546e-01	ci left: 1.432993e-04	ci right 1.714716e-04	k: 488	n:3110000
KS ci ratio: 2.215755e-02	ci left: 9.853258e-03	ci right 1.007434e-02	k: 30986	n:3110000
LRP1   3110000 perm   4796 sec   (648 perm/sec)   p_kst 9.963344e-03   p_cons 1.569132e-04   p_joint 5.112540e-05

Joint ci ratio: 3.098952e-01	ci left: 4.334828e-05	ci right 5.952697e-05	k: 159	n:3120000
Cons ci ratio: 1.770736e-01	ci left: 1.431463e-04	ci right 1.712567e-04	k: 489	n:3120000
KS ci ratio: 2.212476e-02	ci left: 9.851001e-03	ci right 1.007170e-02	k: 31078	n:3120000
LRP1   3120000 perm   4824 sec   (647 perm/sec)   p_kst 9.960897e-03   p_cons 1.567308e-04   p_joint 5.096154e-05

Joint ci ratio: 3.098952e-01	ci left: 4.320979e-05	ci right 5.933679e-05	k: 159	n:3130000
Cons ci ratio: 1.768932e-01	ci left: 1.429943e-04	ci right 1.710432e-04	k: 490	n:3130000
KS ci ratio: 2.209068e-02	ci left: 9.850030e-03	ci right 1.007037e-02	k: 31174	n:3130000
LRP1   3130000 perm   4851 sec   (645 perm/sec)   p_kst 9.959744e-03   p_cons 1.565495e-04   p_joint 5.079872e-05

Joint ci ratio: 3.098953e-01	ci left: 4.307217e-05	ci right 5.914782e-05	k: 159	n:3140000
Cons ci ratio: 1.767134e-01	ci left: 1.428433e-04	ci right 1.708310e-04	k: 491	n:3140000
KS ci ratio: 2.205498e-02	ci left: 9.850648e-03	ci right 1.007064e-02	k: 31275	n:3140000
LRP1   3140000 perm   4879 sec   (644 perm/sec)   p_kst 9.960191e-03   p_cons 1.563694e-04   p_joint 5.063694e-05

Joint ci ratio: 3.079763e-01	ci left: 4.352115e-05	ci right 5.964403e-05	k: 161	n:3150000
Cons ci ratio: 1.763553e-01	ci left: 1.429967e-04	ci right 1.709517e-04	k: 493	n:3150000
KS ci ratio: 2.201201e-02	ci left: 9.857894e-03	ci right 1.007761e-02	k: 31397	n:3150000
LRP1   3150000 perm   4908 sec   (642 perm/sec)   p_kst 9.967302e-03   p_cons 1.565079e-04   p_joint 5.111111e-05

Joint ci ratio: 3.070301e-01	ci left: 4.367546e-05	ci right 5.979608e-05	k: 162	n:3160000
Cons ci ratio: 1.761771e-01	ci left: 1.428466e-04	ci right 1.707411e-04	k: 494	n:3160000
KS ci ratio: 2.198092e-02	ci left: 9.854707e-03	ci right 1.007404e-02	k: 31486	n:3160000
LRP1   3160000 perm   4936 sec   (640 perm/sec)   p_kst 9.963924e-03   p_cons 1.563291e-04   p_joint 5.126582e-05

Joint ci ratio: 3.070302e-01	ci left: 4.353768e-05	ci right 5.960745e-05	k: 162	n:3170000
Cons ci ratio: 1.759994e-01	ci left: 1.426976e-04	ci right 1.705318e-04	k: 495	n:3170000
KS ci ratio: 2.195171e-02	ci left: 9.849972e-03	ci right 1.006891e-02	k: 31570	n:3170000
LRP1   3170000 perm   4963 sec   (639 perm/sec)   p_kst 9.958991e-03   p_cons 1.561514e-04   p_joint 5.110410e-05

Joint ci ratio: 3.070302e-01	ci left: 4.340077e-05	ci right 5.942001e-05	k: 162	n:3180000
Cons ci ratio: 1.754695e-01	ci left: 1.431507e-04	ci right 1.709804e-04	k: 498	n:3180000
KS ci ratio: 2.192122e-02	ci left: 9.846519e-03	ci right 1.006507e-02	k: 31658	n:3180000
LRP1   3180000 perm   4992 sec   (637 perm/sec)   p_kst 9.955346e-03   p_cons 1.566038e-04   p_joint 5.094340e-05

Joint ci ratio: 3.060927e-01	ci left: 4.355409e-05	ci right 5.957126e-05	k: 163	n:3190000
Cons ci ratio: 1.751189e-01	ci left: 1.433014e-04	ci right 1.710989e-04	k: 500	n:3190000
KS ci ratio: 2.188703e-02	ci left: 9.846516e-03	ci right 1.006472e-02	k: 31757	n:3190000
LRP1   3190000 perm   5020 sec   (635 perm/sec)   p_kst 9.955172e-03   p_cons 1.567398e-04   p_joint 5.109718e-05

Joint ci ratio: 3.051637e-01	ci left: 4.370652e-05	ci right 5.972149e-05	k: 164	n:3200000
Cons ci ratio: 1.747704e-01	ci left: 1.434513e-04	ci right 1.712165e-04	k: 502	n:3200000
KS ci ratio: 2.184711e-02	ci left: 9.851798e-03	ci right 1.006972e-02	k: 31873	n:3200000
LRP1   3200000 perm   5048 sec   (634 perm/sec)   p_kst 9.960313e-03   p_cons 1.568750e-04   p_joint 5.125000e-05

Joint ci ratio: 3.051637e-01	ci left: 4.357036e-05	ci right 5.953544e-05	k: 164	n:3210000
Cons ci ratio: 1.745969e-01	ci left: 1.433023e-04	ci right 1.710083e-04	k: 503	n:3210000
KS ci ratio: 2.181602e-02	ci left: 9.849301e-03	ci right 1.006685e-02	k: 31964	n:3210000
LRP1   3210000 perm   5076 sec   (632 perm/sec)   p_kst 9.957632e-03   p_cons 1.566978e-04   p_joint 5.109034e-05

Joint ci ratio: 3.051637e-01	ci left: 4.343505e-05	ci right 5.935055e-05	k: 164	n:3220000
Cons ci ratio: 1.739081e-01	ci left: 1.440453e-04	ci right 1.717735e-04	k: 507	n:3220000
KS ci ratio: 2.178575e-02	ci left: 9.846202e-03	ci right 1.006338e-02	k: 32053	n:3220000
LRP1   3220000 perm   5104 sec   (631 perm/sec)   p_kst 9.954348e-03   p_cons 1.574534e-04   p_joint 5.093168e-05

Joint ci ratio: 3.042431e-01	ci left: 4.358651e-05	ci right 5.949999e-05	k: 165	n:3230000
Cons ci ratio: 1.737372e-01	ci left: 1.438955e-04	ci right 1.715648e-04	k: 508	n:3230000
KS ci ratio: 2.175218e-02	ci left: 9.846202e-03	ci right 1.006304e-02	k: 32152	n:3230000
LRP1   3230000 perm   5132 sec   (629 perm/sec)   p_kst 9.954180e-03   p_cons 1.572755e-04   p_joint 5.108359e-05

Joint ci ratio: 3.042432e-01	ci left: 4.345198e-05	ci right 5.931635e-05	k: 165	n:3240000
Cons ci ratio: 1.733969e-01	ci left: 1.440418e-04	ci right 1.716793e-04	k: 510	n:3240000
KS ci ratio: 2.172081e-02	ci left: 9.844360e-03	ci right 1.006084e-02	k: 32245	n:3240000
LRP1   3240000 perm   5161 sec   (628 perm/sec)   p_kst 9.952160e-03   p_cons 1.574074e-04   p_joint 5.092593e-05

Joint ci ratio: 3.042432e-01	ci left: 4.331828e-05	ci right 5.913384e-05	k: 165	n:3250000
Cons ci ratio: 1.730585e-01	ci left: 1.441873e-04	ci right 1.717931e-04	k: 512	n:3250000
KS ci ratio: 2.168823e-02	ci left: 9.843754e-03	ci right 1.005989e-02	k: 32342	n:3250000
LRP1   3250000 perm   5189 sec   (626 perm/sec)   p_kst 9.951385e-03   p_cons 1.575385e-04   p_joint 5.076923e-05

Joint ci ratio: 3.042432e-01	ci left: 4.318540e-05	ci right 5.895245e-05	k: 165	n:3260000
Cons ci ratio: 1.728901e-01	ci left: 1.440385e-04	ci right 1.715862e-04	k: 513	n:3260000
KS ci ratio: 2.165275e-02	ci left: 9.845898e-03	ci right 1.006172e-02	k: 32448	n:3260000
LRP1   3260000 perm   5218 sec   (625 perm/sec)   p_kst 9.953374e-03   p_cons 1.573620e-04   p_joint 5.061350e-05

Joint ci ratio: 3.042432e-01	ci left: 4.305334e-05	ci right 5.877217e-05	k: 165	n:3270000
Cons ci ratio: 1.728902e-01	ci left: 1.435980e-04	ci right 1.710614e-04	k: 513	n:3270000
KS ci ratio: 2.161946e-02	ci left: 9.846203e-03	ci right 1.006170e-02	k: 32548	n:3270000
LRP1   3270000 perm   5247 sec   (623 perm/sec)   p_kst 9.953517e-03   p_cons 1.568807e-04   p_joint 5.045872e-05

Joint ci ratio: 3.042433e-01	ci left: 4.292208e-05	ci right 5.859298e-05	k: 165	n:3280000
Cons ci ratio: 1.723878e-01	ci left: 1.440353e-04	ci right 1.714940e-04	k: 516	n:3280000
KS ci ratio: 2.158700e-02	ci left: 9.845901e-03	ci right 1.006106e-02	k: 32646	n:3280000
LRP1   3280000 perm   5275 sec   (622 perm/sec)   p_kst 9.953049e-03   p_cons 1.573171e-04   p_joint 5.030488e-05

Joint ci ratio: 3.042433e-01	ci left: 4.279162e-05	ci right 5.841489e-05	k: 165	n:3290000
Cons ci ratio: 1.722213e-01	ci left: 1.438884e-04	ci right 1.712898e-04	k: 517	n:3290000
KS ci ratio: 2.155301e-02	ci left: 9.847113e-03	ci right 1.006196e-02	k: 32749	n:3290000
LRP1   3290000 perm   5304 sec   (620 perm/sec)   p_kst 9.954103e-03   p_cons 1.571429e-04   p_joint 5.015198e-05

Joint ci ratio: 3.042433e-01	ci left: 4.266194e-05	ci right 5.823788e-05	k: 165	n:3300000
Cons ci ratio: 1.722214e-01	ci left: 1.434523e-04	ci right 1.707708e-04	k: 517	n:3300000
KS ci ratio: 2.151952e-02	ci left: 9.848016e-03	ci right 1.006254e-02	k: 32851	n:3300000
LRP1   3300000 perm   5334 sec   (619 perm/sec)   p_kst 9.954848e-03   p_cons 1.566667e-04   p_joint 5.000000e-05

Joint ci ratio: 3.042433e-01	ci left: 4.253305e-05	ci right 5.806193e-05	k: 165	n:3310000
Cons ci ratio: 1.717248e-01	ci left: 1.438863e-04	ci right 1.712002e-04	k: 520	n:3310000
KS ci ratio: 2.148783e-02	ci left: 9.847411e-03	ci right 1.006160e-02	k: 32948	n:3310000
LRP1   3310000 perm   5363 sec   (617 perm/sec)   p_kst 9.954079e-03   p_cons 1.570997e-04   p_joint 4.984894e-05

Joint ci ratio: 3.024269e-01	ci left: 4.296151e-05	ci right 5.853516e-05	k: 167	n:3320000
Cons ci ratio: 1.717248e-01	ci left: 1.434529e-04	ci right 1.706845e-04	k: 520	n:3320000
KS ci ratio: 2.145660e-02	ci left: 9.846510e-03	ci right 1.006037e-02	k: 33044	n:3320000
LRP1   3320000 perm   5392 sec   (616 perm/sec)   p_kst 9.953012e-03   p_cons 1.566265e-04   p_joint 5.030120e-05

Joint ci ratio: 3.015308e-01	ci left: 4.311005e-05	ci right 5.868236e-05	k: 168	n:3330000
Cons ci ratio: 1.715603e-01	ci left: 1.433095e-04	ci right 1.704851e-04	k: 521	n:3330000
KS ci ratio: 2.142388e-02	ci left: 9.847109e-03	ci right 1.006065e-02	k: 33145	n:3330000
LRP1   3330000 perm   5421 sec   (614 perm/sec)   p_kst 9.953453e-03   p_cons 1.564565e-04   p_joint 5.045045e-05

Joint ci ratio: 3.015308e-01	ci left: 4.298098e-05	ci right 5.850667e-05	k: 168	n:3340000
Cons ci ratio: 1.715603e-01	ci left: 1.428804e-04	ci right 1.699747e-04	k: 521	n:3340000
KS ci ratio: 2.139001e-02	ci left: 9.848896e-03	ci right 1.006213e-02	k: 33250	n:3340000
LRP1   3340000 perm   5451 sec   (613 perm/sec)   p_kst 9.955090e-03   p_cons 1.559880e-04   p_joint 5.029940e-05

Joint ci ratio: 3.015308e-01	ci left: 4.285268e-05	ci right 5.833202e-05	k: 168	n:3350000
Cons ci ratio: 1.709067e-01	ci left: 1.435968e-04	ci right 1.707124e-04	k: 525	n:3350000
KS ci ratio: 2.136051e-02	ci left: 9.846812e-03	ci right 1.005971e-02	k: 33342	n:3350000
LRP1   3350000 perm   5480 sec   (611 perm/sec)   p_kst 9.952836e-03   p_cons 1.567164e-04   p_joint 5.014925e-05

Joint ci ratio: 3.006426e-01	ci left: 4.300028e-05	ci right 5.847845e-05	k: 169	n:3360000
Cons ci ratio: 1.707445e-01	ci left: 1.434543e-04	ci right 1.705147e-04	k: 526	n:3360000
KS ci ratio: 2.133596e-02	ci left: 9.840300e-03	ci right 1.005281e-02	k: 33419	n:3360000
LRP1   3360000 perm   5510 sec   (610 perm/sec)   p_kst 9.946131e-03   p_cons 1.565476e-04   p_joint 5.029762e-05

Joint ci ratio: 2.997622e-01	ci left: 4.314707e-05	ci right 5.862394e-05	k: 170	n:3370000
Cons ci ratio: 1.704214e-01	ci left: 1.435968e-04	ci right 1.706275e-04	k: 528	n:3370000
KS ci ratio: 2.130282e-02	ci left: 9.841796e-03	ci right 1.005400e-02	k: 33523	n:3370000
LRP1   3370000 perm   5540 sec   (608 perm/sec)   p_kst 9.947478e-03   p_cons 1.566766e-04   p_joint 5.044510e-05

Joint ci ratio: 2.997623e-01	ci left: 4.301942e-05	ci right 5.845049e-05	k: 170	n:3380000
Cons ci ratio: 1.702605e-01	ci left: 1.434552e-04	ci right 1.704312e-04	k: 529	n:3380000
KS ci ratio: 2.127272e-02	ci left: 9.840635e-03	ci right 1.005251e-02	k: 33618	n:3380000
LRP1   3380000 perm   5570 sec   (607 perm/sec)   p_kst 9.946154e-03   p_cons 1.565089e-04   p_joint 5.029586e-05

Joint ci ratio: 2.988896e-01	ci left: 4.316535e-05	ci right 5.859514e-05	k: 171	n:3390000
Cons ci ratio: 1.697807e-01	ci left: 1.438793e-04	ci right 1.708510e-04	k: 532	n:3390000
KS ci ratio: 2.123511e-02	ci left: 9.846524e-03	ci right 1.005815e-02	k: 33737	n:3390000
LRP1   3390000 perm   5599 sec   (605 perm/sec)   p_kst 9.951917e-03   p_cons 1.569322e-04   p_joint 5.044248e-05

Joint ci ratio: 2.988896e-01	ci left: 4.303840e-05	ci right 5.842281e-05	k: 171	n:3400000
Cons ci ratio: 1.694630e-01	ci left: 1.440194e-04	ci right 1.709617e-04	k: 534	n:3400000
KS ci ratio: 2.120940e-02	ci left: 9.841553e-03	ci right 1.005281e-02	k: 33819	n:3400000
LRP1   3400000 perm   5629 sec   (604 perm/sec)   p_kst 9.946765e-03   p_cons 1.570588e-04   p_joint 5.029412e-05

Joint ci ratio: 2.971668e-01	ci left: 4.345485e-05	ci right 5.888171e-05	k: 173	n:3410000
Cons ci ratio: 1.693049e-01	ci left: 1.438779e-04	ci right 1.707660e-04	k: 535	n:3410000
KS ci ratio: 2.117433e-02	ci left: 9.845363e-03	ci right 1.005635e-02	k: 33931	n:3410000
LRP1   3410000 perm   5658 sec   (603 perm/sec)   p_kst 9.950440e-03   p_cons 1.568915e-04   p_joint 5.073314e-05

Joint ci ratio: 2.971668e-01	ci left: 4.332779e-05	ci right 5.870954e-05	k: 173	n:3420000
Cons ci ratio: 1.689899e-01	ci left: 1.440172e-04	ci right 1.708762e-04	k: 537	n:3420000
KS ci ratio: 2.114790e-02	ci left: 9.841297e-03	ci right 1.005193e-02	k: 34016	n:3420000
LRP1   3420000 perm   5688 sec   (601 perm/sec)   p_kst 9.946199e-03   p_cons 1.570175e-04   p_joint 5.058480e-05

Joint ci ratio: 2.963165e-01	ci left: 4.347131e-05	ci right 5.885156e-05	k: 174	n:3430000
Cons ci ratio: 1.686766e-01	ci left: 1.441558e-04	ci right 1.709857e-04	k: 539	n:3430000
KS ci ratio: 2.111876e-02	ci left: 9.839866e-03	ci right 1.005018e-02	k: 34110	n:3430000
LRP1   3430000 perm   5718 sec   (600 perm/sec)   p_kst 9.944606e-03   p_cons 1.571429e-04   p_joint 5.072886e-05

Joint ci ratio: 2.963166e-01	ci left: 4.334494e-05	ci right 5.868048e-05	k: 174	n:3440000
Cons ci ratio: 1.683651e-01	ci left: 1.442936e-04	ci right 1.710946e-04	k: 541	n:3440000
KS ci ratio: 2.108601e-02	ci left: 9.841913e-03	ci right 1.005194e-02	k: 34216	n:3440000
LRP1   3440000 perm   5748 sec   (598 perm/sec)   p_kst 9.946512e-03   p_cons 1.572674e-04   p_joint 5.058140e-05

Joint ci ratio: 2.963166e-01	ci left: 4.321930e-05	ci right 5.851039e-05	k: 174	n:3450000
Cons ci ratio: 1.682100e-01	ci left: 1.441530e-04	ci right 1.709007e-04	k: 542	n:3450000
KS ci ratio: 2.105867e-02	ci left: 9.839047e-03	ci right 1.004873e-02	k: 34305	n:3450000
LRP1   3450000 perm   5778 sec   (597 perm/sec)   p_kst 9.943478e-03   p_cons 1.571014e-04   p_joint 5.043478e-05

Joint ci ratio: 2.963166e-01	ci left: 4.309439e-05	ci right 5.834129e-05	k: 174	n:3460000
Cons ci ratio: 1.675938e-01	ci left: 1.448439e-04	ci right 1.716114e-04	k: 546	n:3460000
KS ci ratio: 2.103144e-02	ci left: 9.836197e-03	ci right 1.004555e-02	k: 34394	n:3460000
LRP1   3460000 perm   5808 sec   (596 perm/sec)   p_kst 9.940462e-03   p_cons 1.578035e-04   p_joint 5.028902e-05

Joint ci ratio: 2.963166e-01	ci left: 4.297020e-05	ci right 5.817316e-05	k: 174	n:3470000
Cons ci ratio: 1.674409e-01	ci left: 1.447026e-04	ci right 1.714171e-04	k: 547	n:3470000
KS ci ratio: 2.099509e-02	ci left: 9.841965e-03	ci right 1.005107e-02	k: 34513	n:3470000
LRP1   3470000 perm   5844 sec   (594 perm/sec)   p_kst 9.946110e-03   p_cons 1.576369e-04   p_joint 5.014409e-05

Joint ci ratio: 2.963167e-01	ci left: 4.284672e-05	ci right 5.800599e-05	k: 174	n:3480000
Cons ci ratio: 1.674409e-01	ci left: 1.442867e-04	ci right 1.709245e-04	k: 547	n:3480000
KS ci ratio: 2.096351e-02	ci left: 9.843412e-03	ci right 1.005223e-02	k: 34617	n:3480000
LRP1   3480000 perm   5875 sec   (592 perm/sec)   p_kst 9.947414e-03   p_cons 1.571839e-04   p_joint 5.000000e-05

Joint ci ratio: 2.954736e-01	ci left: 4.298922e-05	ci right 5.814753e-05	k: 175	n:3490000
Cons ci ratio: 1.671362e-01	ci left: 1.444224e-04	ci right 1.710318e-04	k: 549	n:3490000
KS ci ratio: 2.093117e-02	ci left: 9.845706e-03	ci right 1.005425e-02	k: 34724	n:3490000
LRP1   3490000 perm   5905 sec   (591 perm/sec)   p_kst 9.949570e-03   p_cons 1.573066e-04   p_joint 5.014327e-05

Joint ci ratio: 2.946378e-01	ci left: 4.313096e-05	ci right 5.828819e-05	k: 176	n:3500000
Cons ci ratio: 1.668331e-01	ci left: 1.445573e-04	ci right 1.711384e-04	k: 551	n:3500000
KS ci ratio: 2.090170e-02	ci left: 9.845429e-03	ci right 1.005367e-02	k: 34822	n:3500000
LRP1   3500000 perm   5935 sec   (590 perm/sec)   p_kst 9.949143e-03   p_cons 1.574286e-04   p_joint 5.028571e-05

Joint ci ratio: 2.921720e-01	ci left: 4.379989e-05	ci right 5.903955e-05	k: 179	n:3510000
Cons ci ratio: 1.668331e-01	ci left: 1.441455e-04	ci right 1.706508e-04	k: 551	n:3510000
KS ci ratio: 2.086934e-02	ci left: 9.847988e-03	ci right 1.005596e-02	k: 34930	n:3510000
LRP1   3510000 perm   5965 sec   (588 perm/sec)   p_kst 9.951567e-03   p_cons 1.569801e-04   p_joint 5.099715e-05

Joint ci ratio: 2.921720e-01	ci left: 4.367546e-05	ci right 5.887182e-05	k: 179	n:3520000
Cons ci ratio: 1.665317e-01	ci left: 1.442804e-04	ci right 1.707579e-04	k: 553	n:3520000
KS ci ratio: 2.083893e-02	ci left: 9.848837e-03	ci right 1.005652e-02	k: 35032	n:3520000
LRP1   3520000 perm   5996 sec   (587 perm/sec)   p_kst 9.952273e-03   p_cons 1.571023e-04   p_joint 5.085227e-05

Joint ci ratio: 2.921721e-01	ci left: 4.355173e-05	ci right 5.870505e-05	k: 179	n:3530000
Cons ci ratio: 1.662319e-01	ci left: 1.444147e-04	ci right 1.708643e-04	k: 555	n:3530000
KS ci ratio: 2.081134e-02	ci left: 9.847145e-03	ci right 1.005451e-02	k: 35125	n:3530000
LRP1   3530000 perm   6027 sec   (586 perm/sec)   p_kst 9.950425e-03   p_cons 1.572238e-04   p_joint 5.070822e-05

Joint ci ratio: 2.913638e-01	ci left: 4.369052e-05	ci right 5.884231e-05	k: 180	n:3540000
Cons ci ratio: 1.656371e-01	ci left: 1.450898e-04	ci right 1.715584e-04	k: 559	n:3540000
KS ci ratio: 2.078357e-02	ci left: 9.845744e-03	ci right 1.005280e-02	k: 35219	n:3540000
LRP1   3540000 perm   6058 sec   (584 perm/sec)   p_kst 9.948870e-03   p_cons 1.579096e-04   p_joint 5.084746e-05

Joint ci ratio: 2.913638e-01	ci left: 4.356745e-05	ci right 5.867656e-05	k: 180	n:3550000
Cons ci ratio: 1.654894e-01	ci left: 1.449511e-04	ci right 1.713685e-04	k: 560	n:3550000
KS ci ratio: 2.075887e-02	ci left: 9.841548e-03	ci right 1.004827e-02	k: 35303	n:3550000
LRP1   3550000 perm   6088 sec   (583 perm/sec)   p_kst 9.944507e-03   p_cons 1.577465e-04   p_joint 5.070423e-05

Joint ci ratio: 2.913639e-01	ci left: 4.344506e-05	ci right 5.851174e-05	k: 180	n:3560000
Cons ci ratio: 1.654895e-01	ci left: 1.445439e-04	ci right 1.708871e-04	k: 560	n:3560000
KS ci ratio: 2.072953e-02	ci left: 9.841847e-03	ci right 1.004828e-02	k: 35403	n:3560000
LRP1   3560000 perm   6119 sec   (582 perm/sec)   p_kst 9.944663e-03   p_cons 1.573034e-04   p_joint 5.056180e-05

Joint ci ratio: 2.913639e-01	ci left: 4.332337e-05	ci right 5.834784e-05	k: 180	n:3570000
Cons ci ratio: 1.650487e-01	ci left: 1.449446e-04	ci right 1.712835e-04	k: 563	n:3570000
KS ci ratio: 2.070208e-02	ci left: 9.840473e-03	ci right 1.004660e-02	k: 35497	n:3570000
LRP1   3570000 perm   6149 sec   (581 perm/sec)   p_kst 9.943137e-03   p_cons 1.577031e-04   p_joint 5.042017e-05

Joint ci ratio: 2.913639e-01	ci left: 4.320235e-05	ci right 5.818486e-05	k: 180	n:3580000
Cons ci ratio: 1.647568e-01	ci left: 1.450753e-04	ci right 1.713868e-04	k: 565	n:3580000
KS ci ratio: 2.066683e-02	ci left: 9.846610e-03	ci right 1.005251e-02	k: 35618	n:3580000
LRP1   3580000 perm   6180 sec   (579 perm/sec)   p_kst 9.949162e-03   p_cons 1.578212e-04   p_joint 5.027933e-05

Joint ci ratio: 2.913639e-01	ci left: 4.308201e-05	ci right 5.802279e-05	k: 180	n:3590000
Cons ci ratio: 1.644665e-01	ci left: 1.452054e-04	ci right 1.714894e-04	k: 567	n:3590000
KS ci ratio: 2.064050e-02	ci left: 9.844400e-03	ci right 1.004999e-02	k: 35709	n:3590000
LRP1   3590000 perm   6211 sec   (578 perm/sec)   p_kst 9.946797e-03   p_cons 1.579387e-04   p_joint 5.013928e-05

Joint ci ratio: 2.905623e-01	ci left: 4.321985e-05	ci right 5.815961e-05	k: 181	n:3600000
Cons ci ratio: 1.640339e-01	ci left: 1.456011e-04	ci right 1.718806e-04	k: 570	n:3600000
KS ci ratio: 2.061253e-02	ci left: 9.843860e-03	ci right 1.004915e-02	k: 35806	n:3600000
LRP1   3600000 perm   6242 sec   (577 perm/sec)   p_kst 9.946111e-03   p_cons 1.583333e-04   p_joint 5.027778e-05

Joint ci ratio: 2.897674e-01	ci left: 4.335698e-05	ci right 5.829561e-05	k: 182	n:3610000
Cons ci ratio: 1.636046e-01	ci left: 1.459947e-04	ci right 1.722695e-04	k: 573	n:3610000
KS ci ratio: 2.058642e-02	ci left: 9.841669e-03	ci right 1.004665e-02	k: 35897	n:3610000
LRP1   3610000 perm   6273 sec   (575 perm/sec)   p_kst 9.943767e-03   p_cons 1.587258e-04   p_joint 5.041551e-05

Joint ci ratio: 2.897674e-01	ci left: 4.323720e-05	ci right 5.813457e-05	k: 182	n:3620000
Cons ci ratio: 1.633203e-01	ci left: 1.461213e-04	ci right 1.723687e-04	k: 575	n:3620000
KS ci ratio: 2.055722e-02	ci left: 9.842514e-03	ci right 1.004722e-02	k: 35999	n:3620000
LRP1   3620000 perm   6304 sec   (574 perm/sec)   p_kst 9.944475e-03   p_cons 1.588398e-04   p_joint 5.027624e-05

Joint ci ratio: 2.897674e-01	ci left: 4.311809e-05	ci right 5.797442e-05	k: 182	n:3630000
Cons ci ratio: 1.631787e-01	ci left: 1.459830e-04	ci right 1.721806e-04	k: 576	n:3630000
KS ci ratio: 2.052902e-02	ci left: 9.842532e-03	ci right 1.004696e-02	k: 36098	n:3630000
LRP1   3630000 perm   6336 sec   (573 perm/sec)   p_kst 9.944353e-03   p_cons 1.586777e-04   p_joint 5.013774e-05

Joint ci ratio: 2.897674e-01	ci left: 4.299964e-05	ci right 5.781515e-05	k: 182	n:3640000
Cons ci ratio: 1.628967e-01	ci left: 1.461090e-04	ci right 1.722794e-04	k: 578	n:3640000
KS ci ratio: 2.049721e-02	ci left: 9.846104e-03	ci right 1.005028e-02	k: 36210	n:3640000
LRP1   3640000 perm   6369 sec   (572 perm/sec)   p_kst 9.947802e-03   p_cons 1.587912e-04   p_joint 5.000000e-05

Joint ci ratio: 2.881968e-01	ci left: 4.339006e-05	ci right 5.824431e-05	k: 184	n:3650000
Cons ci ratio: 1.626160e-01	ci left: 1.462343e-04	ci right 1.723777e-04	k: 580	n:3650000
KS ci ratio: 2.046612e-02	ci left: 9.849111e-03	ci right 1.005304e-02	k: 36320	n:3650000
LRP1   3650000 perm   6399 sec   (570 perm/sec)   p_kst 9.950685e-03   p_cons 1.589041e-04   p_joint 5.041096e-05

Joint ci ratio: 2.874210e-01	ci left: 4.352502e-05	ci right 5.837806e-05	k: 185	n:3660000
Cons ci ratio: 1.626161e-01	ci left: 1.458348e-04	ci right 1.719067e-04	k: 580	n:3660000
KS ci ratio: 2.043318e-02	ci left: 9.854005e-03	ci right 1.005770e-02	k: 36437	n:3660000
LRP1   3660000 perm   6432 sec   (569 perm/sec)   p_kst 9.955464e-03   p_cons 1.584699e-04   p_joint 5.054645e-05

Joint ci ratio: 2.866514e-01	ci left: 4.365929e-05	ci right 5.851103e-05	k: 186	n:3670000
Cons ci ratio: 1.626161e-01	ci left: 1.454374e-04	ci right 1.714383e-04	k: 580	n:3670000
KS ci ratio: 2.040689e-02	ci left: 9.852637e-03	ci right 1.005604e-02	k: 36531	n:3670000
LRP1   3670000 perm   6466 sec   (568 perm/sec)   p_kst 9.953951e-03   p_cons 1.580381e-04   p_joint 5.068120e-05

Joint ci ratio: 2.843793e-01	ci left: 4.429750e-05	ci right 5.922547e-05	k: 189	n:3680000
Cons ci ratio: 1.624764e-01	ci left: 1.453029e-04	ci right 1.712552e-04	k: 581	n:3680000
KS ci ratio: 2.038211e-02	ci left: 9.849925e-03	ci right 1.005302e-02	k: 36620	n:3680000
LRP1   3680000 perm   6497 sec   (566 perm/sec)   p_kst 9.951087e-03   p_cons 1.578804e-04   p_joint 5.135870e-05

Joint ci ratio: 2.836339e-01	ci left: 4.442915e-05	ci right 5.935522e-05	k: 190	n:3690000
Cons ci ratio: 1.619208e-01	ci left: 1.459491e-04	ci right 1.719191e-04	k: 585	n:3690000
KS ci ratio: 2.035714e-02	ci left: 9.847498e-03	ci right 1.005029e-02	k: 36710	n:3690000
LRP1   3690000 perm   6529 sec   (565 perm/sec)   p_kst 9.948509e-03   p_cons 1.585366e-04   p_joint 5.149051e-05

Joint ci ratio: 2.828943e-01	ci left: 4.456015e-05	ci right 5.948421e-05	k: 191	n:3700000
Cons ci ratio: 1.617829e-01	ci left: 1.458140e-04	ci right 1.717356e-04	k: 586	n:3700000
KS ci ratio: 2.033003e-02	ci left: 9.847234e-03	ci right 1.004975e-02	k: 36808	n:3700000
LRP1   3700000 perm   6561 sec   (564 perm/sec)   p_kst 9.948108e-03   p_cons 1.583784e-04   p_joint 5.162162e-05

Joint ci ratio: 2.828943e-01	ci left: 4.444004e-05	ci right 5.932388e-05	k: 191	n:3710000
Cons ci ratio: 1.617829e-01	ci left: 1.454210e-04	ci right 1.712727e-04	k: 586	n:3710000
KS ci ratio: 2.030024e-02	ci left: 9.849655e-03	ci right 1.005192e-02	k: 36916	n:3710000
LRP1   3710000 perm   6593 sec   (563 perm/sec)   p_kst 9.950404e-03   p_cons 1.579515e-04   p_joint 5.148248e-05

Joint ci ratio: 2.814322e-01	ci left: 4.482017e-05	ci right 5.973998e-05	k: 193	n:3720000
Cons ci ratio: 1.616453e-01	ci left: 1.452880e-04	ci right 1.710920e-04	k: 587	n:3720000
KS ci ratio: 2.027723e-02	ci left: 9.845643e-03	ci right 1.004759e-02	k: 37000	n:3720000
LRP1   3720000 perm   6624 sec   (562 perm/sec)   p_kst 9.946237e-03   p_cons 1.577957e-04   p_joint 5.188172e-05

Joint ci ratio: 2.814322e-01	ci left: 4.470001e-05	ci right 5.957982e-05	k: 193	n:3730000
Cons ci ratio: 1.615080e-01	ci left: 1.451557e-04	ci right 1.709123e-04	k: 588	n:3730000
KS ci ratio: 2.024713e-02	ci left: 9.848589e-03	ci right 1.005030e-02	k: 37110	n:3730000
LRP1   3730000 perm   6655 sec   (560 perm/sec)   p_kst 9.949062e-03   p_cons 1.576408e-04   p_joint 5.174263e-05

Joint ci ratio: 2.785749e-01	ci left: 4.557493e-05	ci right 6.056493e-05	k: 197	n:3740000
Cons ci ratio: 1.613711e-01	ci left: 1.450242e-04	ci right 1.707334e-04	k: 589	n:3740000
KS ci ratio: 2.021771e-02	ci left: 9.850987e-03	ci right 1.005245e-02	k: 37218	n:3740000
LRP1   3740000 perm   6686 sec   (559 perm/sec)   p_kst 9.951337e-03   p_cons 1.574866e-04   p_joint 5.267380e-05

Joint ci ratio: 2.778740e-01	ci left: 4.570146e-05	ci right 6.068865e-05	k: 198	n:3750000
Cons ci ratio: 1.612345e-01	ci left: 1.448933e-04	ci right 1.705556e-04	k: 590	n:3750000
KS ci ratio: 2.018841e-02	ci left: 9.853372e-03	ci right 1.005459e-02	k: 37326	n:3750000
LRP1   3750000 perm   6718 sec   (558 perm/sec)   p_kst 9.953600e-03   p_cons 1.573333e-04   p_joint 5.280000e-05

Joint ci ratio: 2.778740e-01	ci left: 4.557991e-05	ci right 6.052724e-05	k: 198	n:3760000
Cons ci ratio: 1.609624e-01	ci left: 1.450185e-04	ci right 1.706553e-04	k: 592	n:3760000
KS ci ratio: 2.015979e-02	ci left: 9.855216e-03	ci right 1.005618e-02	k: 37432	n:3760000
LRP1   3760000 perm   6750 sec   (557 perm/sec)   p_kst 9.955319e-03   p_cons 1.574468e-04   p_joint 5.265957e-05

Joint ci ratio: 2.771785e-01	ci left: 4.570580e-05	ci right 6.065036e-05	k: 199	n:3770000
Cons ci ratio: 1.609624e-01	ci left: 1.446338e-04	ci right 1.702027e-04	k: 592	n:3770000
KS ci ratio: 2.013210e-02	ci left: 9.856258e-03	ci right 1.005696e-02	k: 37535	n:3770000
LRP1   3770000 perm   6782 sec   (556 perm/sec)   p_kst 9.956233e-03   p_cons 1.570292e-04   p_joint 5.278515e-05

Joint ci ratio: 2.771785e-01	ci left: 4.558489e-05	ci right 6.048991e-05	k: 199	n:3780000
Cons ci ratio: 1.608269e-01	ci left: 1.445051e-04	ci right 1.700276e-04	k: 593	n:3780000
KS ci ratio: 2.010777e-02	ci left: 9.854136e-03	ci right 1.005455e-02	k: 37626	n:3780000
LRP1   3780000 perm   6814 sec   (555 perm/sec)   p_kst 9.953968e-03   p_cons 1.568783e-04   p_joint 5.264550e-05

Joint ci ratio: 2.771785e-01	ci left: 4.546461e-05	ci right 6.033030e-05	k: 199	n:3790000
Cons ci ratio: 1.608269e-01	ci left: 1.441238e-04	ci right 1.695790e-04	k: 593	n:3790000
KS ci ratio: 2.008217e-02	ci left: 9.853338e-03	ci right 1.005348e-02	k: 37722	n:3790000
LRP1   3790000 perm   6847 sec   (554 perm/sec)   p_kst 9.953034e-03   p_cons 1.564644e-04   p_joint 5.250660e-05

Joint ci ratio: 2.771785e-01	ci left: 4.534497e-05	ci right 6.017154e-05	k: 199	n:3800000
Cons ci ratio: 1.605568e-01	ci left: 1.442497e-04	ci right 1.696802e-04	k: 595	n:3800000
KS ci ratio: 2.005561e-02	ci left: 9.853592e-03	ci right 1.005347e-02	k: 37822	n:3800000
LRP1   3800000 perm   6880 sec   (552 perm/sec)   p_kst 9.953158e-03   p_cons 1.565789e-04   p_joint 5.236842e-05

Joint ci ratio: 2.771785e-01	ci left: 4.522595e-05	ci right 6.001361e-05	k: 199	n:3810000
Cons ci ratio: 1.605569e-01	ci left: 1.438711e-04	ci right 1.692348e-04	k: 595	n:3810000
KS ci ratio: 2.003262e-02	ci left: 9.850450e-03	ci right 1.005003e-02	k: 37909	n:3810000
LRP1   3810000 perm   6913 sec   (551 perm/sec)   p_kst 9.949869e-03   p_cons 1.561680e-04   p_joint 5.223097e-05

Joint ci ratio: 2.764882e-01	ci left: 4.535117e-05	ci right 6.013641e-05	k: 200	n:3820000
Cons ci ratio: 1.602882e-01	ci left: 1.439970e-04	ci right 1.693363e-04	k: 597	n:3820000
KS ci ratio: 2.000651e-02	ci left: 9.850450e-03	ci right 1.004977e-02	k: 38008	n:3820000
LRP1   3820000 perm   6945 sec   (550 perm/sec)   p_kst 9.949738e-03   p_cons 1.562827e-04   p_joint 5.235602e-05

Joint ci ratio: 2.764882e-01	ci left: 4.523276e-05	ci right 5.997940e-05	k: 200	n:3830000
Cons ci ratio: 1.601543e-01	ci left: 1.438716e-04	ci right 1.691658e-04	k: 598	n:3830000
KS ci ratio: 1.997865e-02	ci left: 9.852268e-03	ci right 1.005135e-02	k: 38114	n:3830000
LRP1   3830000 perm   6978 sec   (549 perm/sec)   p_kst 9.951436e-03   p_cons 1.561358e-04   p_joint 5.221932e-05

Joint ci ratio: 2.758029e-01	ci left: 4.535735e-05	ci right 6.010160e-05	k: 201	n:3840000
Cons ci ratio: 1.596222e-01	ci left: 1.444970e-04	ci right 1.698085e-04	k: 602	n:3840000
KS ci ratio: 1.995118e-02	ci left: 9.853819e-03	ci right 1.005265e-02	k: 38219	n:3840000
LRP1   3840000 perm   7011 sec   (548 perm/sec)   p_kst 9.952865e-03   p_cons 1.567708e-04   p_joint 5.234375e-05

Joint ci ratio: 2.744476e-01	ci left: 4.572319e-05	ci right 6.050072e-05	k: 203	n:3850000
Cons ci ratio: 1.590953e-01	ci left: 1.451192e-04	ci right 1.704478e-04	k: 606	n:3850000
KS ci ratio: 1.992828e-02	ci left: 9.850968e-03	ci right 1.004951e-02	k: 38307	n:3850000
LRP1   3850000 perm   7042 sec   (547 perm/sec)   p_kst 9.949870e-03   p_cons 1.574026e-04   p_joint 5.272727e-05

Joint ci ratio: 2.731120e-01	ci left: 4.608731e-05	ci right 6.089759e-05	k: 205	n:3860000
Cons ci ratio: 1.587036e-01	ci left: 1.454895e-04	ci right 1.708143e-04	k: 609	n:3860000
KS ci ratio: 1.989996e-02	ci left: 9.853545e-03	ci right 1.005185e-02	k: 38416	n:3860000
LRP1   3860000 perm   7075 sec   (546 perm/sec)   p_kst 9.952332e-03   p_cons 1.577720e-04   p_joint 5.310881e-05

Joint ci ratio: 2.731120e-01	ci left: 4.596822e-05	ci right 6.074024e-05	k: 205	n:3870000
Cons ci ratio: 1.587036e-01	ci left: 1.451136e-04	ci right 1.703730e-04	k: 609	n:3870000
KS ci ratio: 1.986916e-02	ci left: 9.858680e-03	ci right 1.005678e-02	k: 38535	n:3870000
LRP1   3870000 perm   7107 sec   (545 perm/sec)   p_kst 9.957364e-03   p_cons 1.573643e-04   p_joint 5.297158e-05

Joint ci ratio: 2.731121e-01	ci left: 4.584974e-05	ci right 6.058369e-05	k: 205	n:3880000
Cons ci ratio: 1.585737e-01	ci left: 1.449871e-04	ci right 1.702018e-04	k: 610	n:3880000
KS ci ratio: 1.984706e-02	ci left: 9.855326e-03	ci right 1.005314e-02	k: 38621	n:3880000
LRP1   3880000 perm   7139 sec   (543 perm/sec)   p_kst 9.953866e-03   p_cons 1.572165e-04   p_joint 5.283505e-05

Joint ci ratio: 2.731121e-01	ci left: 4.573188e-05	ci right 6.042795e-05	k: 205	n:3890000
Cons ci ratio: 1.584441e-01	ci left: 1.448612e-04	ci right 1.700315e-04	k: 611	n:3890000
KS ci ratio: 1.981651e-02	ci left: 9.860431e-03	ci right 1.005804e-02	k: 38740	n:3890000
LRP1   3890000 perm   7171 sec   (542 perm/sec)   p_kst 9.958869e-03   p_cons 1.570694e-04   p_joint 5.269923e-05

Joint ci ratio: 2.731121e-01	ci left: 4.561462e-05	ci right 6.027301e-05	k: 205	n:3900000
Cons ci ratio: 1.583148e-01	ci left: 1.447360e-04	ci right 1.698621e-04	k: 612	n:3900000
KS ci ratio: 1.979227e-02	ci left: 9.859386e-03	ci right 1.005673e-02	k: 38835	n:3900000
LRP1   3900000 perm   7204 sec   (541 perm/sec)   p_kst 9.957692e-03   p_cons 1.569231e-04   p_joint 5.256410e-05

Joint ci ratio: 2.731121e-01	ci left: 4.549795e-05	ci right 6.011886e-05	k: 205	n:3910000
Cons ci ratio: 1.581859e-01	ci left: 1.446115e-04	ci right 1.696936e-04	k: 613	n:3910000
KS ci ratio: 1.977043e-02	ci left: 9.856056e-03	ci right 1.005311e-02	k: 38921	n:3910000
LRP1   3910000 perm   7237 sec   (540 perm/sec)   p_kst 9.954220e-03   p_cons 1.567775e-04   p_joint 5.242967e-05

Joint ci ratio: 2.731121e-01	ci left: 4.538189e-05	ci right 5.996549e-05	k: 205	n:3920000
Cons ci ratio: 1.580572e-01	ci left: 1.444876e-04	ci right 1.695259e-04	k: 614	n:3920000
KS ci ratio: 1.974508e-02	ci left: 9.856297e-03	ci right 1.005310e-02	k: 39021	n:3920000
LRP1   3920000 perm   7270 sec   (539 perm/sec)   p_kst 9.954337e-03   p_cons 1.566327e-04   p_joint 5.229592e-05

Joint ci ratio: 2.724516e-01	ci left: 4.550346e-05	ci right 6.008472e-05	k: 206	n:3930000
Cons ci ratio: 1.578008e-01	ci left: 1.446087e-04	ci right 1.696235e-04	k: 616	n:3930000
KS ci ratio: 1.971677e-02	ci left: 9.859576e-03	ci right 1.005616e-02	k: 39133	n:3930000
LRP1   3930000 perm   7303 sec   (538 perm/sec)   p_kst 9.957506e-03   p_cons 1.567430e-04   p_joint 5.241730e-05

Joint ci ratio: 2.724516e-01	ci left: 4.538797e-05	ci right 5.993222e-05	k: 206	n:3940000
Cons ci ratio: 1.578009e-01	ci left: 1.442417e-04	ci right 1.691930e-04	k: 616	n:3940000
KS ci ratio: 1.968782e-02	ci left: 9.863596e-03	ci right 1.005997e-02	k: 39248	n:3940000
LRP1   3940000 perm   7337 sec   (537 perm/sec)   p_kst 9.961421e-03   p_cons 1.563452e-04   p_joint 5.228426e-05

Joint ci ratio: 2.717959e-01	ci left: 4.550896e-05	ci right 6.005089e-05	k: 207	n:3950000
Cons ci ratio: 1.576732e-01	ci left: 1.441197e-04	ci right 1.690278e-04	k: 617	n:3950000
KS ci ratio: 1.966683e-02	ci left: 9.859786e-03	ci right 1.005587e-02	k: 39332	n:3950000
LRP1   3950000 perm   7369 sec   (536 perm/sec)   p_kst 9.957468e-03   p_cons 1.562025e-04   p_joint 5.240506e-05

Joint ci ratio: 2.711449e-01	ci left: 4.562938e-05	ci right 6.016891e-05	k: 208	n:3960000
Cons ci ratio: 1.571653e-01	ci left: 1.447261e-04	ci right 1.696508e-04	k: 621	n:3960000
KS ci ratio: 1.964389e-02	ci left: 9.858005e-03	ci right 1.005382e-02	k: 39424	n:3960000
LRP1   3960000 perm   7402 sec   (535 perm/sec)   p_kst 9.955556e-03   p_cons 1.568182e-04   p_joint 5.252525e-05

Joint ci ratio: 2.704985e-01	ci left: 4.574923e-05	ci right 6.028631e-05	k: 209	n:3970000
Cons ci ratio: 1.566623e-01	ci left: 1.453295e-04	ci right 1.702706e-04	k: 625	n:3970000
KS ci ratio: 1.962027e-02	ci left: 9.856986e-03	ci right 1.005255e-02	k: 39519	n:3970000
LRP1   3970000 perm   7436 sec   (534 perm/sec)   p_kst 9.954408e-03   p_cons 1.574307e-04   p_joint 5.264484e-05

Joint ci ratio: 2.698567e-01	ci left: 4.586852e-05	ci right 6.040307e-05	k: 210	n:3980000
Cons ci ratio: 1.565374e-01	ci left: 1.452058e-04	ci right 1.701038e-04	k: 626	n:3980000
KS ci ratio: 1.959425e-02	ci left: 9.858472e-03	ci right 1.005380e-02	k: 39624	n:3980000
LRP1   3980000 perm   7472 sec   (533 perm/sec)   p_kst 9.955779e-03   p_cons 1.572864e-04   p_joint 5.276382e-05

Joint ci ratio: 2.698568e-01	ci left: 4.575356e-05	ci right 6.025168e-05	k: 210	n:3990000
Cons ci ratio: 1.562883e-01	ci left: 1.453235e-04	ci right 1.701984e-04	k: 628	n:3990000
KS ci ratio: 1.956634e-02	ci left: 9.861947e-03	ci right 1.005706e-02	k: 39737	n:3990000
LRP1   3990000 perm   7506 sec   (532 perm/sec)   p_kst 9.959148e-03   p_cons 1.573935e-04   p_joint 5.263158e-05

Joint ci ratio: 2.692195e-01	ci left: 4.587229e-05	ci right 6.036790e-05	k: 211	n:4000000
Cons ci ratio: 1.562883e-01	ci left: 1.449602e-04	ci right 1.697729e-04	k: 628	n:4000000
KS ci ratio: 1.954251e-02	ci left: 9.861423e-03	ci right 1.005629e-02	k: 39834	n:4000000
LRP1   4000000 perm   7538 sec   (531 perm/sec)   p_kst 9.958500e-03   p_cons 1.570000e-04   p_joint 5.275000e-05

Joint ci ratio: 3.548947e-01	ci left: 2.503811e-05	ci right 3.605465e-05	k: 121	n:4010000
Cons ci ratio: 1.557937e-01	ci left: 1.455573e-04	ci right 1.703859e-04	k: 632	n:4010000
KS ci ratio: 1.951827e-02	ci left: 9.861399e-03	ci right 1.005602e-02	k: 39933	n:4010000
LRP1   4010000 perm   7572 sec   (530 perm/sec)   p_kst 9.958354e-03   p_cons 1.576060e-04   p_joint 3.017456e-05

Joint ci ratio: 3.548947e-01	ci left: 2.497583e-05	ci right 3.596496e-05	k: 121	n:4020000
Cons ci ratio: 1.555481e-01	ci left: 1.456733e-04	ci right 1.704790e-04	k: 634	n:4020000
KS ci ratio: 1.949215e-02	ci left: 9.863355e-03	ci right 1.005775e-02	k: 40040	n:4020000
LRP1   4020000 perm   7605 sec   (529 perm/sec)   p_kst 9.960199e-03   p_cons 1.577114e-04   p_joint 3.009950e-05

Joint ci ratio: 3.520209e-01	ci left: 2.536607e-05	ci right 3.641588e-05	k: 123	n:4030000
Cons ci ratio: 1.551820e-01	ci left: 1.460273e-04	ci right 1.708293e-04	k: 637	n:4030000
KS ci ratio: 1.946614e-02	ci left: 9.865302e-03	ci right 1.005947e-02	k: 40147	n:4030000
LRP1   4030000 perm   7639 sec   (528 perm/sec)   p_kst 9.962035e-03   p_cons 1.580645e-04   p_joint 3.052109e-05

Joint ci ratio: 3.520209e-01	ci left: 2.530329e-05	ci right 3.632574e-05	k: 123	n:4040000
Cons ci ratio: 1.551820e-01	ci left: 1.456659e-04	ci right 1.704064e-04	k: 637	n:4040000
KS ci ratio: 1.944463e-02	ci left: 9.862806e-03	ci right 1.005671e-02	k: 40236	n:4040000
LRP1   4040000 perm   7674 sec   (526 perm/sec)   p_kst 9.959406e-03   p_cons 1.576733e-04   p_joint 3.044554e-05

Joint ci ratio: 3.520210e-01	ci left: 2.524081e-05	ci right 3.623605e-05	k: 123	n:4050000
Cons ci ratio: 1.551820e-01	ci left: 1.453062e-04	ci right 1.699857e-04	k: 637	n:4050000
KS ci ratio: 1.941492e-02	ci left: 9.868676e-03	ci right 1.006240e-02	k: 40359	n:4050000
LRP1   4050000 perm   7707 sec   (525 perm/sec)   p_kst 9.965185e-03   p_cons 1.572840e-04   p_joint 3.037037e-05

Joint ci ratio: 2.667151e-01	ci left: 4.611341e-05	ci right 6.052702e-05	k: 215	n:4060000
Cons ci ratio: 1.548184e-01	ci left: 1.456585e-04	ci right 1.703345e-04	k: 640	n:4060000
KS ci ratio: 1.939140e-02	ci left: 9.868390e-03	ci right 1.006187e-02	k: 40457	n:4060000
LRP1   4060000 perm   7741 sec   (524 perm/sec)   p_kst 9.964778e-03   p_cons 1.576355e-04   p_joint 5.295567e-05

Joint ci ratio: 2.667151e-01	ci left: 4.600011e-05	ci right 6.037830e-05	k: 215	n:4070000
Cons ci ratio: 1.548185e-01	ci left: 1.453007e-04	ci right 1.699160e-04	k: 640	n:4070000
KS ci ratio: 1.936579e-02	ci left: 9.870306e-03	ci right 1.006356e-02	k: 40564	n:4070000
LRP1   4070000 perm   7776 sec   (523 perm/sec)   p_kst 9.966585e-03   p_cons 1.572482e-04   p_joint 5.282555e-05

Joint ci ratio: 2.667151e-01	ci left: 4.588737e-05	ci right 6.023032e-05	k: 215	n:4080000
Cons ci ratio: 1.544574e-01	ci left: 1.456514e-04	ci right 1.702633e-04	k: 643	n:4080000
KS ci ratio: 1.934292e-02	ci left: 9.869529e-03	ci right 1.006254e-02	k: 40660	n:4080000
LRP1   4080000 perm   7810 sec   (522 perm/sec)   p_kst 9.965686e-03   p_cons 1.575980e-04   p_joint 5.269608e-05

Joint ci ratio: 2.667151e-01	ci left: 4.577517e-05	ci right 6.008305e-05	k: 215	n:4090000
Cons ci ratio: 1.539799e-01	ci left: 1.462355e-04	ci right 1.708627e-04	k: 647	n:4090000
KS ci ratio: 1.932085e-02	ci left: 9.868027e-03	ci right 1.006079e-02	k: 40753	n:4090000
LRP1   4090000 perm   7844 sec   (521 perm/sec)   p_kst 9.964059e-03   p_cons 1.581907e-04   p_joint 5.256724e-05

Joint ci ratio: 2.654888e-01	ci left: 4.611879e-05	ci right 6.045678e-05	k: 217	n:4100000
Cons ci ratio: 1.535068e-01	ci left: 1.468169e-04	ci right 1.714591e-04	k: 651	n:4100000
KS ci ratio: 1.929457e-02	ci left: 9.870901e-03	ci right 1.006345e-02	k: 40864	n:4100000
LRP1   4100000 perm   7878 sec   (520 perm/sec)   p_kst 9.966829e-03   p_cons 1.587805e-04   p_joint 5.292683e-05

Joint ci ratio: 2.654888e-01	ci left: 4.600658e-05	ci right 6.030968e-05	k: 217	n:4110000
Cons ci ratio: 1.533892e-01	ci left: 1.466937e-04	ci right 1.712945e-04	k: 652	n:4110000
KS ci ratio: 1.927195e-02	ci left: 9.870129e-03	ci right 1.006244e-02	k: 40960	n:4110000
LRP1   4110000 perm   7913 sec   (519 perm/sec)   p_kst 9.965937e-03   p_cons 1.586375e-04   p_joint 5.279805e-05

Joint ci ratio: 2.648820e-01	ci left: 4.612150e-05	ci right 6.042212e-05	k: 218	n:4120000
Cons ci ratio: 1.531549e-01	ci left: 1.468044e-04	ci right 1.713828e-04	k: 654	n:4120000
KS ci ratio: 1.925250e-02	ci left: 9.866221e-03	ci right 1.005825e-02	k: 41043	n:4120000
LRP1   4120000 perm   7947 sec   (518 perm/sec)   p_kst 9.961893e-03   p_cons 1.587379e-04   p_joint 5.291262e-05

Joint ci ratio: 2.648820e-01	ci left: 4.600982e-05	ci right 6.027582e-05	k: 218	n:4130000
Cons ci ratio: 1.526893e-01	ci left: 1.473805e-04	ci right 1.719734e-04	k: 658	n:4130000
KS ci ratio: 1.923074e-02	ci left: 9.864742e-03	ci right 1.005653e-02	k: 41136	n:4130000
LRP1   4130000 perm   7981 sec   (517 perm/sec)   p_kst 9.960291e-03   p_cons 1.593220e-04   p_joint 5.278450e-05

Joint ci ratio: 2.648820e-01	ci left: 4.589869e-05	ci right 6.013022e-05	k: 218	n:4140000
Cons ci ratio: 1.525736e-01	ci left: 1.472568e-04	ci right 1.718088e-04	k: 659	n:4140000
KS ci ratio: 1.920411e-02	ci left: 9.868318e-03	ci right 1.005990e-02	k: 41250	n:4140000
LRP1   4140000 perm   8016 sec   (516 perm/sec)   p_kst 9.963768e-03   p_cons 1.591787e-04   p_joint 5.265700e-05

Joint ci ratio: 2.648820e-01	ci left: 4.578809e-05	ci right 5.998533e-05	k: 218	n:4150000
Cons ci ratio: 1.523430e-01	ci left: 1.473655e-04	ci right 1.718951e-04	k: 661	n:4150000
KS ci ratio: 1.917854e-02	ci left: 9.870918e-03	ci right 1.006230e-02	k: 41360	n:4150000
LRP1   4150000 perm   8051 sec   (515 perm/sec)   p_kst 9.966265e-03   p_cons 1.592771e-04   p_joint 5.253012e-05

Joint ci ratio: 2.648820e-01	ci left: 4.567802e-05	ci right 5.984114e-05	k: 218	n:4160000
Cons ci ratio: 1.521133e-01	ci left: 1.474737e-04	ci right 1.719809e-04	k: 663	n:4160000
KS ci ratio: 1.915399e-02	ci left: 9.872549e-03	ci right 1.006371e-02	k: 41466	n:4160000
LRP1   4160000 perm   8086 sec   (514 perm/sec)   p_kst 9.967788e-03   p_cons 1.593750e-04   p_joint 5.240385e-05

Joint ci ratio: 2.636807e-01	ci left: 4.601633e-05	ci right 6.020895e-05	k: 220	n:4170000
Cons ci ratio: 1.519989e-01	ci left: 1.473507e-04	ci right 1.718174e-04	k: 664	n:4170000
KS ci ratio: 1.913047e-02	ci left: 9.873217e-03	ci right 1.006416e-02	k: 41568	n:4170000
LRP1   4170000 perm   8121 sec   (513 perm/sec)   p_kst 9.968345e-03   p_cons 1.592326e-04   p_joint 5.275779e-05

Joint ci ratio: 2.624956e-01	ci left: 4.635316e-05	ci right 6.057486e-05	k: 222	n:4180000
Cons ci ratio: 1.519990e-01	ci left: 1.469982e-04	ci right 1.714064e-04	k: 664	n:4180000
KS ci ratio: 1.910936e-02	ci left: 9.871501e-03	ci right 1.006219e-02	k: 41660	n:4180000
LRP1   4180000 perm   8157 sec   (512 perm/sec)   p_kst 9.966507e-03   p_cons 1.588517e-04   p_joint 5.311005e-05

Joint ci ratio: 2.619090e-01	ci left: 4.646551e-05	ci right 6.068460e-05	k: 223	n:4190000
Cons ci ratio: 1.517709e-01	ci left: 1.471066e-04	ci right 1.714927e-04	k: 666	n:4190000
KS ci ratio: 1.908415e-02	ci left: 9.874069e-03	ci right 1.006456e-02	k: 41770	n:4190000
LRP1   4190000 perm   8192 sec   (511 perm/sec)   p_kst 9.968974e-03   p_cons 1.589499e-04   p_joint 5.322196e-05

Joint ci ratio: 2.619090e-01	ci left: 4.635488e-05	ci right 6.054011e-05	k: 223	n:4200000
Cons ci ratio: 1.517709e-01	ci left: 1.467563e-04	ci right 1.710844e-04	k: 666	n:4200000
KS ci ratio: 1.905790e-02	ci left: 9.877810e-03	ci right 1.006810e-02	k: 41885	n:4200000
LRP1   4200000 perm   8228 sec   (510 perm/sec)   p_kst 9.972619e-03   p_cons 1.585714e-04   p_joint 5.309524e-05

Joint ci ratio: 2.619090e-01	ci left: 4.624477e-05	ci right 6.039631e-05	k: 223	n:4210000
Cons ci ratio: 1.516573e-01	ci left: 1.466362e-04	ci right 1.709246e-04	k: 667	n:4210000
KS ci ratio: 1.903153e-02	ci left: 9.881770e-03	ci right 1.007187e-02	k: 42001	n:4210000
LRP1   4210000 perm   8264 sec   (509 perm/sec)   p_kst 9.976485e-03   p_cons 1.584323e-04   p_joint 5.296912e-05

Joint ci ratio: 2.619090e-01	ci left: 4.613518e-05	ci right 6.025319e-05	k: 223	n:4220000
Cons ci ratio: 1.516573e-01	ci left: 1.462888e-04	ci right 1.705196e-04	k: 667	n:4220000
KS ci ratio: 1.900618e-02	ci left: 9.884767e-03	ci right 1.007467e-02	k: 42113	n:4220000
LRP1   4220000 perm   8299 sec   (508 perm/sec)   p_kst 9.979384e-03   p_cons 1.580569e-04   p_joint 5.284360e-05

Joint ci ratio: 2.613264e-01	ci left: 4.624702e-05	ci right 6.036263e-05	k: 224	n:4230000
Cons ci ratio: 1.515440e-01	ci left: 1.461704e-04	ci right 1.703618e-04	k: 668	n:4230000
KS ci ratio: 1.898252e-02	ci left: 9.886104e-03	ci right 1.007580e-02	k: 42218	n:4230000
LRP1   4230000 perm   8335 sec   (508 perm/sec)   p_kst 9.980615e-03   p_cons 1.579196e-04   p_joint 5.295508e-05

Joint ci ratio: 2.601725e-01	ci left: 4.657882e-05	ci right 6.072272e-05	k: 226	n:4240000
Cons ci ratio: 1.512053e-01	ci left: 1.465064e-04	ci right 1.706943e-04	k: 671	n:4240000
KS ci ratio: 1.896076e-02	ci left: 9.885557e-03	ci right 1.007502e-02	k: 42315	n:4240000
LRP1   4240000 perm   8370 sec   (507 perm/sec)   p_kst 9.979953e-03   p_cons 1.582547e-04   p_joint 5.330189e-05

Joint ci ratio: 2.590339e-01	ci left: 4.690919e-05	ci right 6.108098e-05	k: 228	n:4250000
Cons ci ratio: 1.509808e-01	ci left: 1.466144e-04	ci right 1.707811e-04	k: 673	n:4250000
KS ci ratio: 1.893186e-02	ci left: 9.892506e-03	ci right 1.008181e-02	k: 42444	n:4250000
LRP1   4250000 perm   8406 sec   (506 perm/sec)   p_kst 9.986824e-03   p_cons 1.583529e-04   p_joint 5.364706e-05

Joint ci ratio: 2.584701e-01	ci left: 4.701860e-05	ci right 6.118753e-05	k: 229	n:4260000
Cons ci ratio: 1.508689e-01	ci left: 1.464962e-04	ci right 1.706238e-04	k: 674	n:4260000
KS ci ratio: 1.890735e-02	ci left: 9.894984e-03	ci right 1.008409e-02	k: 42554	n:4260000
LRP1   4260000 perm   8441 sec   (505 perm/sec)   p_kst 9.989202e-03   p_cons 1.582160e-04   p_joint 5.375587e-05

Joint ci ratio: 2.579101e-01	ci left: 4.712752e-05	ci right 6.129355e-05	k: 230	n:4270000
Cons ci ratio: 1.507573e-01	ci left: 1.463784e-04	ci right 1.704672e-04	k: 675	n:4270000
KS ci ratio: 1.888338e-02	ci left: 9.896984e-03	ci right 1.008588e-02	k: 42662	n:4270000
LRP1   4270000 perm   8476 sec   (504 perm/sec)   p_kst 9.991101e-03   p_cons 1.580796e-04   p_joint 5.386417e-05

Joint ci ratio: 2.579101e-01	ci left: 4.701741e-05	ci right 6.115034e-05	k: 230	n:4280000
Cons ci ratio: 1.503132e-01	ci left: 1.469358e-04	ci right 1.710387e-04	k: 679	n:4280000
KS ci ratio: 1.885795e-02	ci left: 9.900602e-03	ci right 1.008931e-02	k: 42777	n:4280000
LRP1   4280000 perm   8513 sec   (503 perm/sec)   p_kst 9.994626e-03   p_cons 1.586449e-04   p_joint 5.373832e-05

Joint ci ratio: 2.573536e-01	ci left: 4.712586e-05	ci right 6.125592e-05	k: 231	n:4290000
Cons ci ratio: 1.499827e-01	ci left: 1.472663e-04	ci right 1.713655e-04	k: 682	n:4290000
KS ci ratio: 1.883595e-02	ci left: 9.900724e-03	ci right 1.008922e-02	k: 42877	n:4290000
LRP1   4290000 perm   8550 sec   (502 perm/sec)   p_kst 9.994639e-03   p_cons 1.589744e-04   p_joint 5.384615e-05

Joint ci ratio: 2.573536e-01	ci left: 4.701627e-05	ci right 6.111346e-05	k: 231	n:4300000
Cons ci ratio: 1.499827e-01	ci left: 1.469238e-04	ci right 1.709670e-04	k: 682	n:4300000
KS ci ratio: 1.881071e-02	ci left: 9.904318e-03	ci right 1.009262e-02	k: 42992	n:4300000
LRP1   4300000 perm   8589 sec   (501 perm/sec)   p_kst 9.998140e-03   p_cons 1.586047e-04   p_joint 5.372093e-05

Joint ci ratio: 2.573537e-01	ci left: 4.690718e-05	ci right 6.097167e-05	k: 231	n:4310000
Cons ci ratio: 1.498730e-01	ci left: 1.468063e-04	ci right 1.708111e-04	k: 683	n:4310000
KS ci ratio: 1.878579e-02	ci left: 9.907664e-03	ci right 1.009578e-02	k: 43106	n:4310000
LRP1   4310000 perm   8625 sec   (500 perm/sec)   p_kst 1.000139e-02   p_cons 1.584687e-04   p_joint 5.359629e-05

Joint ci ratio: 2.573537e-01	ci left: 4.679860e-05	ci right 6.083053e-05	k: 231	n:4320000
Cons ci ratio: 1.496544e-01	ci left: 1.469121e-04	ci right 1.708960e-04	k: 685	n:4320000
KS ci ratio: 1.876228e-02	ci left: 9.909612e-03	ci right 1.009753e-02	k: 43214	n:4320000
LRP1   4320000 perm   8662 sec   (499 perm/sec)   p_kst 1.000324e-02   p_cons 1.585648e-04   p_joint 5.347222e-05

Joint ci ratio: 2.573537e-01	ci left: 4.669052e-05	ci right 6.069005e-05	k: 231	n:4330000
Cons ci ratio: 1.491119e-01	ci left: 1.476843e-04	ci right 1.716991e-04	k: 690	n:4330000
KS ci ratio: 1.874236e-02	ci left: 9.907874e-03	ci right 1.009555e-02	k: 43306	n:4330000
LRP1   4330000 perm   8699 sec   (498 perm/sec)   p_kst 1.000139e-02   p_cons 1.593533e-04   p_joint 5.334873e-05

Joint ci ratio: 2.573537e-01	ci left: 4.658293e-05	ci right 6.055021e-05	k: 231	n:4340000
Cons ci ratio: 1.491119e-01	ci left: 1.473441e-04	ci right 1.713035e-04	k: 690	n:4340000
KS ci ratio: 1.871705e-02	ci left: 9.911877e-03	ci right 1.009938e-02	k: 43423	n:4340000
LRP1   4340000 perm   8735 sec   (497 perm/sec)   p_kst 1.000530e-02   p_cons 1.589862e-04   p_joint 5.322581e-05

Joint ci ratio: 2.568008e-01	ci left: 4.669092e-05	ci right 6.065568e-05	k: 232	n:4350000
Cons ci ratio: 1.490042e-01	ci left: 1.472266e-04	ci right 1.711482e-04	k: 691	n:4350000
KS ci ratio: 1.869424e-02	ci left: 9.913345e-03	ci right 1.010064e-02	k: 43529	n:4350000
LRP1   4350000 perm   8772 sec   (496 perm/sec)   p_kst 1.000667e-02   p_cons 1.588506e-04   p_joint 5.333333e-05

Joint ci ratio: 2.568008e-01	ci left: 4.658383e-05	ci right 6.051656e-05	k: 232	n:4360000
Cons ci ratio: 1.487893e-01	ci left: 1.473306e-04	ci right 1.712314e-04	k: 693	n:4360000
KS ci ratio: 1.866826e-02	ci left: 9.918231e-03	ci right 1.010536e-02	k: 43650	n:4360000
LRP1   4360000 perm   8808 sec   (495 perm/sec)   p_kst 1.001147e-02   p_cons 1.589450e-04   p_joint 5.321101e-05

Joint ci ratio: 2.568009e-01	ci left: 4.647723e-05	ci right 6.037808e-05	k: 232	n:4370000
Cons ci ratio: 1.484687e-01	ci left: 1.476544e-04	ci right 1.715516e-04	k: 696	n:4370000
KS ci ratio: 1.864649e-02	ci left: 9.918767e-03	ci right 1.010568e-02	k: 43752	n:4370000
LRP1   4370000 perm   8844 sec   (494 perm/sec)   p_kst 1.001190e-02   p_cons 1.592677e-04   p_joint 5.308924e-05

Joint ci ratio: 2.568009e-01	ci left: 4.637112e-05	ci right 6.024023e-05	k: 232	n:4380000
Cons ci ratio: 1.482562e-01	ci left: 1.477570e-04	ci right 1.716335e-04	k: 698	n:4380000
KS ci ratio: 1.862607e-02	ci left: 9.917937e-03	ci right 1.010463e-02	k: 43848	n:4380000
LRP1   4380000 perm   8881 sec   (493 perm/sec)   p_kst 1.001096e-02   p_cons 1.593607e-04   p_joint 5.296804e-05

Joint ci ratio: 2.568009e-01	ci left: 4.626549e-05	ci right 6.010301e-05	k: 232	n:4390000
Cons ci ratio: 1.481502e-01	ci left: 1.476398e-04	ci right 1.714788e-04	k: 699	n:4390000
KS ci ratio: 1.860530e-02	ci left: 9.917564e-03	ci right 1.010404e-02	k: 43946	n:4390000
LRP1   4390000 perm   8918 sec   (492 perm/sec)   p_kst 1.001048e-02   p_cons 1.592255e-04   p_joint 5.284738e-05

Joint ci ratio: 2.568009e-01	ci left: 4.616034e-05	ci right 5.996641e-05	k: 232	n:4400000
Cons ci ratio: 1.481503e-01	ci left: 1.473042e-04	ci right 1.710890e-04	k: 699	n:4400000
KS ci ratio: 1.858481e-02	ci left: 9.916967e-03	ci right 1.010322e-02	k: 44043	n:4400000
LRP1   4400000 perm   8954 sec   (491 perm/sec)   p_kst 1.000977e-02   p_cons 1.588636e-04   p_joint 5.272727e-05

Joint ci ratio: 2.568009e-01	ci left: 4.605567e-05	ci right 5.983043e-05	k: 232	n:4410000
Cons ci ratio: 1.480446e-01	ci left: 1.471885e-04	ci right 1.709362e-04	k: 700	n:4410000
KS ci ratio: 1.856077e-02	ci left: 9.920210e-03	ci right 1.010628e-02	k: 44157	n:4410000
LRP1   4410000 perm   8991 sec   (490 perm/sec)   p_kst 1.001293e-02   p_cons 1.587302e-04   p_joint 5.260771e-05

Joint ci ratio: 2.562516e-01	ci left: 4.616317e-05	ci right 5.993583e-05	k: 233	n:4420000
Cons ci ratio: 1.479391e-01	ci left: 1.470734e-04	ci right 1.707841e-04	k: 701	n:4420000
KS ci ratio: 1.854360e-02	ci left: 9.916232e-03	ci right 1.010206e-02	k: 44239	n:4420000
LRP1   4420000 perm   9027 sec   (490 perm/sec)   p_kst 1.000882e-02   p_cons 1.585973e-04   p_joint 5.271493e-05

Joint ci ratio: 2.557058e-01	ci left: 4.627022e-05	ci right 6.004072e-05	k: 234	n:4430000
Cons ci ratio: 1.475194e-01	ci left: 1.476110e-04	ci right 1.713349e-04	k: 705	n:4430000
KS ci ratio: 1.852226e-02	ci left: 9.916766e-03	ci right 1.010239e-02	k: 44341	n:4430000
LRP1   4430000 perm   9065 sec   (489 perm/sec)   p_kst 1.000926e-02   p_cons 1.591422e-04   p_joint 5.282167e-05

Joint ci ratio: 2.557058e-01	ci left: 4.616600e-05	ci right 5.990549e-05	k: 234	n:4440000
Cons ci ratio: 1.473109e-01	ci left: 1.477123e-04	ci right 1.714160e-04	k: 707	n:4440000
KS ci ratio: 1.849930e-02	ci left: 9.919091e-03	ci right 1.010452e-02	k: 44451	n:4440000
LRP1   4440000 perm   9104 sec   (488 perm/sec)   p_kst 1.001149e-02   p_cons 1.592342e-04   p_joint 5.270270e-05

Joint ci ratio: 2.546246e-01	ci left: 4.648296e-05	ci right 6.024899e-05	k: 236	n:4450000
Cons ci ratio: 1.472069e-01	ci left: 1.475968e-04	ci right 1.712638e-04	k: 708	n:4450000
KS ci ratio: 1.847686e-02	ci left: 9.920959e-03	ci right 1.010620e-02	k: 44559	n:4450000
LRP1   4450000 perm   9142 sec   (487 perm/sec)   p_kst 1.001326e-02   p_cons 1.591011e-04   p_joint 5.303371e-05

Joint ci ratio: 2.540891e-01	ci left: 4.658866e-05	ci right 6.035238e-05	k: 237	n:4460000
Cons ci ratio: 1.471033e-01	ci left: 1.474819e-04	ci right 1.711123e-04	k: 709	n:4460000
KS ci ratio: 1.845553e-02	ci left: 9.921702e-03	ci right 1.010674e-02	k: 44662	n:4460000
LRP1   4460000 perm   9180 sec   (486 perm/sec)   p_kst 1.001390e-02   p_cons 1.589686e-04   p_joint 5.313901e-05

Joint ci ratio: 2.540891e-01	ci left: 4.648443e-05	ci right 6.021736e-05	k: 237	n:4470000
Cons ci ratio: 1.468965e-01	ci left: 1.475829e-04	ci right 1.711934e-04	k: 711	n:4470000
KS ci ratio: 1.843303e-02	ci left: 9.923778e-03	ci right 1.010862e-02	k: 44771	n:4470000
LRP1   4470000 perm   9217 sec   (485 perm/sec)   p_kst 1.001588e-02   p_cons 1.590604e-04   p_joint 5.302013e-05

Joint ci ratio: 2.535569e-01	ci left: 4.658969e-05	ci right 6.032033e-05	k: 238	n:4480000
Cons ci ratio: 1.467935e-01	ci left: 1.474685e-04	ci right 1.710426e-04	k: 712	n:4480000
KS ci ratio: 1.841124e-02	ci left: 9.925179e-03	ci right 1.010983e-02	k: 44877	n:4480000
LRP1   4480000 perm   9255 sec   (484 perm/sec)   p_kst 1.001719e-02   p_cons 1.589286e-04   p_joint 5.312500e-05

Joint ci ratio: 2.530281e-01	ci left: 4.669451e-05	ci right 6.042281e-05	k: 239	n:4490000
Cons ci ratio: 1.467935e-01	ci left: 1.471401e-04	ci right 1.706617e-04	k: 712	n:4490000
KS ci ratio: 1.839241e-02	ci left: 9.923469e-03	ci right 1.010790e-02	k: 44969	n:4490000
LRP1   4490000 perm   9293 sec   (483 perm/sec)   p_kst 1.001537e-02   p_cons 1.585746e-04   p_joint 5.322940e-05

Joint ci ratio: 2.525026e-01	ci left: 4.679889e-05	ci right 6.052481e-05	k: 240	n:4500000
Cons ci ratio: 1.467935e-01	ci left: 1.468131e-04	ci right 1.702825e-04	k: 712	n:4500000
KS ci ratio: 1.837488e-02	ci left: 9.920440e-03	ci right 1.010464e-02	k: 45055	n:4500000
LRP1   4500000 perm   9332 sec   (482 perm/sec)   p_kst 1.001222e-02   p_cons 1.582222e-04   p_joint 5.333333e-05

Joint ci ratio: 2.525026e-01	ci left: 4.669512e-05	ci right 6.039061e-05	k: 240	n:4510000
Cons ci ratio: 1.466907e-01	ci left: 1.467011e-04	ci right 1.701348e-04	k: 713	n:4510000
KS ci ratio: 1.835637e-02	ci left: 9.918529e-03	ci right 1.010250e-02	k: 45146	n:4510000
LRP1   4510000 perm   9372 sec   (481 perm/sec)   p_kst 1.001020e-02   p_cons 1.580931e-04   p_joint 5.321508e-05

Joint ci ratio: 2.519804e-01	ci left: 4.679907e-05	ci right 6.049220e-05	k: 241	n:4520000
Cons ci ratio: 1.463835e-01	ci left: 1.470160e-04	ci right 1.704464e-04	k: 716	n:4520000
KS ci ratio: 1.833465e-02	ci left: 9.920149e-03	ci right 1.010393e-02	k: 45253	n:4520000
LRP1   4520000 perm   9410 sec   (480 perm/sec)   p_kst 1.001173e-02   p_cons 1.584071e-04   p_joint 5.331858e-05

Joint ci ratio: 2.519804e-01	ci left: 4.669576e-05	ci right 6.035866e-05	k: 241	n:4530000
Cons ci ratio: 1.461797e-01	ci left: 1.471168e-04	ci right 1.705278e-04	k: 718	n:4530000
KS ci ratio: 1.831565e-02	ci left: 9.918906e-03	ci right 1.010247e-02	k: 45347	n:4530000
LRP1   4530000 perm   9448 sec   (479 perm/sec)   p_kst 1.001038e-02   p_cons 1.584989e-04   p_joint 5.320088e-05

Joint ci ratio: 2.519804e-01	ci left: 4.659290e-05	ci right 6.022571e-05	k: 241	n:4540000
Cons ci ratio: 1.460782e-01	ci left: 1.470049e-04	ci right 1.703805e-04	k: 719	n:4540000
KS ci ratio: 1.829406e-02	ci left: 9.920518e-03	ci right 1.010390e-02	k: 45454	n:4540000
LRP1   4540000 perm   9486 sec   (479 perm/sec)   p_kst 1.001189e-02   p_cons 1.583700e-04   p_joint 5.308370e-05

Joint ci ratio: 2.514614e-01	ci left: 4.669642e-05	ci right 6.032696e-05	k: 242	n:4550000
Cons ci ratio: 1.458757e-01	ci left: 1.471053e-04	ci right 1.704616e-04	k: 721	n:4550000
KS ci ratio: 1.827539e-02	ci left: 9.919061e-03	ci right 1.010222e-02	k: 45547	n:4550000
LRP1   4550000 perm   9524 sec   (478 perm/sec)   p_kst 1.001033e-02   p_cons 1.584615e-04   p_joint 5.318681e-05

Joint ci ratio: 2.514614e-01	ci left: 4.659401e-05	ci right 6.019467e-05	k: 242	n:4560000
Cons ci ratio: 1.457748e-01	ci left: 1.469940e-04	ci right 1.703151e-04	k: 722	n:4560000
KS ci ratio: 1.825496e-02	ci left: 9.919575e-03	ci right 1.010254e-02	k: 45649	n:4560000
LRP1   4560000 perm   9564 sec   (477 perm/sec)   p_kst 1.001075e-02   p_cons 1.583333e-04   p_joint 5.307018e-05

Joint ci ratio: 2.514614e-01	ci left: 4.649206e-05	ci right 6.006295e-05	k: 242	n:4570000
Cons ci ratio: 1.455736e-01	ci left: 1.470941e-04	ci right 1.703960e-04	k: 724	n:4570000
KS ci ratio: 1.823339e-02	ci left: 9.921394e-03	ci right 1.010417e-02	k: 45757	n:4570000
LRP1   4570000 perm   9606 sec   (476 perm/sec)   p_kst 1.001247e-02   p_cons 1.584245e-04   p_joint 5.295405e-05

Joint ci ratio: 2.514614e-01	ci left: 4.639054e-05	ci right 5.993181e-05	k: 242	n:4580000
Cons ci ratio: 1.454733e-01	ci left: 1.469833e-04	ci right 1.702502e-04	k: 725	n:4580000
KS ci ratio: 1.821229e-02	ci left: 9.922770e-03	ci right 1.010536e-02	k: 45863	n:4580000
LRP1   4580000 perm   9644 sec   (475 perm/sec)   p_kst 1.001376e-02   p_cons 1.582969e-04   p_joint 5.283843e-05

Joint ci ratio: 2.509456e-01	ci left: 4.649363e-05	ci right 6.003279e-05	k: 243	n:4590000
Cons ci ratio: 1.454733e-01	ci left: 1.466631e-04	ci right 1.698793e-04	k: 725	n:4590000
KS ci ratio: 1.819307e-02	ci left: 9.922189e-03	ci right 1.010457e-02	k: 45960	n:4590000
LRP1   4590000 perm   9684 sec   (474 perm/sec)   p_kst 1.001307e-02   p_cons 1.579521e-04   p_joint 5.294118e-05

Joint ci ratio: 2.504329e-01	ci left: 4.659629e-05	ci right 6.013331e-05	k: 244	n:4600000
Cons ci ratio: 1.452734e-01	ci left: 1.467632e-04	ci right 1.699606e-04	k: 727	n:4600000
KS ci ratio: 1.817271e-02	ci left: 9.922908e-03	ci right 1.010510e-02	k: 46063	n:4600000
LRP1   4600000 perm   9723 sec   (473 perm/sec)   p_kst 1.001370e-02   p_cons 1.580435e-04   p_joint 5.304348e-05

Joint ci ratio: 2.504329e-01	ci left: 4.649521e-05	ci right 6.000287e-05	k: 244	n:4610000
Cons ci ratio: 1.452734e-01	ci left: 1.464449e-04	ci right 1.695919e-04	k: 727	n:4610000
KS ci ratio: 1.815421e-02	ci left: 9.921681e-03	ci right 1.010366e-02	k: 46157	n:4610000
LRP1   4610000 perm   9762 sec   (472 perm/sec)   p_kst 1.001236e-02   p_cons 1.577007e-04   p_joint 5.292842e-05

Joint ci ratio: 2.504329e-01	ci left: 4.639457e-05	ci right 5.987299e-05	k: 244	n:4620000
Cons ci ratio: 1.452734e-01	ci left: 1.461279e-04	ci right 1.692248e-04	k: 727	n:4620000
KS ci ratio: 1.813319e-02	ci left: 9.923261e-03	ci right 1.010506e-02	k: 46264	n:4620000
LRP1   4620000 perm   9801 sec   (471 perm/sec)   p_kst 1.001385e-02   p_cons 1.573593e-04   p_joint 5.281385e-05

Joint ci ratio: 2.499234e-01	ci left: 4.649681e-05	ci right 5.997317e-05	k: 245	n:4630000
Cons ci ratio: 1.450743e-01	ci left: 1.462285e-04	ci right 1.693070e-04	k: 729	n:4630000
KS ci ratio: 1.811718e-02	ci left: 9.919458e-03	ci right 1.010103e-02	k: 46346	n:4630000
LRP1   4630000 perm   9841 sec   (470 perm/sec)   p_kst 1.000994e-02   p_cons 1.574514e-04   p_joint 5.291577e-05

Joint ci ratio: 2.499234e-01	ci left: 4.639660e-05	ci right 5.984392e-05	k: 245	n:4640000
Cons ci ratio: 1.448759e-01	ci left: 1.463288e-04	ci right 1.693888e-04	k: 731	n:4640000
KS ci ratio: 1.809845e-02	ci left: 9.918676e-03	ci right 1.010004e-02	k: 46442	n:4640000
LRP1   4640000 perm   9880 sec   (470 perm/sec)   p_kst 1.000905e-02   p_cons 1.575431e-04   p_joint 5.280172e-05

Joint ci ratio: 2.499234e-01	ci left: 4.629682e-05	ci right 5.971522e-05	k: 245	n:4650000
Cons ci ratio: 1.445799e-01	ci left: 1.466359e-04	ci right 1.696930e-04	k: 734	n:4650000
KS ci ratio: 1.808194e-02	ci left: 9.915543e-03	ci right 1.009668e-02	k: 46527	n:4650000
LRP1   4650000 perm   9919 sec   (469 perm/sec)   p_kst 1.000581e-02   p_cons 1.578495e-04   p_joint 5.268817e-05

Joint ci ratio: 2.499234e-01	ci left: 4.619747e-05	ci right 5.958708e-05	k: 245	n:4660000
Cons ci ratio: 1.444817e-01	ci left: 1.465281e-04	ci right 1.695512e-04	k: 735	n:4660000
KS ci ratio: 1.806333e-02	ci left: 9.914772e-03	ci right 1.009571e-02	k: 46623	n:4660000
LRP1   4660000 perm   9958 sec   (468 perm/sec)   p_kst 1.000494e-02   p_cons 1.577253e-04   p_joint 5.257511e-05

Joint ci ratio: 2.494170e-01	ci left: 4.629929e-05	ci right 5.968698e-05	k: 246	n:4670000
Cons ci ratio: 1.443836e-01	ci left: 1.464207e-04	ci right 1.694100e-04	k: 736	n:4670000
KS ci ratio: 1.804496e-02	ci left: 9.913792e-03	ci right 1.009452e-02	k: 46718	n:4670000
LRP1   4670000 perm   9998 sec   (467 perm/sec)   p_kst 1.000385e-02   p_cons 1.576017e-04   p_joint 5.267666e-05

Joint ci ratio: 2.489136e-01	ci left: 4.640069e-05	ci right 5.978644e-05	k: 247	n:4680000
Cons ci ratio: 1.438963e-01	ci left: 1.471377e-04	ci right 1.701549e-04	k: 741	n:4680000
KS ci ratio: 1.802160e-02	ci left: 9.918347e-03	ci right 1.009893e-02	k: 46839	n:4680000
LRP1   4680000 perm   10037 sec   (466 perm/sec)   p_kst 1.000833e-02   p_cons 1.583333e-04   p_joint 5.277778e-05

Joint ci ratio: 2.484133e-01	ci left: 4.650169e-05	ci right 5.988544e-05	k: 248	n:4690000
Cons ci ratio: 1.437028e-01	ci left: 1.472351e-04	ci right 1.702338e-04	k: 743	n:4690000
KS ci ratio: 1.799910e-02	ci left: 9.922034e-03	ci right 1.010245e-02	k: 46956	n:4690000
LRP1   4690000 perm   10077 sec   (465 perm/sec)   p_kst 1.001194e-02   p_cons 1.584222e-04   p_joint 5.287846e-05

Joint ci ratio: 2.484133e-01	ci left: 4.640275e-05	ci right 5.975803e-05	k: 248	n:4700000
Cons ci ratio: 1.437028e-01	ci left: 1.469218e-04	ci right 1.698716e-04	k: 743	n:4700000
KS ci ratio: 1.798132e-02	ci left: 9.920621e-03	ci right 1.010083e-02	k: 47049	n:4700000
LRP1   4700000 perm   10117 sec   (465 perm/sec)   p_kst 1.001043e-02   p_cons 1.580851e-04   p_joint 5.276596e-05

Joint ci ratio: 2.484133e-01	ci left: 4.630423e-05	ci right 5.963115e-05	k: 248	n:4710000
Cons ci ratio: 1.436063e-01	ci left: 1.468145e-04	ci right 1.697309e-04	k: 744	n:4710000
KS ci ratio: 1.796166e-02	ci left: 9.921329e-03	ci right 1.010136e-02	k: 47152	n:4710000
LRP1   4710000 perm   10156 sec   (464 perm/sec)   p_kst 1.001104e-02   p_cons 1.579618e-04   p_joint 5.265393e-05

Joint ci ratio: 2.464417e-01	ci left: 4.700104e-05	ci right 6.040471e-05	k: 252	n:4720000
Cons ci ratio: 1.435100e-01	ci left: 1.467077e-04	ci right 1.695908e-04	k: 745	n:4720000
KS ci ratio: 1.794188e-02	ci left: 9.922244e-03	ci right 1.010209e-02	k: 47256	n:4720000
LRP1   4720000 perm   10196 sec   (463 perm/sec)   p_kst 1.001186e-02   p_cons 1.578390e-04   p_joint 5.338983e-05

Joint ci ratio: 2.464417e-01	ci left: 4.690168e-05	ci right 6.027700e-05	k: 252	n:4730000
Cons ci ratio: 1.435101e-01	ci left: 1.463976e-04	ci right 1.692323e-04	k: 745	n:4730000
KS ci ratio: 1.792350e-02	ci left: 9.921682e-03	ci right 1.010133e-02	k: 47353	n:4730000
LRP1   4730000 perm   10235 sec   (462 perm/sec)   p_kst 1.001121e-02   p_cons 1.575053e-04   p_joint 5.327696e-05

Joint ci ratio: 2.464417e-01	ci left: 4.680273e-05	ci right 6.014984e-05	k: 252	n:4740000
Cons ci ratio: 1.431268e-01	ci left: 1.469023e-04	ci right 1.697493e-04	k: 749	n:4740000
KS ci ratio: 1.790708e-02	ci left: 9.919022e-03	ci right 1.009845e-02	k: 47440	n:4740000
LRP1   4740000 perm   10275 sec   (461 perm/sec)   p_kst 1.000844e-02   p_cons 1.580169e-04   p_joint 5.316456e-05

Joint ci ratio: 2.464417e-01	ci left: 4.670419e-05	ci right 6.002320e-05	k: 252	n:4750000
Cons ci ratio: 1.429364e-01	ci left: 1.469991e-04	ci right 1.698281e-04	k: 751	n:4750000
KS ci ratio: 1.788919e-02	ci left: 9.918051e-03	ci right 1.009728e-02	k: 47535	n:4750000
LRP1   4750000 perm   10315 sec   (461 perm/sec)   p_kst 1.000737e-02   p_cons 1.581053e-04   p_joint 5.305263e-05

Joint ci ratio: 2.464417e-01	ci left: 4.660608e-05	ci right 5.989711e-05	k: 252	n:4760000
Cons ci ratio: 1.427467e-01	ci left: 1.470954e-04	ci right 1.699065e-04	k: 753	n:4760000
KS ci ratio: 1.787135e-02	ci left: 9.917083e-03	ci right 1.009612e-02	k: 47630	n:4760000
LRP1   4760000 perm   10355 sec   (460 perm/sec)   p_kst 1.000630e-02   p_cons 1.581933e-04   p_joint 5.294118e-05

Joint ci ratio: 2.464417e-01	ci left: 4.650837e-05	ci right 5.977154e-05	k: 252	n:4770000
Cons ci ratio: 1.425577e-01	ci left: 1.471913e-04	ci right 1.699845e-04	k: 755	n:4770000
KS ci ratio: 1.785337e-02	ci left: 9.916329e-03	ci right 1.009517e-02	k: 47726	n:4770000
LRP1   4770000 perm   10395 sec   (459 perm/sec)   p_kst 1.000545e-02   p_cons 1.582809e-04   p_joint 5.283019e-05

Joint ci ratio: 2.459561e-01	ci left: 4.660737e-05	ci right 5.986858e-05	k: 253	n:4780000
Cons ci ratio: 1.425577e-01	ci left: 1.468834e-04	ci right 1.696289e-04	k: 755	n:4780000
KS ci ratio: 1.783282e-02	ci left: 9.918493e-03	ci right 1.009716e-02	k: 47836	n:4780000
LRP1   4780000 perm   10436 sec   (458 perm/sec)   p_kst 1.000753e-02   p_cons 1.579498e-04   p_joint 5.292887e-05

Joint ci ratio: 2.459561e-01	ci left: 4.651007e-05	ci right 5.974359e-05	k: 253	n:4790000
Cons ci ratio: 1.424635e-01	ci left: 1.467781e-04	ci right 1.694910e-04	k: 756	n:4790000
KS ci ratio: 1.781646e-02	ci left: 9.916076e-03	ci right 1.009454e-02	k: 47924	n:4790000
LRP1   4790000 perm   10477 sec   (457 perm/sec)   p_kst 1.000501e-02   p_cons 1.578288e-04   p_joint 5.281837e-05

Joint ci ratio: 2.454734e-01	ci left: 4.660868e-05	ci right 5.984026e-05	k: 254	n:4800000
Cons ci ratio: 1.420886e-01	ci left: 1.472760e-04	ci right 1.700009e-04	k: 760	n:4800000
KS ci ratio: 1.779977e-02	ci left: 9.914084e-03	ci right 1.009234e-02	k: 48014	n:4800000
LRP1   4800000 perm   10517 sec   (456 perm/sec)   p_kst 1.000292e-02   p_cons 1.583333e-04   p_joint 5.291667e-05

Joint ci ratio: 2.449935e-01	ci left: 4.670691e-05	ci right 5.993650e-05	k: 255	n:4810000
Cons ci ratio: 1.420886e-01	ci left: 1.469698e-04	ci right 1.696474e-04	k: 760	n:4810000
KS ci ratio: 1.778239e-02	ci left: 9.912928e-03	ci right 1.009099e-02	k: 48108	n:4810000
LRP1   4810000 perm   10558 sec   (456 perm/sec)   p_kst 1.000166e-02   p_cons 1.580042e-04   p_joint 5.301455e-05

Joint ci ratio: 2.440420e-01	ci left: 4.699952e-05	ci right 6.025246e-05	k: 257	n:4820000
Cons ci ratio: 1.417166e-01	ci left: 1.474653e-04	ci right 1.701548e-04	k: 764	n:4820000
KS ci ratio: 1.776486e-02	ci left: 9.911984e-03	ci right 1.008985e-02	k: 48203	n:4820000
LRP1   4820000 perm   10598 sec   (455 perm/sec)   p_kst 1.000062e-02   p_cons 1.585062e-04   p_joint 5.331950e-05

Joint ci ratio: 2.440420e-01	ci left: 4.690221e-05	ci right 6.012772e-05	k: 257	n:4830000
Cons ci ratio: 1.416241e-01	ci left: 1.473597e-04	ci right 1.700169e-04	k: 765	n:4830000
KS ci ratio: 1.774721e-02	ci left: 9.911250e-03	ci right 1.008892e-02	k: 48299	n:4830000
LRP1   4830000 perm   10638 sec   (454 perm/sec)   p_kst 9.999793e-03   p_cons 1.583851e-04   p_joint 5.320911e-05

Joint ci ratio: 2.426353e-01	ci left: 4.738735e-05	ci right 6.066104e-05	k: 260	n:4840000
Cons ci ratio: 1.415318e-01	ci left: 1.472545e-04	ci right 1.698795e-04	k: 766	n:4840000
KS ci ratio: 1.772572e-02	ci left: 9.914838e-03	ci right 1.009236e-02	k: 48416	n:4840000
LRP1   4840000 perm   10679 sec   (453 perm/sec)   p_kst 1.000331e-02   p_cons 1.582645e-04   p_joint 5.371901e-05

Joint ci ratio: 2.426354e-01	ci left: 4.728965e-05	ci right 6.053596e-05	k: 260	n:4850000
Cons ci ratio: 1.411641e-01	ci left: 1.477465e-04	ci right 1.703831e-04	k: 770	n:4850000
KS ci ratio: 1.771076e-02	ci left: 9.911228e-03	ci right 1.008853e-02	k: 48498	n:4850000
LRP1   4850000 perm   10720 sec   (452 perm/sec)   p_kst 9.999588e-03   p_cons 1.587629e-04   p_joint 5.360825e-05

Joint ci ratio: 2.421719e-01	ci left: 4.738561e-05	ci right 6.062964e-05	k: 261	n:4860000
Cons ci ratio: 1.407993e-01	ci left: 1.482365e-04	ci right 1.708846e-04	k: 774	n:4860000
KS ci ratio: 1.769216e-02	ci left: 9.911729e-03	ci right 1.008886e-02	k: 48600	n:4860000
LRP1   4860000 perm   10761 sec   (452 perm/sec)   p_kst 1.000000e-02   p_cons 1.592593e-04   p_joint 5.370370e-05

Joint ci ratio: 2.421719e-01	ci left: 4.728830e-05	ci right 6.050514e-05	k: 261	n:4870000
Cons ci ratio: 1.405276e-01	ci left: 1.485264e-04	ci right 1.711714e-04	k: 777	n:4870000
KS ci ratio: 1.767656e-02	ci left: 9.908957e-03	ci right 1.008588e-02	k: 48686	n:4870000
LRP1   4870000 perm   10801 sec   (451 perm/sec)   p_kst 9.997125e-03   p_cons 1.595483e-04   p_joint 5.359343e-05

Joint ci ratio: 2.421719e-01	ci left: 4.719140e-05	ci right 6.038116e-05	k: 261	n:4880000
Cons ci ratio: 1.403473e-01	ci left: 1.486175e-04	ci right 1.712449e-04	k: 779	n:4880000
KS ci ratio: 1.765971e-02	ci left: 9.907625e-03	ci right 1.008435e-02	k: 48779	n:4880000
LRP1   4880000 perm   10841 sec   (450 perm/sec)   p_kst 9.995697e-03   p_cons 1.596311e-04   p_joint 5.348361e-05

Joint ci ratio: 2.417110e-01	ci left: 4.728700e-05	ci right 6.047455e-05	k: 262	n:4890000
Cons ci ratio: 1.400781e-01	ci left: 1.489056e-04	ci right 1.715297e-04	k: 782	n:4890000
KS ci ratio: 1.764000e-02	ci left: 9.909556e-03	ci right 1.008612e-02	k: 48888	n:4890000
LRP1   4890000 perm   10881 sec   (449 perm/sec)   p_kst 9.997546e-03   p_cons 1.599182e-04   p_joint 5.357873e-05

Joint ci ratio: 2.412528e-01	ci left: 4.738223e-05	ci right 6.056754e-05	k: 263	n:4900000
Cons ci ratio: 1.399888e-01	ci left: 1.487986e-04	ci right 1.713908e-04	k: 783	n:4900000
KS ci ratio: 1.762417e-02	ci left: 9.907213e-03	ci right 1.008357e-02	k: 48976	n:4900000
LRP1   4900000 perm   10922 sec   (449 perm/sec)   p_kst 9.995102e-03   p_cons 1.597959e-04   p_joint 5.367347e-05

Joint ci ratio: 2.412528e-01	ci left: 4.728573e-05	ci right 6.044418e-05	k: 263	n:4910000
Cons ci ratio: 1.398996e-01	ci left: 1.486921e-04	ci right 1.712526e-04	k: 784	n:4910000
KS ci ratio: 1.760674e-02	ci left: 9.906704e-03	ci right 1.008288e-02	k: 49073	n:4910000
LRP1   4910000 perm   10964 sec   (448 perm/sec)   p_kst 9.994501e-03   p_cons 1.596741e-04   p_joint 5.356415e-05

Joint ci ratio: 2.412528e-01	ci left: 4.718962e-05	ci right 6.032133e-05	k: 263	n:4920000
Cons ci ratio: 1.398106e-01	ci left: 1.485860e-04	ci right 1.711148e-04	k: 785	n:4920000
KS ci ratio: 1.758865e-02	ci left: 9.907006e-03	ci right 1.008300e-02	k: 49174	n:4920000
LRP1   4920000 perm   11005 sec   (447 perm/sec)   p_kst 9.994715e-03   p_cons 1.595528e-04   p_joint 5.345528e-05

Joint ci ratio: 2.412528e-01	ci left: 4.709390e-05	ci right 6.019898e-05	k: 263	n:4930000
Cons ci ratio: 1.397217e-01	ci left: 1.484804e-04	ci right 1.709777e-04	k: 786	n:4930000
KS ci ratio: 1.757116e-02	ci left: 9.906702e-03	ci right 1.008252e-02	k: 49272	n:4930000
LRP1   4930000 perm   11046 sec   (446 perm/sec)   p_kst 9.994320e-03   p_cons 1.594320e-04   p_joint 5.334686e-05

Joint ci ratio: 2.407972e-01	ci left: 4.718877e-05	ci right 6.029175e-05	k: 264	n:4940000
Cons ci ratio: 1.395445e-01	ci left: 1.485705e-04	ci right 1.710506e-04	k: 788	n:4940000
KS ci ratio: 1.755245e-02	ci left: 9.907809e-03	ci right 1.008345e-02	k: 49377	n:4940000
LRP1   4940000 perm   11088 sec   (446 perm/sec)   p_kst 9.995344e-03   p_cons 1.595142e-04   p_joint 5.344130e-05

Joint ci ratio: 2.407972e-01	ci left: 4.709344e-05	ci right 6.016994e-05	k: 264	n:4950000
Cons ci ratio: 1.395446e-01	ci left: 1.482704e-04	ci right 1.707050e-04	k: 788	n:4950000
KS ci ratio: 1.753954e-02	ci left: 9.902476e-03	ci right 1.007790e-02	k: 49450	n:4950000
LRP1   4950000 perm   11130 sec   (445 perm/sec)   p_kst 9.989899e-03   p_cons 1.591919e-04   p_joint 5.333333e-05

Joint ci ratio: 2.403442e-01	ci left: 4.718795e-05	ci right 6.026238e-05	k: 265	n:4960000
Cons ci ratio: 1.391921e-01	ci left: 1.487498e-04	ci right 1.711954e-04	k: 792	n:4960000
KS ci ratio: 1.752487e-02	ci left: 9.899172e-03	ci right 1.007438e-02	k: 49533	n:4960000
LRP1   4960000 perm   11171 sec   (444 perm/sec)   p_kst 9.986492e-03   p_cons 1.596774e-04   p_joint 5.342742e-05

Joint ci ratio: 2.403442e-01	ci left: 4.709301e-05	ci right 6.014112e-05	k: 265	n:4970000
Cons ci ratio: 1.389296e-01	ci left: 1.490331e-04	ci right 1.714755e-04	k: 795	n:4970000
KS ci ratio: 1.750365e-02	ci left: 9.903293e-03	ci right 1.007836e-02	k: 49653	n:4970000
LRP1   4970000 perm   11213 sec   (443 perm/sec)   p_kst 9.990543e-03   p_cons 1.599598e-04   p_joint 5.331992e-05

Joint ci ratio: 2.398936e-01	ci left: 4.718717e-05	ci right 6.023322e-05	k: 266	n:4980000
Cons ci ratio: 1.387554e-01	ci left: 1.491215e-04	ci right 1.715468e-04	k: 797	n:4980000
KS ci ratio: 1.748480e-02	ci left: 9.904799e-03	ci right 1.007971e-02	k: 49760	n:4980000
LRP1   4980000 perm   11254 sec   (442 perm/sec)   p_kst 9.991968e-03   p_cons 1.600402e-04   p_joint 5.341365e-05

Joint ci ratio: 2.394457e-01	ci left: 4.728097e-05	ci right 6.032492e-05	k: 267	n:4990000
Cons ci ratio: 1.386685e-01	ci left: 1.490161e-04	ci right 1.714103e-04	k: 798	n:4990000
KS ci ratio: 1.746797e-02	ci left: 9.904104e-03	ci right 1.007883e-02	k: 49856	n:4990000
LRP1   4990000 perm   11296 sec   (442 perm/sec)   p_kst 9.991182e-03   p_cons 1.599198e-04   p_joint 5.350701e-05

Joint ci ratio: 2.390002e-01	ci left: 4.737442e-05	ci right 6.041624e-05	k: 268	n:5000000
Cons ci ratio: 1.386685e-01	ci left: 1.487181e-04	ci right 1.710675e-04	k: 798	n:5000000
KS ci ratio: 1.744854e-02	ci left: 9.906399e-03	ci right 1.008097e-02	k: 49967	n:5000000
LRP1   5000000 perm   11338 sec   (441 perm/sec)   p_kst 9.993400e-03   p_cons 1.596000e-04   p_joint 5.360000e-05

Outputting figure to mutsig2_images.part000000000098/LRP1.2_13991_5000000_0.0099934_0.0001596_5.36e-05.png
                gene_name: LRP1
               theta_stop: 0.24 
                    nperm: 5000000 
                     p_ks: 0.0100 
        ci_ks_bounds_left: 0.0099 
       ci_ks_bounds_right: 0.010 
                   p_cons: 0.00016 
      ci_cons_bounds_left: 0.00015 
     ci_cons_bounds_right: 0.00017 
                  p_joint: 5.36e-05 
     ci_joint_bounds_left: 4.74e-05 
    ci_joint_bounds_right: 6.04e-05 

Current progress: 73 percent done.
LRP11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.930177e-02	ci left: 6.320107e-01	ci right 6.509069e-01	k: 6415	n:10000
Cons ci ratio: 2.833421e-03	ci left: 9.932998e-01	ci right 9.962004e-01	k: 9949	n:10000
KS ci ratio: 8.928483e-02	ci left: 1.543368e-01	ci right 1.688609e-01	k: 1615	n:10000
LRP11   10000 perm   2 sec   (6504 perm/sec)   p_kst 1.615000e-01   p_cons 9.949000e-01   p_joint 6.415000e-01

Outputting figure to mutsig2_images.part000000000098/LRP11.2_1531_10000_0.1615_0.9949_0.6415.png
                gene_name: LRP11
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 82 percent done.
LRP2
Processing conservation and coverage...
70% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.856483e-03	ci left: 9.668882e-01	ci right 9.736342e-01	k: 9704	n:10000
KS ci ratio: 6.724503e-03	ci left: 9.680482e-01	ci right 9.746734e-01	k: 9715	n:10000
LRP2   10000 perm   3 sec   (3277 perm/sec)   p_kst 9.715000e-01   p_cons 9.704000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000098/LRP2.2_14284_10000_0.9715_0.9704_1.png
                gene_name: LRP2
               theta_stop: 0.0069 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 91 percent done.
LRRC16B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.437769e-02	ci left: 4.284445e-01	ci right 4.479915e-01	k: 4382	n:10000
Cons ci ratio: 3.373175e-02	ci left: 5.647390e-01	ci right 5.842175e-01	k: 5745	n:10000
KS ci ratio: 5.112967e-02	ci left: 3.606257e-01	ci right 3.796501e-01	k: 3701	n:10000
LRRC16B   10000 perm   2 sec   (5481 perm/sec)   p_kst 3.701000e-01   p_cons 5.745000e-01   p_joint 4.382000e-01

Outputting figure to mutsig2_images.part000000000098/LRRC16B.2_4279_10000_0.3701_0.5745_0.4382.png
                gene_name: LRRC16B
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000098
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 98 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4398112: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000099> was used as the working directory.
Started at Wed Oct 24 16:13:36 2012
Results reported at Wed Oct 24 16:15:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000099.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000099.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 99  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000099.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    128.89 sec.
    Max Memory :      1192 MB
    Max Swap   :      3963 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
99
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 99
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 99: processing genes 8793 - 8881
Calculating significance of each gene.
Using projection method.
8793	LRRC18	1
8794	LRRC19	1
8795	LRRC2	1
8796	LRRC20	1
8797	LRRC23	1
8798	LRRC24	1
8799	LRRC25	1
8800	LRRC27	1
8801	LRRC28	1
8802	LRRC29	1
8803	LRRC3	1
8804	LRRC30	1
8805	LRRC31	2.858992e-02
8806	LRRC32	1
8807	LRRC33	1
8808	LRRC34	1.455777e-01
8809	LRRC36	1
8810	LRRC37A2	1
8811	LRRC37A3	3.373575e-01
8812	LRRC37B	1
8813	LRRC39	1
8814	LRRC3B	1
8815	LRRC4	1
8816	LRRC40	1.599069e-02
8817	LRRC41	1.754091e-01
8818	LRRC42	1
8819	LRRC43	1
8820	LRRC45	1
8821	LRRC46	1
8822	LRRC47	1.421271e-01
8823	LRRC48	1
8824	LRRC49	1
8825	LRRC4B	1
8826	LRRC4C	1
8827	LRRC50	2.850648e-01
8828	LRRC52	1.609014e-01
8829	LRRC55	1
8830	LRRC56	1
8831	LRRC57	1
8832	LRRC58	1
8833	LRRC59	3.925784e-02
8834	LRRC6	1
8835	LRRC61	1
8836	LRRC66	1
8837	LRRC67	1
8838	LRRC7	2.130089e-01
8839	LRRC8A	1
8840	LRRC8B	1.498822e-01
8841	LRRC8C	1
8842	LRRC8D	1
In gene LRRC8E the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 2399    n = 1	mu =   4.43e-07
8843	LRRC8E	9.178651e-02
8844	LRRCC1	1
8845	LRRFIP1	1
8846	LRRFIP2	1
8847	LRRIQ1	2.412327e-01
8848	LRRIQ3	1
8849	LRRIQ4	1
8850	LRRK1	3.474128e-01
8851	LRRK2	1
8852	LRRN1	1.457253e-01
8853	LRRN2	1
8854	LRRN3	1
8855	LRRN4	1
8856	LRRN4CL	1
8857	LRRTM1	2.777236e-02
8858	LRRTM2	1
8859	LRRTM3	2.653225e-01
8860	LRRTM4	1
8861	LRSAM1	2.593750e-01
8862	LRTM1	1
8863	LRTM2	1
8864	LRTOMT	1
8865	LRWD1	1
8866	LSAMP	1.791668e-01
8867	LSG1	1
8868	LSM1	1
8869	LSM10	1
8870	LSM11	1
8871	LSM12	1
8872	LSM14A	1
8873	LSM14B	1
8874	LSM2	1
8875	LSM3	1
8876	LSM4	1
8877	LSM5	5.195969e-02
8878	LSM6	1
8879	LSM7	1
8880	LSMD1	1
8881	LSP1	1
Done

Running MutSig 2:
Scatter job 99: processing genes 8793 - 8881
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LRRC31
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.451724e-02	ci left: 7.098755e-01	ci right 7.275970e-01	k: 7188	n:10000
Cons ci ratio: 2.474777e-02	ci left: 7.060407e-01	ci right 7.238339e-01	k: 7150	n:10000
KS ci ratio: 4.413521e-02	ci left: 4.311373e-01	ci right 4.506972e-01	k: 4409	n:10000
LRRC31   10000 perm   2 sec   (6141 perm/sec)   p_kst 4.409000e-01   p_cons 7.150000e-01   p_joint 7.188000e-01

Outputting figure to mutsig2_images.part000000000099/LRRC31.3_1695_10000_0.4409_0.715_0.7188.png
                gene_name: LRRC31
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.71 
    ci_joint_bounds_right: 0.73 

Current progress: 25 percent done.
LRRC40
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.219129e-02	ci left: 7.487731e-01	ci right 7.656768e-01	k: 7573	n:10000
KS ci ratio: 6.798590e-02	ci left: 2.409439e-01	ci right 2.580023e-01	k: 2494	n:10000
LRRC40   10000 perm   2 sec   (6382 perm/sec)   p_kst 2.494000e-01   p_cons 7.573000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000099/LRRC40.2_1869_10000_0.2494_0.7573_1.png
                gene_name: LRRC40
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
LRRC8B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.796730e-02	ci left: 3.046112e-01	ci right 3.228974e-01	k: 3137	n:10000
KS ci ratio: 6.613156e-02	ci left: 2.513249e-01	ci right 2.686151e-01	k: 2599	n:10000
LRRC8B   10000 perm   2 sec   (6354 perm/sec)   p_kst 2.599000e-01   p_cons 3.137000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000099/LRRC8B.2_2420_10000_0.2599_0.3137_1.png
                gene_name: LRRC8B
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
LRRK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.391093e-02	ci left: 8.818604e-01	ci right 8.943125e-01	k: 8882	n:10000
KS ci ratio: 2.277655e-02	ci left: 7.389648e-01	ci right 7.560908e-01	k: 7476	n:10000
LRRK1   10000 perm   2 sec   (4933 perm/sec)   p_kst 7.476000e-01   p_cons 8.882000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000099/LRRK1.2_6180_10000_0.7476_0.8882_1.png
                gene_name: LRRK1
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000099
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 99 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4398115: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000100> was used as the working directory.
Started at Wed Oct 24 16:13:39 2012
Results reported at Wed Oct 24 16:15:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000100.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000100.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 100  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000100.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    136.24 sec.
    Max Memory :      1509 MB
    Max Swap   :      4073 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
100
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 100
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 100: processing genes 8882 - 8971
Calculating significance of each gene.
Using projection method.
8882	LSR	1
8883	LSS	1
8884	LST-3TM12	1
8885	LST1	1
8886	LTA	1
8887	LTA4H	1
8888	LTB	1
8889	LTB4R	1
8890	LTB4R2	1
8891	LTBP1	1
8892	LTBP2	1
8893	LTBP3	1
8894	LTBP4	1.337259e-01
8895	LTBR	1
8896	LTC4S	1
8897	LTF	1
8898	LTK	1
8899	LTV1	1
8900	LUC7L	1
8901	LUC7L2	1
8902	LUC7L3	1
8903	LUM	1
8904	LUZP1	1
8905	LUZP2	1
8906	LUZP4	1
8907	LXN	1
8908	LY6D	1
8909	LY6E	1
8910	LY6G5B	1
8911	LY6G5C	1
8912	LY6G6C	1
8913	LY6G6D	1
8914	LY6G6F	1
8915	LY6H	1
8916	LY6K	1
8917	LY75	2.791107e-01
8918	LY86	1
8919	LY9	1
8920	LY96	9.134440e-03
8921	LYAR	1
8922	LYG1	1
8923	LYG2	1
8924	LYN	1
8925	LYNX1	1
8926	LYPD1	1
8927	LYPD2	1
8928	LYPD3	1.208624e-02
8929	LYPD4	1
8930	LYPD5	5.763105e-02
8931	LYPD6	1
8932	LYPD6B	1
8933	LYPLA1	1
8934	LYPLA2	1
8935	LYPLAL1	1
8936	LYRM1	1
8937	LYRM2	1
8938	LYRM4	1
8939	LYRM5	1
8940	LYRM7	1
8941	LYSMD1	1
8942	LYSMD2	1
8943	LYSMD3	1
8944	LYSMD4	1
8945	LYST	2.380143e-01
8946	LYVE1	1
8947	LYZ	1
8948	LYZL1	3.781503e-03
8949	LYZL2	1
8950	LYZL4	1
8951	LYZL6	1
8952	LZIC	1
8953	LZTFL1	1
8954	LZTR1	1
8955	LZTS1	1
8956	LZTS2	1
8957	M6PR	1.419655e-01
8958	MAB21L1	1
8959	MAB21L2	1
8960	MACC1	1
8961	MACF1	1
8962	MACROD1	1
8963	MACROD2	1
8964	MAD1L1	1
8965	MAD2L1	1
8966	MAD2L1BP	1
8967	MAD2L2	1
8968	MADCAM1	1
8969	MADD	1
8970	MAEA	1
8971	MAEL	7.605987e-03
Done

Running MutSig 2:
Scatter job 100: processing genes 8882 - 8971
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LYST
Processing conservation and coverage...
86% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.286912e-01	ci left: 7.941135e-02	ci right 9.043186e-02	k: 848	n:10000
Cons ci ratio: 1.417551e-02	ci left: 8.779709e-01	ci right 8.906043e-01	k: 8844	n:10000
KS ci ratio: 2.473410e-01	ci left: 2.146516e-02	ci right 2.761609e-02	k: 244	n:10000
LYST   10000 perm   3 sec   (3390 perm/sec)   p_kst 2.440000e-02   p_cons 8.844000e-01   p_joint 8.480000e-02

Joint ci ratio: 1.030640e-01	ci left: 6.396343e-02	ci right 7.096296e-02	k: 1348	n:20000
Cons ci ratio: 9.993046e-03	ci left: 8.804976e-01	ci right 8.893901e-01	k: 17700	n:20000
KS ci ratio: 1.835317e-01	ci left: 2.025053e-02	ci right 2.438996e-02	k: 445	n:20000
LYST   20000 perm   8 sec   (2397 perm/sec)   p_kst 2.225000e-02   p_cons 8.850000e-01   p_joint 6.740000e-02

Joint ci ratio: 9.656684e-02	ci left: 4.954696e-02	ci right 5.460690e-02	k: 1561	n:30000
Cons ci ratio: 8.140266e-03	ci left: 8.818090e-01	ci right 8.890495e-01	k: 26564	n:30000
KS ci ratio: 1.461008e-01	ci left: 2.171899e-02	ci right 2.517415e-02	k: 702	n:30000
LYST   30000 perm   12 sec   (2528 perm/sec)   p_kst 2.340000e-02   p_cons 8.854667e-01   p_joint 5.203333e-02

Joint ci ratio: 8.803601e-02	ci left: 4.514222e-02	ci right 4.932383e-02	k: 1888	n:40000
Cons ci ratio: 7.017069e-03	ci left: 8.832497e-01	ci right 8.894941e-01	k: 35456	n:40000
KS ci ratio: 1.312915e-01	ci left: 2.036703e-02	ci right 2.325297e-02	k: 871	n:40000
LYST   40000 perm   15 sec   (2598 perm/sec)   p_kst 2.177500e-02   p_cons 8.864000e-01   p_joint 4.720000e-02

Joint ci ratio: 7.647861e-02	ci left: 4.800765e-02	ci right 5.184482e-02	k: 2495	n:50000
Cons ci ratio: 6.272444e-03	ci left: 8.837074e-01	ci right 8.892876e-01	k: 44326	n:50000
KS ci ratio: 1.117934e-01	ci left: 2.265673e-02	ci right 2.535892e-02	k: 1199	n:50000
LYST   50000 perm   19 sec   (2630 perm/sec)   p_kst 2.398000e-02   p_cons 8.865200e-01   p_joint 4.990000e-02

Joint ci ratio: 7.300386e-02	ci left: 4.417370e-02	ci right 4.753708e-02	k: 2750	n:60000
Cons ci ratio: 5.747301e-03	ci left: 8.831944e-01	ci right 8.883015e-01	k: 53146	n:60000
KS ci ratio: 1.022716e-01	ci left: 2.267635e-02	ci right 2.513666e-02	k: 1433	n:60000
LYST   60000 perm   23 sec   (2645 perm/sec)   p_kst 2.388333e-02   p_cons 8.857667e-01   p_joint 4.583333e-02

Joint ci ratio: 7.010370e-02	ci left: 4.125623e-02	ci right 4.426753e-02	k: 2992	n:70000
Cons ci ratio: 5.296369e-03	ci left: 8.843288e-01	ci right 8.890391e-01	k: 62069	n:70000
KS ci ratio: 9.506432e-02	ci left: 2.258579e-02	ci right 2.485393e-02	k: 1659	n:70000
LYST   70000 perm   26 sec   (2647 perm/sec)   p_kst 2.370000e-02   p_cons 8.867000e-01   p_joint 4.274286e-02

Outputting figure to mutsig2_images.part000000000100/LYST.4_11610_70000_0.0237_0.8867_0.042743.png
                gene_name: LYST
               theta_stop: 0.095 
                    nperm: 70000 
                     p_ks: 0.024 
        ci_ks_bounds_left: 0.023 
       ci_ks_bounds_right: 0.025 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.043 
     ci_joint_bounds_left: 0.041 
    ci_joint_bounds_right: 0.044 

Current progress: 20 percent done.
LTBP4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.787716e-02	ci left: 2.415369e-01	ci right 2.586089e-01	k: 2500	n:10000
Cons ci ratio: 1.413391e-02	ci left: 8.785849e-01	ci right 8.911899e-01	k: 8850	n:10000
KS ci ratio: 2.696112e-01	ci left: 1.790635e-02	ci right 2.357766e-02	k: 206	n:10000
LTBP4   10000 perm   2 sec   (5261 perm/sec)   p_kst 2.060000e-02   p_cons 8.850000e-01   p_joint 2.500000e-01

Joint ci ratio: 5.379374e-02	ci left: 2.041251e-01	ci right 2.154594e-01	k: 4195	n:20000
Cons ci ratio: 1.069440e-02	ci left: 8.657171e-01	ci right 8.750749e-01	k: 17409	n:20000
KS ci ratio: 1.845928e-01	ci left: 2.001183e-02	ci right 2.412875e-02	k: 440	n:20000
LTBP4   20000 perm   4 sec   (4745 perm/sec)   p_kst 2.200000e-02   p_cons 8.704500e-01   p_joint 2.097500e-01

Joint ci ratio: 2.198106e-02	ci left: 5.088933e-01	ci right 5.202372e-01	k: 15437	n:30000
Cons ci ratio: 8.352776e-03	ci left: 8.764044e-01	ci right 8.837885e-01	k: 26404	n:30000
KS ci ratio: 1.465282e-01	ci left: 2.159043e-02	ci right 2.503607e-02	k: 698	n:30000
LTBP4   30000 perm   7 sec   (4538 perm/sec)   p_kst 2.326667e-02   p_cons 8.801333e-01   p_joint 5.145667e-01

Joint ci ratio: 3.319337e-02	ci left: 2.542147e-01	ci right 2.628204e-01	k: 10340	n:40000
Cons ci ratio: 7.191824e-03	ci left: 8.781408e-01	ci right 8.845038e-01	k: 35254	n:40000
KS ci ratio: 1.276003e-01	ci left: 2.157740e-02	ci right 2.454240e-02	k: 921	n:40000
LTBP4   40000 perm   9 sec   (4397 perm/sec)   p_kst 2.302500e-02   p_cons 8.813500e-01   p_joint 2.585000e-01

Joint ci ratio: 2.701386e-02	ci left: 2.923194e-01	ci right 3.003442e-01	k: 14816	n:50000
Cons ci ratio: 6.411257e-03	ci left: 8.791805e-01	ci right 8.848551e-01	k: 44102	n:50000
KS ci ratio: 1.138517e-01	ci left: 2.183991e-02	ci right 2.449585e-02	k: 1157	n:50000
LTBP4   50000 perm   12 sec   (4284 perm/sec)   p_kst 2.314000e-02   p_cons 8.820400e-01   p_joint 2.963200e-01

Joint ci ratio: 3.226384e-02	ci left: 1.942546e-01	ci right 2.006414e-01	k: 11846	n:60000
Cons ci ratio: 5.844355e-03	ci left: 8.797283e-01	ci right 8.849013e-01	k: 52940	n:60000
KS ci ratio: 1.035740e-01	ci left: 2.210770e-02	ci right 2.453871e-02	k: 1398	n:60000
LTBP4   60000 perm   14 sec   (4189 perm/sec)   p_kst 2.330000e-02   p_cons 8.823333e-01   p_joint 1.974333e-01

Joint ci ratio: 2.658317e-02	ci left: 2.338536e-01	ci right 2.401682e-01	k: 16590	n:70000
Cons ci ratio: 5.399000e-03	ci left: 8.803797e-01	ci right 8.851599e-01	k: 61795	n:70000
KS ci ratio: 9.619818e-02	ci left: 2.205562e-02	ci right 2.429843e-02	k: 1621	n:70000
LTBP4   70000 perm   17 sec   (4100 perm/sec)   p_kst 2.315714e-02   p_cons 8.827857e-01   p_joint 2.370000e-01

Outputting figure to mutsig2_images.part000000000100/LTBP4.2_5299_70000_0.023157_0.88279_0.237.png
                gene_name: LTBP4
               theta_stop: 0.096 
                    nperm: 70000 
                     p_ks: 0.023 
        ci_ks_bounds_left: 0.022 
       ci_ks_bounds_right: 0.024 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 40 percent done.
LYPD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.779278e-02	ci left: 5.083526e-01	ci right 5.280368e-01	k: 5182	n:10000
KS ci ratio: 2.072783e-02	ci left: 7.732695e-01	ci right 7.895662e-01	k: 7815	n:10000
LYPD3   10000 perm   1 sec   (6841 perm/sec)   p_kst 7.815000e-01   p_cons 5.182000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000100/LYPD3.2_1061_10000_0.7815_0.5182_1.png
                gene_name: LYPD3
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
LYZL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.212332e-02	ci left: 5.885136e-01	ci right 6.078292e-01	k: 5982	n:10000
KS ci ratio: 2.236629e-02	ci left: 7.458401e-01	ci right 7.628115e-01	k: 7544	n:10000
LYZL1   10000 perm   1 sec   (7164 perm/sec)   p_kst 7.544000e-01   p_cons 5.982000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000100/LYZL1.2_605_10000_0.7544_0.5982_1.png
                gene_name: LYZL1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
MAEL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.816456e-02	ci left: 6.501168e-01	ci right 6.687903e-01	k: 6595	n:10000
Cons ci ratio: 4.100724e-02	ci left: 4.675680e-01	ci right 4.872452e-01	k: 4774	n:10000
KS ci ratio: 1.007820e-01	ci left: 1.247387e-01	ci right 1.380768e-01	k: 1313	n:10000
MAEL   10000 perm   2 sec   (6533 perm/sec)   p_kst 1.313000e-01   p_cons 4.774000e-01   p_joint 6.595000e-01

Joint ci ratio: 2.646173e-02	ci left: 5.162000e-01	ci right 5.300933e-01	k: 10463	n:20000
Cons ci ratio: 2.913279e-02	ci left: 4.681581e-01	ci right 4.820491e-01	k: 9502	n:20000
KS ci ratio: 7.148428e-02	ci left: 1.260082e-01	ci right 1.353995e-01	k: 2613	n:20000
MAEL   20000 perm   3 sec   (5761 perm/sec)   p_kst 1.306500e-01   p_cons 4.751000e-01   p_joint 5.231500e-01

Outputting figure to mutsig2_images.part000000000100/MAEL.2_1353_20000_0.13065_0.4751_0.52315.png
                gene_name: MAEL
               theta_stop: 0.071 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.52 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.53 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000100
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 100 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4398117: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000101> was used as the working directory.
Started at Wed Oct 24 16:14:00 2012
Results reported at Wed Oct 24 16:16:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000101.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000101.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 101  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000101.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    130.23 sec.
    Max Memory :      1554 MB
    Max Swap   :      3971 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
101
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 101
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 101: processing genes 8972 - 9061
Calculating significance of each gene.
Using projection method.
8972	MAF	1
8973	MAF1	1
8974	MAFB	1
8975	MAFF	1
8976	MAFG	1
8977	MAFK	1
8978	MAG	1.214138e-01
8979	MAGEA1	5.469363e-02
8980	MAGEA10	4.526821e-02
8981	MAGEA11	2.298246e-01
8982	MAGEA12	1.016846e-01
8983	MAGEA3	3.517324e-02
8984	MAGEA4	1
8985	MAGEA5	1
8986	MAGEA6	1
8987	MAGEA8	1
8988	MAGEB1	1
8989	MAGEB10	2.179473e-02
8990	MAGEB16	1
8991	MAGEB18	1.255817e-01
8992	MAGEB2	1
8993	MAGEB3	1
8994	MAGEB4	1
8995	MAGEB6	1
8996	MAGEC1	1.980400e-02
8997	MAGEC2	1
8998	MAGEC3	1.446715e-02
8999	MAGED1	1
9000/17942 9000	MAGED2	1
9001	MAGEE1	1
9002	MAGEE2	1
9003	MAGEF1	1.321817e-01
9004	MAGEH1	8.608382e-02
9005	MAGEL2	1
9006	MAGI1	1
9007	MAGI2	1.174262e-01
9008	MAGI3	5.447442e-01
9009	MAGIX	1
9010	MAGOH	1
9011	MAGOHB	1
9012	MAGT1	5.010619e-04
9013	MAK	1
9014	MAK16	1
9015	MAL	1
9016	MAL2	1
9017	MALL	1
9018	MALT1	1
9019	MAMDC2	1
9020	MAMDC4	1
9021	MAML1	1.683691e-01
9022	MAML2	3.687900e-01
9023	MAML3	9.156225e-02
9024	MAMLD1	1
9025	MAMSTR	1
9026	MAN1A1	1
9027	MAN1A2	2.393305e-01
9028	MAN1B1	1
9029	MAN1C1	1
9030	MAN2A1	1
9031	MAN2A2	1
9032	MAN2B1	1
9033	MAN2B2	1
9034	MAN2C1	1
9035	MANBA	2.564434e-01
9036	MANBAL	1
9037	MANEA	1
9038	MANEAL	1
9039	MANF	1
9040	MANSC1	1
9041	MAOA	2.469105e-01
9042	MAOB	1
9043	MAP1A	1
9044	MAP1B	2.136984e-01
9045	MAP1D	1
9046	MAP1LC3A	3.421649e-02
9047	MAP1LC3B	1
9048	MAP1LC3B2	1
9049	MAP1LC3C	1
9050	MAP1S	1
9051	MAP2	2.774270e-01
9052	MAP2K1	1
9053	MAP2K2	1
9054	MAP2K3	1
9055	MAP2K4	1
9056	MAP2K5	1
9057	MAP2K6	1
9058	MAP2K7	1
9059	MAP3K1	1
9060	MAP3K10	1
9061	MAP3K11	1
Done

Running MutSig 2:
Scatter job 101: processing genes 8972 - 9061
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MAGEC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.997394e-02	ci left: 6.214554e-01	ci right 6.404682e-01	k: 6310	n:10000
Cons ci ratio: 1.657893e-02	ci left: 8.411177e-01	ci right 8.552788e-01	k: 8483	n:10000
KS ci ratio: 5.267779e-02	ci left: 3.469066e-01	ci right 3.657772e-01	k: 3563	n:10000
MAGEC1   10000 perm   2 sec   (5326 perm/sec)   p_kst 3.563000e-01   p_cons 8.483000e-01   p_joint 6.310000e-01

Outputting figure to mutsig2_images.part000000000101/MAGEC1.3_3437_10000_0.3563_0.8483_0.631.png
                gene_name: MAGEC1
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 17 percent done.
MAGEC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.812068e-02	ci left: 6.508212e-01	ci right 6.694854e-01	k: 6602	n:10000
Cons ci ratio: 2.104303e-02	ci left: 7.680025e-01	ci right 7.844363e-01	k: 7763	n:10000
KS ci ratio: 4.859582e-02	ci left: 3.845045e-01	ci right 4.037572e-01	k: 3941	n:10000
MAGEC3   10000 perm   2 sec   (5958 perm/sec)   p_kst 3.941000e-01   p_cons 7.763000e-01   p_joint 6.602000e-01

Outputting figure to mutsig2_images.part000000000101/MAGEC3.2_2330_10000_0.3941_0.7763_0.6602.png
                gene_name: MAGEC3
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 33 percent done.
MAGT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.113034e-02	ci left: 6.035728e-01	ci right 6.227612e-01	k: 6132	n:10000
KS ci ratio: 2.344045e-02	ci left: 7.278487e-01	ci right 7.452133e-01	k: 7366	n:10000
MAGT1   10000 perm   1 sec   (6847 perm/sec)   p_kst 7.366000e-01   p_cons 6.132000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000101/MAGT1.2_1144_10000_0.7366_0.6132_1.png
                gene_name: MAGT1
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
MAML3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.998711e-02	ci left: 3.711691e-01	ci right 3.903004e-01	k: 3807	n:10000
KS ci ratio: 8.990802e-03	ci left: 9.456495e-01	ci right 9.542860e-01	k: 9501	n:10000
MAML3   10000 perm   2 sec   (5824 perm/sec)   p_kst 9.501000e-01   p_cons 3.807000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000101/MAML3.2_3429_10000_0.9501_0.3807_1.png
                gene_name: MAML3
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
MANBA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.761639e-02	ci left: 8.245259e-01	ci right 8.392802e-01	k: 8320	n:10000
KS ci ratio: 4.656160e-02	ci left: 4.050199e-01	ci right 4.244298e-01	k: 4147	n:10000
MANBA   10000 perm   2 sec   (5924 perm/sec)   p_kst 4.147000e-01   p_cons 8.320000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000101/MANBA.2_2708_10000_0.4147_0.832_1.png
                gene_name: MANBA
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.84 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
MAP1B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.527085e-03	ci left: 9.396240e-01	ci right 9.487151e-01	k: 9443	n:10000
Cons ci ratio: 5.540393e-02	ci left: 3.242591e-01	ci right 3.428380e-01	k: 3335	n:10000
KS ci ratio: 6.356810e-02	ci left: 2.666610e-01	ci right 2.842700e-01	k: 2754	n:10000
MAP1B   10000 perm   2 sec   (4471 perm/sec)   p_kst 2.754000e-01   p_cons 3.335000e-01   p_joint 9.443000e-01

Outputting figure to mutsig2_images.part000000000101/MAP1B.2_7435_10000_0.2754_0.3335_0.9443.png
                gene_name: MAP1B
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000101
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 101 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4398120: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000102> was used as the working directory.
Started at Wed Oct 24 16:14:03 2012
Results reported at Wed Oct 24 19:33:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000102.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000102.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 102  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000102.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :  12894.99 sec.
    Max Memory :      1743 MB
    Max Swap   :      4015 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
102
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 102
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 102: processing genes 9062 - 9150
Calculating significance of each gene.
Using projection method.
9062	MAP3K12	1
9063	MAP3K13	1.926859e-01
9064	MAP3K14	1
9065	MAP3K15	5.805365e-02
9066	MAP3K2	1
9067	MAP3K3	1
9068	MAP3K4	4.861429e-02
9069	MAP3K5	5.247442e-01
9070	MAP3K6	1.215724e-01
9071	MAP3K7	1
9072	MAP3K8	2.353437e-01
9073	MAP3K9	2.607347e-01
9074	MAP4	1
9075	MAP4K1	1
9076	MAP4K2	1
9077	MAP4K3	4.756677e-02
9078	MAP4K4	1
9079	MAP4K5	1
9080	MAP6	1
9081	MAP7	1
9082	MAP7D1	4.009244e-02
9083	MAP7D2	3.111470e-02
9084	MAP7D3	3.010216e-02
9085	MAP9	1
9086	MAPK1	6.730619e-04
9087	MAPK10	1
9088	MAPK11	3.203405e-02
9089	MAPK12	1
9090	MAPK13	1
9091	MAPK14	1
9092	MAPK15	1
9093	MAPK1IP1L	1
9094	MAPK3	1
9095	MAPK4	1
9096	MAPK6	1
9097	MAPK7	1.676467e-01
9098	MAPK8	1
9099	MAPK8IP1	1
9100	MAPK8IP2	1
9101	MAPK8IP3	1
9102	MAPK9	1
9103	MAPKAP1	1
9104	MAPKAPK2	1
9105	MAPKAPK3	1
9106	MAPKAPK5	1
9107	MAPKBP1	1
9108	MAPKSP1	1
9109	MAPRE1	1
9110	MAPRE2	1
9111	MAPRE3	1
9112	MAPT	1
9113	MARCH1	1
9114	MARCH10	1
9115	MARCH11	4.626176e-02
9116	MARCH2	1
9117	MARCH3	1
9118	MARCH4	1
9119	MARCH5	1
9120	MARCH6	3.996668e-03
9121	MARCH7	1
9122	MARCH8	1
9123	MARCH9	1
9124	MARCKS	1
9125	MARCKSL1	1
9126	MARCO	2.389586e-01
9127	MARK1	3.059860e-02
9128	MARK2	6.179822e-02
9129	MARK3	1
9130	MARK4	2.698672e-01
9131	MARS	1
9132	MARS2	1
9133	MARVELD2	1
9134	MARVELD3	1
9135	MAS1	1.441930e-01
9136	MAS1L	1
9137	MASP1	1
9138	MASP2	1
9139	MAST1	2.583213e-01
9140	MAST2	1
9141	MAST3	4.068327e-01
9142	MAST4	8.892196e-02
9143	MASTL	1
9144	MAT1A	1
9145	MAT2A	1
9146	MAT2B	1
9147	MATK	1
9148	MATN1	1
9149	MATN2	1
9150	MATN3	1
Done

Running MutSig 2:
Scatter job 102: processing genes 9062 - 9150
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MAPK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.385306e+00	ci left: 2.814811e-04	ci right 1.441732e-03	k: 7	n:10000
Cons ci ratio: 9.412510e-02	ci left: 1.407993e-01	ci right 1.548065e-01	k: 1477	n:10000
KS ci ratio: 2.771443e+00	ci left: 2.531778e-06	ci right 5.570370e-04	k: 1	n:10000
MAPK1   10000 perm   2 sec   (5871 perm/sec)   p_kst 1.000000e-04   p_cons 1.477000e-01   p_joint 7.000000e-04

Joint ci ratio: 1.385617e+00	ci left: 1.407294e-04	ci right 7.210000e-04	k: 7	n:20000
Cons ci ratio: 6.719905e-02	ci left: 1.404921e-01	ci right 1.503112e-01	k: 2907	n:20000
KS ci ratio: 2.262987e+00	ci left: 1.211069e-05	ci right 3.611872e-04	k: 2	n:20000
MAPK1   20000 perm   6 sec   (3099 perm/sec)   p_kst 1.000000e-04   p_cons 1.453500e-01   p_joint 3.500000e-04

Joint ci ratio: 1.239386e+00	ci left: 1.371880e-04	ci right 5.694167e-04	k: 9	n:30000
Cons ci ratio: 5.475798e-02	ci left: 1.418902e-01	ci right 1.499118e-01	k: 4376	n:30000
KS ci ratio: 1.752902e+00	ci left: 3.633000e-05	ci right 3.413508e-04	k: 4	n:30000
MAPK1   30000 perm   8 sec   (3556 perm/sec)   p_kst 1.333333e-04   p_cons 1.458667e-01   p_joint 3.000000e-04

Joint ci ratio: 1.385773e+00	ci left: 7.036188e-05	ci right 3.605334e-04	k: 7	n:40000
Cons ci ratio: 4.746479e-02	ci left: 1.422064e-01	ci right 1.491451e-01	k: 5826	n:40000
KS ci ratio: 1.600193e+00	ci left: 4.058837e-05	ci right 2.916840e-04	k: 5	n:40000
MAPK1   40000 perm   10 sec   (3818 perm/sec)   p_kst 1.250000e-04   p_cons 1.456500e-01   p_joint 1.750000e-04

Joint ci ratio: 1.600221e+00	ci left: 3.247050e-05	ci right 2.333511e-04	k: 5	n:50000
Cons ci ratio: 4.253850e-02	ci left: 1.420830e-01	ci right 1.482782e-01	k: 7258	n:50000
KS ci ratio: 1.600221e+00	ci left: 3.247050e-05	ci right 2.333511e-04	k: 5	n:50000
MAPK1   50000 perm   13 sec   (3963 perm/sec)   p_kst 1.000000e-04   p_cons 1.451600e-01   p_joint 1.000000e-04

Joint ci ratio: 1.600240e+00	ci left: 2.705864e-05	ci right 1.944614e-04	k: 5	n:60000
Cons ci ratio: 3.881865e-02	ci left: 1.424395e-01	ci right 1.480948e-01	k: 8715	n:60000
KS ci ratio: 1.600240e+00	ci left: 2.705864e-05	ci right 1.944614e-04	k: 5	n:60000
MAPK1   60000 perm   15 sec   (4040 perm/sec)   p_kst 8.333333e-05   p_cons 1.452500e-01   p_joint 8.333333e-05

Joint ci ratio: 1.385840e+00	ci left: 4.020610e-05	ci right 2.060273e-04	k: 7	n:70000
Cons ci ratio: 3.590332e-02	ci left: 1.428955e-01	ci right 1.481339e-01	k: 10185	n:70000
KS ci ratio: 1.385840e+00	ci left: 4.020610e-05	ci right 2.060273e-04	k: 7	n:70000
MAPK1   70000 perm   17 sec   (4028 perm/sec)   p_kst 1.000000e-04   p_cons 1.455000e-01   p_joint 1.000000e-04

Joint ci ratio: 7.686455e-01	ci left: 2.022434e-04	ci right 4.612773e-04	k: 25	n:80000
Cons ci ratio: 3.362024e-02	ci left: 1.428026e-01	ci right 1.476982e-01	k: 11619	n:80000
KS ci ratio: 1.181836e+00	ci left: 5.994393e-05	ci right 2.298674e-04	k: 10	n:80000
MAPK1   80000 perm   20 sec   (4012 perm/sec)   p_kst 1.250000e-04   p_cons 1.452375e-01   p_joint 3.125000e-04

Joint ci ratio: 1.181846e+00	ci left: 5.328334e-05	ci right 2.043278e-04	k: 10	n:90000
Cons ci ratio: 3.180358e-02	ci left: 1.421206e-01	ci right 1.467246e-01	k: 12997	n:90000
KS ci ratio: 1.181846e+00	ci left: 5.328334e-05	ci right 2.043278e-04	k: 10	n:90000
MAPK1   90000 perm   22 sec   (4012 perm/sec)   p_kst 1.111111e-04   p_cons 1.444111e-01   p_joint 1.111111e-04

Joint ci ratio: 1.131533e+00	ci left: 5.491284e-05	ci right 1.968118e-04	k: 11	n:100000
Cons ci ratio: 3.013766e-02	ci left: 1.425150e-01	ci right 1.468857e-01	k: 14469	n:100000
KS ci ratio: 1.131533e+00	ci left: 5.491284e-05	ci right 1.968118e-04	k: 11	n:100000
MAPK1   100000 perm   25 sec   (4003 perm/sec)   p_kst 1.100000e-04   p_cons 1.446900e-01   p_joint 1.100000e-04

Joint ci ratio: 9.799243e-01	ci left: 7.632364e-05	ci right 2.249011e-04	k: 15	n:110000
Cons ci ratio: 2.872776e-02	ci left: 1.426801e-01	ci right 1.468477e-01	k: 15923	n:110000
KS ci ratio: 9.799243e-01	ci left: 7.632364e-05	ci right 2.249011e-04	k: 15	n:110000
MAPK1   110000 perm   28 sec   (3981 perm/sec)   p_kst 1.363636e-04   p_cons 1.447545e-01   p_joint 1.363636e-04

Joint ci ratio: 9.799306e-01	ci left: 6.996318e-05	ci right 2.061601e-04	k: 15	n:120000
Cons ci ratio: 2.746191e-02	ci left: 1.431531e-01	ci right 1.471474e-01	k: 17417	n:120000
KS ci ratio: 9.799306e-01	ci left: 6.996318e-05	ci right 2.061601e-04	k: 15	n:120000
MAPK1   120000 perm   31 sec   (3933 perm/sec)   p_kst 1.250000e-04   p_cons 1.451417e-01   p_joint 1.250000e-04

Joint ci ratio: 9.506738e-01	ci left: 7.035068e-05	ci right 1.998615e-04	k: 16	n:130000
Cons ci ratio: 2.635393e-02	ci left: 1.435185e-01	ci right 1.473589e-01	k: 18906	n:130000
KS ci ratio: 9.506738e-01	ci left: 7.035068e-05	ci right 1.998615e-04	k: 16	n:130000
MAPK1   130000 perm   34 sec   (3860 perm/sec)   p_kst 1.230769e-04   p_cons 1.454308e-01   p_joint 1.230769e-04

Joint ci ratio: 8.764729e-01	ci left: 8.171078e-05	ci right 2.119266e-04	k: 19	n:140000
Cons ci ratio: 2.539629e-02	ci left: 1.435786e-01	ci right 1.472789e-01	k: 20359	n:140000
KS ci ratio: 8.764729e-01	ci left: 8.171078e-05	ci right 2.119266e-04	k: 19	n:140000
MAPK1   140000 perm   37 sec   (3824 perm/sec)   p_kst 1.357143e-04   p_cons 1.454214e-01   p_joint 1.357143e-04

Joint ci ratio: 8.764773e-01	ci left: 7.626328e-05	ci right 1.977987e-04	k: 19	n:150000
Cons ci ratio: 2.452285e-02	ci left: 1.437656e-01	ci right 1.473415e-01	k: 21832	n:150000
KS ci ratio: 8.764773e-01	ci left: 7.626328e-05	ci right 1.977987e-04	k: 19	n:150000
MAPK1   150000 perm   40 sec   (3785 perm/sec)   p_kst 1.266667e-04   p_cons 1.455467e-01   p_joint 1.266667e-04

Joint ci ratio: 8.764811e-01	ci left: 7.149672e-05	ci right 1.854367e-04	k: 19	n:160000
Cons ci ratio: 2.377853e-02	ci left: 1.434646e-01	ci right 1.469232e-01	k: 23230	n:160000
KS ci ratio: 8.764811e-01	ci left: 7.149672e-05	ci right 1.854367e-04	k: 19	n:160000
MAPK1   160000 perm   43 sec   (3743 perm/sec)   p_kst 1.187500e-04   p_cons 1.451875e-01   p_joint 1.187500e-04

Joint ci ratio: 8.553588e-01	ci left: 7.186331e-05	ci right 1.816905e-04	k: 20	n:170000
Cons ci ratio: 2.304069e-02	ci left: 1.438153e-01	ci right 1.471733e-01	k: 24733	n:170000
KS ci ratio: 8.553588e-01	ci left: 7.186331e-05	ci right 1.816905e-04	k: 20	n:170000
MAPK1   170000 perm   46 sec   (3696 perm/sec)   p_kst 1.176471e-04   p_cons 1.454882e-01   p_joint 1.176471e-04

Joint ci ratio: 8.356934e-01	ci left: 7.221991e-05	ci right 1.783319e-04	k: 21	n:180000
Cons ci ratio: 2.239701e-02	ci left: 1.438021e-01	ci right 1.470648e-01	k: 26177	n:180000
KS ci ratio: 8.356934e-01	ci left: 7.221991e-05	ci right 1.783319e-04	k: 21	n:180000
MAPK1   180000 perm   49 sec   (3653 perm/sec)   p_kst 1.166667e-04   p_cons 1.454278e-01   p_joint 1.166667e-04

Joint ci ratio: 8.173249e-01	ci left: 7.256602e-05	ci right 1.753014e-04	k: 22	n:190000
Cons ci ratio: 2.179980e-02	ci left: 1.438440e-01	ci right 1.470195e-01	k: 27631	n:190000
KS ci ratio: 8.173249e-01	ci left: 7.256602e-05	ci right 1.753014e-04	k: 22	n:190000
MAPK1   190000 perm   53 sec   (3605 perm/sec)   p_kst 1.157895e-04   p_cons 1.454263e-01   p_joint 1.157895e-04

Joint ci ratio: 8.173275e-01	ci left: 6.893766e-05	ci right 1.665366e-04	k: 22	n:200000
Cons ci ratio: 2.123344e-02	ci left: 1.440519e-01	ci right 1.471484e-01	k: 29119	n:200000
KS ci ratio: 8.173275e-01	ci left: 6.893766e-05	ci right 1.665366e-04	k: 22	n:200000
MAPK1   200000 perm   56 sec   (3559 perm/sec)   p_kst 1.100000e-04   p_cons 1.455950e-01   p_joint 1.100000e-04

Joint ci ratio: 8.001190e-01	ci left: 6.942993e-05	ci right 1.643350e-04	k: 23	n:210000
Cons ci ratio: 2.070982e-02	ci left: 1.442315e-01	ci right 1.472545e-01	k: 30605	n:210000
KS ci ratio: 8.001190e-01	ci left: 6.942993e-05	ci right 1.643350e-04	k: 23	n:210000
MAPK1   210000 perm   60 sec   (3515 perm/sec)   p_kst 1.095238e-04   p_cons 1.457381e-01   p_joint 1.095238e-04

Joint ci ratio: 7.839537e-01	ci left: 6.989781e-05	ci right 1.623143e-04	k: 24	n:220000
Cons ci ratio: 2.024455e-02	ci left: 1.441331e-01	ci right 1.470853e-01	k: 32033	n:220000
KS ci ratio: 7.839537e-01	ci left: 6.989781e-05	ci right 1.623143e-04	k: 24	n:220000
MAPK1   220000 perm   64 sec   (3463 perm/sec)   p_kst 1.090909e-04   p_cons 1.456045e-01   p_joint 1.090909e-04

Joint ci ratio: 7.543584e-01	ci left: 7.384504e-05	ci right 1.656305e-04	k: 26	n:230000
Cons ci ratio: 1.981102e-02	ci left: 1.440223e-01	ci right 1.469084e-01	k: 33456	n:230000
KS ci ratio: 7.543584e-01	ci left: 7.384504e-05	ci right 1.656305e-04	k: 26	n:230000
MAPK1   230000 perm   67 sec   (3421 perm/sec)   p_kst 1.130435e-04   p_cons 1.454609e-01   p_joint 1.130435e-04

Joint ci ratio: 7.543603e-01	ci left: 7.076811e-05	ci right 1.587294e-04	k: 26	n:240000
Cons ci ratio: 1.938469e-02	ci left: 1.441704e-01	ci right 1.469965e-01	k: 34939	n:240000
KS ci ratio: 7.543603e-01	ci left: 7.076811e-05	ci right 1.587294e-04	k: 26	n:240000
MAPK1   240000 perm   71 sec   (3381 perm/sec)   p_kst 1.083333e-04   p_cons 1.455792e-01   p_joint 1.083333e-04

Joint ci ratio: 7.040077e-01	ci left: 8.096491e-05	ci right 1.713031e-04	k: 30	n:250000
Cons ci ratio: 1.902114e-02	ci left: 1.438331e-01	ci right 1.465992e-01	k: 36303	n:250000
KS ci ratio: 7.040077e-01	ci left: 8.096491e-05	ci right 1.713031e-04	k: 30	n:250000
MAPK1   250000 perm   75 sec   (3337 perm/sec)   p_kst 1.200000e-04   p_cons 1.452120e-01   p_joint 1.200000e-04

Joint ci ratio: 6.929207e-01	ci left: 8.101292e-05	ci right 1.692343e-04	k: 31	n:260000
Cons ci ratio: 1.866800e-02	ci left: 1.436448e-01	ci right 1.463554e-01	k: 37699	n:260000
KS ci ratio: 6.929207e-01	ci left: 8.101292e-05	ci right 1.692343e-04	k: 31	n:260000
MAPK1   260000 perm   79 sec   (3291 perm/sec)   p_kst 1.192308e-04   p_cons 1.449962e-01   p_joint 1.192308e-04

Joint ci ratio: 4.354894e-01	ci left: 2.349513e-04	ci right 3.687530e-04	k: 80	n:270000
Cons ci ratio: 1.832205e-02	ci left: 1.436296e-01	ci right 1.462892e-01	k: 39138	n:270000
KS ci ratio: 6.722309e-01	ci left: 8.413360e-05	ci right 1.716412e-04	k: 33	n:270000
MAPK1   270000 perm   83 sec   (3253 perm/sec)   p_kst 1.222222e-04   p_cons 1.449556e-01   p_joint 2.962963e-04

Joint ci ratio: 6.722324e-01	ci left: 8.112878e-05	ci right 1.655113e-04	k: 33	n:280000
Cons ci ratio: 1.799153e-02	ci left: 1.436586e-01	ci right 1.462702e-01	k: 40589	n:280000
KS ci ratio: 6.722324e-01	ci left: 8.112878e-05	ci right 1.655113e-04	k: 33	n:280000
MAPK1   280000 perm   87 sec   (3213 perm/sec)   p_kst 1.178571e-04   p_cons 1.449607e-01   p_joint 1.178571e-04

Joint ci ratio: 6.722339e-01	ci left: 7.833119e-05	ci right 1.598041e-04	k: 33	n:290000
Cons ci ratio: 1.769650e-02	ci left: 1.434317e-01	ci right 1.459960e-01	k: 41966	n:290000
KS ci ratio: 6.722339e-01	ci left: 7.833119e-05	ci right 1.598041e-04	k: 33	n:290000
MAPK1   290000 perm   91 sec   (3174 perm/sec)   p_kst 1.137931e-04   p_cons 1.447103e-01   p_joint 1.137931e-04

Joint ci ratio: 6.532930e-01	ci left: 8.126391e-05	ci right 1.622514e-04	k: 35	n:300000
Cons ci ratio: 1.739441e-02	ci left: 1.435193e-01	ci right 1.460409e-01	k: 43433	n:300000
KS ci ratio: 6.532930e-01	ci left: 8.126391e-05	ci right 1.622514e-04	k: 35	n:300000
MAPK1   300000 perm   96 sec   (3137 perm/sec)   p_kst 1.166667e-04   p_cons 1.447767e-01   p_joint 1.166667e-04

Joint ci ratio: 6.358680e-01	ci left: 8.403817e-05	ci right 1.645112e-04	k: 37	n:310000
Cons ci ratio: 1.711485e-02	ci left: 1.434922e-01	ci right 1.459725e-01	k: 44866	n:310000
KS ci ratio: 6.358680e-01	ci left: 8.403817e-05	ci right 1.645112e-04	k: 37	n:310000
MAPK1   310000 perm   100 sec   (3098 perm/sec)   p_kst 1.193548e-04   p_cons 1.447290e-01   p_joint 1.193548e-04

Joint ci ratio: 6.276631e-01	ci left: 8.403590e-05	ci right 1.629900e-04	k: 38	n:320000
Cons ci ratio: 1.684155e-02	ci left: 1.435668e-01	ci right 1.460083e-01	k: 46331	n:320000
KS ci ratio: 6.276631e-01	ci left: 8.403590e-05	ci right 1.629900e-04	k: 38	n:320000
MAPK1   320000 perm   105 sec   (3060 perm/sec)   p_kst 1.187500e-04   p_cons 1.447844e-01   p_joint 1.187500e-04

Joint ci ratio: 6.276643e-01	ci left: 8.148931e-05	ci right 1.580511e-04	k: 38	n:330000
Cons ci ratio: 1.659271e-02	ci left: 1.434621e-01	ci right 1.458654e-01	k: 47738	n:330000
KS ci ratio: 6.276643e-01	ci left: 8.148931e-05	ci right 1.580511e-04	k: 38	n:330000
MAPK1   330000 perm   109 sec   (3022 perm/sec)   p_kst 1.151515e-04   p_cons 1.446606e-01   p_joint 1.151515e-04

Joint ci ratio: 6.276654e-01	ci left: 7.909253e-05	ci right 1.534026e-04	k: 38	n:340000
Cons ci ratio: 1.633517e-02	ci left: 1.436568e-01	ci right 1.460257e-01	k: 49245	n:340000
KS ci ratio: 6.276654e-01	ci left: 7.909253e-05	ci right 1.534026e-04	k: 38	n:340000
MAPK1   340000 perm   114 sec   (2986 perm/sec)   p_kst 1.117647e-04   p_cons 1.448382e-01   p_joint 1.117647e-04

Joint ci ratio: 6.197701e-01	ci left: 7.923777e-05	ci right 1.523234e-04	k: 39	n:350000
Cons ci ratio: 1.609778e-02	ci left: 1.437097e-01	ci right 1.460447e-01	k: 50706	n:350000
KS ci ratio: 6.197701e-01	ci left: 7.923777e-05	ci right 1.523234e-04	k: 39	n:350000
MAPK1   350000 perm   119 sec   (2950 perm/sec)   p_kst 1.114286e-04   p_cons 1.448743e-01   p_joint 1.114286e-04

Joint ci ratio: 6.121654e-01	ci left: 7.938056e-05	ci right 1.512988e-04	k: 40	n:360000
Cons ci ratio: 1.587027e-02	ci left: 1.437627e-01	ci right 1.460652e-01	k: 52168	n:360000
KS ci ratio: 6.121654e-01	ci left: 7.938056e-05	ci right 1.512988e-04	k: 40	n:360000
MAPK1   360000 perm   124 sec   (2914 perm/sec)   p_kst 1.111111e-04   p_cons 1.449111e-01   p_joint 1.111111e-04

Joint ci ratio: 6.048340e-01	ci left: 7.952089e-05	ci right 1.503244e-04	k: 41	n:370000
Cons ci ratio: 1.565556e-02	ci left: 1.437592e-01	ci right 1.460302e-01	k: 53610	n:370000
KS ci ratio: 6.048340e-01	ci left: 7.952089e-05	ci right 1.503244e-04	k: 41	n:370000
MAPK1   370000 perm   129 sec   (2879 perm/sec)   p_kst 1.108108e-04   p_cons 1.448919e-01   p_joint 1.108108e-04

Joint ci ratio: 6.048349e-01	ci left: 7.742820e-05	ci right 1.463686e-04	k: 41	n:380000
Cons ci ratio: 1.544753e-02	ci left: 1.437848e-01	ci right 1.460258e-01	k: 55063	n:380000
KS ci ratio: 6.048349e-01	ci left: 7.742820e-05	ci right 1.463686e-04	k: 41	n:380000
MAPK1   380000 perm   134 sec   (2844 perm/sec)   p_kst 1.078947e-04   p_cons 1.449026e-01   p_joint 1.078947e-04

Joint ci ratio: 5.977607e-01	ci left: 7.761621e-05	ci right 1.455660e-04	k: 42	n:390000
Cons ci ratio: 1.524552e-02	ci left: 1.438426e-01	ci right 1.460550e-01	k: 56529	n:390000
KS ci ratio: 5.977607e-01	ci left: 7.761621e-05	ci right 1.455660e-04	k: 42	n:390000
MAPK1   390000 perm   139 sec   (2814 perm/sec)   p_kst 1.076923e-04   p_cons 1.449462e-01   p_joint 1.076923e-04

Joint ci ratio: 5.843255e-01	ci left: 7.992727e-05	ci right 1.476671e-04	k: 44	n:400000
Cons ci ratio: 1.504730e-02	ci left: 1.439625e-01	ci right 1.461476e-01	k: 58021	n:400000
KS ci ratio: 5.843255e-01	ci left: 7.992727e-05	ci right 1.476671e-04	k: 44	n:400000
MAPK1   400000 perm   144 sec   (2781 perm/sec)   p_kst 1.100000e-04   p_cons 1.450525e-01   p_joint 1.100000e-04

Joint ci ratio: 5.843263e-01	ci left: 7.797780e-05	ci right 1.440655e-04	k: 44	n:410000
Cons ci ratio: 1.486026e-02	ci left: 1.440159e-01	ci right 1.461745e-01	k: 59488	n:410000
KS ci ratio: 5.843263e-01	ci left: 7.797780e-05	ci right 1.440655e-04	k: 44	n:410000
MAPK1   410000 perm   149 sec   (2749 perm/sec)   p_kst 1.073171e-04   p_cons 1.450927e-01   p_joint 1.073171e-04

Joint ci ratio: 5.779401e-01	ci left: 7.815178e-05	ci right 1.433630e-04	k: 45	n:420000
Cons ci ratio: 1.468848e-02	ci left: 1.439245e-01	ci right 1.460566e-01	k: 60895	n:420000
KS ci ratio: 5.779401e-01	ci left: 7.815178e-05	ci right 1.433630e-04	k: 45	n:420000
MAPK1   420000 perm   155 sec   (2718 perm/sec)   p_kst 1.071429e-04   p_cons 1.449881e-01   p_joint 1.071429e-04

Joint ci ratio: 5.779409e-01	ci left: 7.633427e-05	ci right 1.400290e-04	k: 45	n:430000
Cons ci ratio: 1.451326e-02	ci left: 1.439952e-01	ci right 1.461026e-01	k: 62370	n:430000
KS ci ratio: 5.779409e-01	ci left: 7.633427e-05	ci right 1.400290e-04	k: 45	n:430000
MAPK1   430000 perm   160 sec   (2689 perm/sec)   p_kst 1.046512e-04   p_cons 1.450465e-01   p_joint 1.046512e-04

Joint ci ratio: 5.599682e-01	ci left: 8.043609e-05	ci right 1.446361e-04	k: 48	n:440000
Cons ci ratio: 1.434417e-02	ci left: 1.440628e-01	ci right 1.461464e-01	k: 63845	n:440000
KS ci ratio: 5.599682e-01	ci left: 8.043609e-05	ci right 1.446361e-04	k: 48	n:440000
MAPK1   440000 perm   165 sec   (2660 perm/sec)   p_kst 1.090909e-04   p_cons 1.451023e-01   p_joint 1.090909e-04

Joint ci ratio: 5.543403e-01	ci left: 8.055765e-05	ci right 1.439544e-04	k: 49	n:450000
Cons ci ratio: 1.417857e-02	ci left: 1.441674e-01	ci right 1.462283e-01	k: 65338	n:450000
KS ci ratio: 5.543403e-01	ci left: 8.055765e-05	ci right 1.439544e-04	k: 49	n:450000
MAPK1   450000 perm   171 sec   (2631 perm/sec)   p_kst 1.088889e-04   p_cons 1.451956e-01   p_joint 1.088889e-04

Joint ci ratio: 5.488788e-01	ci left: 8.067705e-05	ci right 1.432992e-04	k: 50	n:460000
Cons ci ratio: 1.401783e-02	ci left: 1.442806e-01	ci right 1.463195e-01	k: 66837	n:460000
KS ci ratio: 5.488788e-01	ci left: 8.067705e-05	ci right 1.432992e-04	k: 50	n:460000
MAPK1   460000 perm   177 sec   (2604 perm/sec)   p_kst 1.086957e-04   p_cons 1.452978e-01   p_joint 1.086957e-04

Joint ci ratio: 5.435755e-01	ci left: 8.079433e-05	ci right 1.426690e-04	k: 51	n:470000
Cons ci ratio: 1.387004e-02	ci left: 1.442533e-01	ci right 1.462702e-01	k: 68272	n:470000
KS ci ratio: 5.435755e-01	ci left: 8.079433e-05	ci right 1.426690e-04	k: 51	n:470000
MAPK1   470000 perm   182 sec   (2577 perm/sec)   p_kst 1.085106e-04   p_cons 1.452596e-01   p_joint 1.085106e-04

Joint ci ratio: 5.384231e-01	ci left: 8.090954e-05	ci right 1.420624e-04	k: 52	n:480000
Cons ci ratio: 1.371935e-02	ci left: 1.443623e-01	ci right 1.463586e-01	k: 69772	n:480000
KS ci ratio: 5.384231e-01	ci left: 8.090954e-05	ci right 1.420624e-04	k: 52	n:480000
MAPK1   480000 perm   188 sec   (2550 perm/sec)   p_kst 1.083333e-04   p_cons 1.453583e-01   p_joint 1.083333e-04

Joint ci ratio: 3.221730e-01	ci left: 2.534700e-04	ci right 3.525960e-04	k: 147	n:490000
Cons ci ratio: 1.358105e-02	ci left: 1.443286e-01	ci right 1.463042e-01	k: 71204	n:490000
KS ci ratio: 5.285425e-01	ci left: 8.278975e-05	ci right 1.437900e-04	k: 54	n:490000
MAPK1   490000 perm   194 sec   (2524 perm/sec)   p_kst 1.102041e-04   p_cons 1.453143e-01   p_joint 3.000000e-04

Joint ci ratio: 3.189566e-01	ci left: 2.539179e-04	ci right 3.520252e-04	k: 150	n:500000
Cons ci ratio: 1.344392e-02	ci left: 1.443502e-01	ci right 1.463059e-01	k: 72663	n:500000
KS ci ratio: 5.238022e-01	ci left: 8.286810e-05	ci right 1.431777e-04	k: 55	n:500000
MAPK1   500000 perm   200 sec   (2498 perm/sec)   p_kst 1.100000e-04   p_cons 1.453260e-01   p_joint 3.000000e-04

Joint ci ratio: 3.148138e-01	ci left: 2.561586e-04	ci right 3.535875e-04	k: 154	n:510000
Cons ci ratio: 1.331223e-02	ci left: 1.443456e-01	ci right 1.462820e-01	k: 74109	n:510000
KS ci ratio: 5.191872e-01	ci left: 8.294573e-05	ci right 1.425872e-04	k: 56	n:510000
MAPK1   510000 perm   206 sec   (2473 perm/sec)   p_kst 1.098039e-04   p_cons 1.453118e-01   p_joint 3.019608e-04

Joint ci ratio: 5.146920e-01	ci left: 8.302265e-05	ci right 1.420171e-04	k: 57	n:520000
Cons ci ratio: 1.317933e-02	ci left: 1.444352e-01	ci right 1.463533e-01	k: 75604	n:520000
KS ci ratio: 5.146920e-01	ci left: 8.302265e-05	ci right 1.420171e-04	k: 57	n:520000
MAPK1   520000 perm   212 sec   (2448 perm/sec)   p_kst 1.096154e-04   p_cons 1.453923e-01   p_joint 1.096154e-04

Joint ci ratio: 5.103116e-01	ci left: 8.309881e-05	ci right 1.414665e-04	k: 58	n:530000
Cons ci ratio: 1.304925e-02	ci left: 1.445423e-01	ci right 1.464427e-01	k: 77110	n:530000
KS ci ratio: 5.103116e-01	ci left: 8.309881e-05	ci right 1.414665e-04	k: 58	n:530000
MAPK1   530000 perm   219 sec   (2424 perm/sec)   p_kst 1.094340e-04   p_cons 1.454906e-01   p_joint 1.094340e-04

Joint ci ratio: 5.103122e-01	ci left: 8.155993e-05	ci right 1.388468e-04	k: 58	n:540000
Cons ci ratio: 1.292824e-02	ci left: 1.445439e-01	ci right 1.464266e-01	k: 78561	n:540000
KS ci ratio: 5.103122e-01	ci left: 8.155993e-05	ci right 1.388468e-04	k: 58	n:540000
MAPK1   540000 perm   225 sec   (2400 perm/sec)   p_kst 1.074074e-04   p_cons 1.454833e-01   p_joint 1.074074e-04

Joint ci ratio: 5.103127e-01	ci left: 8.007700e-05	ci right 1.363223e-04	k: 58	n:550000
Cons ci ratio: 1.280959e-02	ci left: 1.445637e-01	ci right 1.464292e-01	k: 80022	n:550000
KS ci ratio: 5.103127e-01	ci left: 8.007700e-05	ci right 1.363223e-04	k: 58	n:550000
MAPK1   550000 perm   232 sec   (2375 perm/sec)   p_kst 1.054545e-04   p_cons 1.454945e-01   p_joint 1.054545e-04

Joint ci ratio: 5.060423e-01	ci left: 8.020368e-05	ci right 1.359010e-04	k: 59	n:560000
Cons ci ratio: 1.268969e-02	ci left: 1.446700e-01	ci right 1.465193e-01	k: 81532	n:560000
KS ci ratio: 5.060423e-01	ci left: 8.020368e-05	ci right 1.359010e-04	k: 59	n:560000
MAPK1   560000 perm   238 sec   (2352 perm/sec)   p_kst 1.053571e-04   p_cons 1.455929e-01   p_joint 1.053571e-04

Joint ci ratio: 5.060427e-01	ci left: 7.879658e-05	ci right 1.335168e-04	k: 59	n:570000
Cons ci ratio: 1.258152e-02	ci left: 1.446066e-01	ci right 1.464392e-01	k: 82947	n:570000
KS ci ratio: 5.060427e-01	ci left: 7.879658e-05	ci right 1.335168e-04	k: 59	n:570000
MAPK1   570000 perm   245 sec   (2330 perm/sec)   p_kst 1.035088e-04   p_cons 1.455211e-01   p_joint 1.035088e-04

Joint ci ratio: 4.978135e-01	ci left: 8.044949e-05	ci right 1.350963e-04	k: 61	n:580000
Cons ci ratio: 1.247261e-02	ci left: 1.446141e-01	ci right 1.464308e-01	k: 84402	n:580000
KS ci ratio: 4.978135e-01	ci left: 8.044949e-05	ci right 1.350963e-04	k: 61	n:580000
MAPK1   580000 perm   252 sec   (2306 perm/sec)   p_kst 1.051724e-04   p_cons 1.455207e-01   p_joint 1.051724e-04

Joint ci ratio: 2.962799e-01	ci left: 2.527273e-04	ci right 3.421303e-04	k: 174	n:590000
Cons ci ratio: 1.236428e-02	ci left: 1.446654e-01	ci right 1.464669e-01	k: 85883	n:590000
KS ci ratio: 4.938468e-01	ci left: 8.056879e-05	ci right 1.347119e-04	k: 62	n:590000
MAPK1   590000 perm   258 sec   (2284 perm/sec)   p_kst 1.050847e-04   p_cons 1.455644e-01   p_joint 2.949153e-04

Joint ci ratio: 2.946015e-01	ci left: 2.516015e-04	ci right 3.400079e-04	k: 176	n:600000
Cons ci ratio: 1.225783e-02	ci left: 1.447334e-01	ci right 1.465201e-01	k: 87375	n:600000
KS ci ratio: 4.938472e-01	ci left: 7.922596e-05	ci right 1.324667e-04	k: 62	n:600000
MAPK1   600000 perm   265 sec   (2263 perm/sec)   p_kst 1.033333e-04   p_cons 1.456250e-01   p_joint 2.933333e-04

Joint ci ratio: 2.929513e-01	ci left: 2.505139e-04	ci right 3.379536e-04	k: 178	n:610000
Cons ci ratio: 1.216337e-02	ci left: 1.446095e-01	ci right 1.463808e-01	k: 88751	n:610000
KS ci ratio: 4.938477e-01	ci left: 7.792716e-05	ci right 1.302952e-04	k: 62	n:610000
MAPK1   610000 perm   272 sec   (2242 perm/sec)   p_kst 1.016393e-04   p_cons 1.454934e-01   p_joint 2.918033e-04

Joint ci ratio: 4.938481e-01	ci left: 7.667026e-05	ci right 1.281937e-04	k: 62	n:620000
Cons ci ratio: 1.206691e-02	ci left: 1.445749e-01	ci right 1.463316e-01	k: 90180	n:620000
KS ci ratio: 4.938481e-01	ci left: 7.667026e-05	ci right 1.281937e-04	k: 62	n:620000
MAPK1   620000 perm   279 sec   (2219 perm/sec)   p_kst 1.000000e-04   p_cons 1.454516e-01   p_joint 1.000000e-04

Joint ci ratio: 4.938485e-01	ci left: 7.545326e-05	ci right 1.261589e-04	k: 62	n:630000
Cons ci ratio: 1.197294e-02	ci left: 1.445367e-01	ci right 1.462792e-01	k: 91606	n:630000
KS ci ratio: 4.938485e-01	ci left: 7.545326e-05	ci right 1.261589e-04	k: 62	n:630000
MAPK1   630000 perm   287 sec   (2198 perm/sec)   p_kst 9.841270e-05   p_cons 1.454063e-01   p_joint 9.841270e-05

Joint ci ratio: 4.824934e-01	ci left: 7.838464e-05	ci right 1.294479e-04	k: 65	n:640000
Cons ci ratio: 1.187546e-02	ci left: 1.446183e-01	ci right 1.463475e-01	k: 93108	n:640000
KS ci ratio: 4.824934e-01	ci left: 7.838464e-05	ci right 1.294479e-04	k: 65	n:640000
MAPK1   640000 perm   294 sec   (2176 perm/sec)   p_kst 1.015625e-04   p_cons 1.454813e-01   p_joint 1.015625e-04

Joint ci ratio: 4.788792e-01	ci left: 7.853068e-05	ci right 1.291800e-04	k: 66	n:650000
Cons ci ratio: 1.178411e-02	ci left: 1.446175e-01	ci right 1.463333e-01	k: 94558	n:650000
KS ci ratio: 4.788792e-01	ci left: 7.853068e-05	ci right 1.291800e-04	k: 66	n:650000
MAPK1   650000 perm   301 sec   (2156 perm/sec)   p_kst 1.015385e-04   p_cons 1.454738e-01   p_joint 1.015385e-04

Joint ci ratio: 4.788796e-01	ci left: 7.734081e-05	ci right 1.272228e-04	k: 66	n:660000
Cons ci ratio: 1.169419e-02	ci left: 1.446305e-01	ci right 1.463332e-01	k: 96017	n:660000
KS ci ratio: 4.788796e-01	ci left: 7.734081e-05	ci right 1.272228e-04	k: 66	n:660000
MAPK1   660000 perm   309 sec   (2137 perm/sec)   p_kst 1.000000e-04   p_cons 1.454803e-01   p_joint 1.000000e-04

Joint ci ratio: 4.788799e-01	ci left: 7.618646e-05	ci right 1.253240e-04	k: 66	n:670000
Cons ci ratio: 1.160679e-02	ci left: 1.446327e-01	ci right 1.463226e-01	k: 97469	n:670000
KS ci ratio: 4.788799e-01	ci left: 7.618646e-05	ci right 1.253240e-04	k: 66	n:670000
MAPK1   670000 perm   316 sec   (2119 perm/sec)   p_kst 9.850746e-05   p_cons 1.454761e-01   p_joint 9.850746e-05

Joint ci ratio: 4.788803e-01	ci left: 7.506606e-05	ci right 1.234810e-04	k: 66	n:680000
Cons ci ratio: 1.151996e-02	ci left: 1.446642e-01	ci right 1.463418e-01	k: 98941	n:680000
KS ci ratio: 4.788803e-01	ci left: 7.506606e-05	ci right 1.234810e-04	k: 66	n:680000
MAPK1   680000 perm   324 sec   (2100 perm/sec)   p_kst 9.705882e-05   p_cons 1.455015e-01   p_joint 9.705882e-05

Joint ci ratio: 4.788806e-01	ci left: 7.397813e-05	ci right 1.216914e-04	k: 66	n:690000
Cons ci ratio: 1.143744e-02	ci left: 1.446428e-01	ci right 1.463080e-01	k: 100377	n:690000
KS ci ratio: 4.788806e-01	ci left: 7.397813e-05	ci right 1.216914e-04	k: 66	n:690000
MAPK1   690000 perm   331 sec   (2082 perm/sec)   p_kst 9.565217e-05   p_cons 1.454739e-01   p_joint 9.565217e-05

Joint ci ratio: 4.753464e-01	ci left: 7.417800e-05	ci right 1.215522e-04	k: 67	n:700000
Cons ci ratio: 1.135713e-02	ci left: 1.446120e-01	ci right 1.462652e-01	k: 101806	n:700000
KS ci ratio: 4.753464e-01	ci left: 7.417800e-05	ci right 1.215522e-04	k: 67	n:700000
MAPK1   700000 perm   339 sec   (2064 perm/sec)   p_kst 9.571429e-05   p_cons 1.454371e-01   p_joint 9.571429e-05

Joint ci ratio: 4.753467e-01	ci left: 7.313323e-05	ci right 1.198402e-04	k: 67	n:710000
Cons ci ratio: 1.128092e-02	ci left: 1.445288e-01	ci right 1.461699e-01	k: 103197	n:710000
KS ci ratio: 4.753467e-01	ci left: 7.313323e-05	ci right 1.198402e-04	k: 67	n:710000
MAPK1   710000 perm   347 sec   (2046 perm/sec)   p_kst 9.436620e-05   p_cons 1.453479e-01   p_joint 9.436620e-05

Joint ci ratio: 4.718896e-01	ci left: 7.334053e-05	ci right 1.197293e-04	k: 68	n:720000
Cons ci ratio: 1.120484e-02	ci left: 1.444784e-01	ci right 1.461078e-01	k: 104610	n:720000
KS ci ratio: 4.718896e-01	ci left: 7.334053e-05	ci right 1.197293e-04	k: 68	n:720000
MAPK1   720000 perm   355 sec   (2029 perm/sec)   p_kst 9.444444e-05   p_cons 1.452917e-01   p_joint 9.444444e-05

Joint ci ratio: 4.685068e-01	ci left: 7.354335e-05	ci right 1.196203e-04	k: 69	n:730000
Cons ci ratio: 1.112826e-02	ci left: 1.444746e-01	ci right 1.460926e-01	k: 106056	n:730000
KS ci ratio: 4.685068e-01	ci left: 7.354335e-05	ci right 1.196203e-04	k: 69	n:730000
MAPK1   730000 perm   363 sec   (2012 perm/sec)   p_kst 9.452055e-05   p_cons 1.452822e-01   p_joint 9.452055e-05

Joint ci ratio: 4.685071e-01	ci left: 7.254951e-05	ci right 1.180038e-04	k: 69	n:740000
Cons ci ratio: 1.105298e-02	ci left: 1.444762e-01	ci right 1.460833e-01	k: 107506	n:740000
KS ci ratio: 4.685071e-01	ci left: 7.254951e-05	ci right 1.180038e-04	k: 69	n:740000
MAPK1   740000 perm   371 sec   (1995 perm/sec)   p_kst 9.324324e-05   p_cons 1.452784e-01   p_joint 9.324324e-05

Joint ci ratio: 4.651961e-01	ci left: 7.275861e-05	ci right 1.179196e-04	k: 70	n:750000
Cons ci ratio: 1.098252e-02	ci left: 1.444034e-01	ci right 1.459994e-01	k: 108900	n:750000
KS ci ratio: 4.651961e-01	ci left: 7.275861e-05	ci right 1.179196e-04	k: 70	n:750000
MAPK1   750000 perm   379 sec   (1978 perm/sec)   p_kst 9.333333e-05   p_cons 1.452000e-01   p_joint 9.333333e-05

Joint ci ratio: 4.619542e-01	ci left: 7.296332e-05	ci right 1.178365e-04	k: 71	n:760000
Cons ci ratio: 1.090835e-02	ci left: 1.444467e-01	ci right 1.460323e-01	k: 110381	n:760000
KS ci ratio: 4.619542e-01	ci left: 7.296332e-05	ci right 1.178365e-04	k: 71	n:760000
MAPK1   760000 perm   387 sec   (1962 perm/sec)   p_kst 9.342105e-05   p_cons 1.452382e-01   p_joint 9.342105e-05

Joint ci ratio: 4.619545e-01	ci left: 7.201573e-05	ci right 1.163062e-04	k: 71	n:770000
Cons ci ratio: 1.083521e-02	ci left: 1.444993e-01	ci right 1.460748e-01	k: 111870	n:770000
KS ci ratio: 4.619545e-01	ci left: 7.201573e-05	ci right 1.163062e-04	k: 71	n:770000
MAPK1   770000 perm   396 sec   (1946 perm/sec)   p_kst 9.220779e-05   p_cons 1.452857e-01   p_joint 9.220779e-05

Joint ci ratio: 4.619548e-01	ci left: 7.109244e-05	ci right 1.148151e-04	k: 71	n:780000
Cons ci ratio: 1.076513e-02	ci left: 1.445135e-01	ci right 1.460789e-01	k: 113330	n:780000
KS ci ratio: 4.619548e-01	ci left: 7.109244e-05	ci right 1.148151e-04	k: 71	n:780000
MAPK1   780000 perm   404 sec   (1930 perm/sec)   p_kst 9.102564e-05   p_cons 1.452949e-01   p_joint 9.102564e-05

Joint ci ratio: 4.556691e-01	ci left: 7.243150e-05	ci right 1.161841e-04	k: 73	n:790000
Cons ci ratio: 1.069324e-02	ci left: 1.446006e-01	ci right 1.461564e-01	k: 114848	n:790000
KS ci ratio: 4.556691e-01	ci left: 7.243150e-05	ci right 1.161841e-04	k: 73	n:790000
MAPK1   790000 perm   413 sec   (1915 perm/sec)   p_kst 9.240506e-05   p_cons 1.453772e-01   p_joint 9.240506e-05

Joint ci ratio: 4.556694e-01	ci left: 7.152609e-05	ci right 1.147318e-04	k: 73	n:800000
Cons ci ratio: 1.062565e-02	ci left: 1.446182e-01	ci right 1.461643e-01	k: 116312	n:800000
KS ci ratio: 4.556694e-01	ci left: 7.152609e-05	ci right 1.147318e-04	k: 73	n:800000
MAPK1   800000 perm   421 sec   (1899 perm/sec)   p_kst 9.125000e-05   p_cons 1.453900e-01   p_joint 9.125000e-05

Joint ci ratio: 4.526214e-01	ci left: 7.173636e-05	ci right 1.146903e-04	k: 74	n:810000
Cons ci ratio: 1.056085e-02	ci left: 1.445997e-01	ci right 1.461361e-01	k: 117747	n:810000
KS ci ratio: 4.526214e-01	ci left: 7.173636e-05	ci right 1.146903e-04	k: 74	n:810000
MAPK1   810000 perm   430 sec   (1884 perm/sec)   p_kst 9.135802e-05   p_cons 1.453667e-01   p_joint 9.135802e-05

Joint ci ratio: 4.526216e-01	ci left: 7.086152e-05	ci right 1.132916e-04	k: 74	n:820000
Cons ci ratio: 1.049366e-02	ci left: 1.446657e-01	ci right 1.461929e-01	k: 119251	n:820000
KS ci ratio: 4.526216e-01	ci left: 7.086152e-05	ci right 1.132916e-04	k: 74	n:820000
MAPK1   820000 perm   439 sec   (1869 perm/sec)   p_kst 9.024390e-05   p_cons 1.454280e-01   p_joint 9.024390e-05

Joint ci ratio: 4.526219e-01	ci left: 7.000776e-05	ci right 1.119267e-04	k: 74	n:830000
Cons ci ratio: 1.043158e-02	ci left: 1.446387e-01	ci right 1.461566e-01	k: 120679	n:830000
KS ci ratio: 4.526219e-01	ci left: 7.000776e-05	ci right 1.119267e-04	k: 74	n:830000
MAPK1   830000 perm   448 sec   (1853 perm/sec)   p_kst 8.915663e-05   p_cons 1.453964e-01   p_joint 8.915663e-05

Joint ci ratio: 4.526221e-01	ci left: 6.917432e-05	ci right 1.105943e-04	k: 74	n:840000
Cons ci ratio: 1.036866e-02	ci left: 1.446587e-01	ci right 1.461676e-01	k: 122146	n:840000
KS ci ratio: 4.526221e-01	ci left: 6.917432e-05	ci right 1.105943e-04	k: 74	n:840000
MAPK1   840000 perm   457 sec   (1839 perm/sec)   p_kst 8.809524e-05   p_cons 1.454119e-01   p_joint 8.809524e-05

Joint ci ratio: 4.526224e-01	ci left: 6.836050e-05	ci right 1.092932e-04	k: 74	n:850000
Cons ci ratio: 1.030915e-02	ci left: 1.446231e-01	ci right 1.461229e-01	k: 123566	n:850000
KS ci ratio: 4.526224e-01	ci left: 6.836050e-05	ci right 1.092932e-04	k: 74	n:850000
MAPK1   850000 perm   466 sec   (1824 perm/sec)   p_kst 8.705882e-05   p_cons 1.453718e-01   p_joint 8.705882e-05

Joint ci ratio: 4.496347e-01	ci left: 6.859625e-05	ci right 1.093164e-04	k: 75	n:860000
Cons ci ratio: 1.024989e-02	ci left: 1.446069e-01	ci right 1.460978e-01	k: 125002	n:860000
KS ci ratio: 4.496347e-01	ci left: 6.859625e-05	ci right 1.093164e-04	k: 75	n:860000
MAPK1   860000 perm   475 sec   (1809 perm/sec)   p_kst 8.720930e-05   p_cons 1.453512e-01   p_joint 8.720930e-05

Joint ci ratio: 4.467054e-01	ci left: 6.882744e-05	ci right 1.093383e-04	k: 76	n:870000
Cons ci ratio: 1.019239e-02	ci left: 1.445727e-01	ci right 1.460549e-01	k: 126422	n:870000
KS ci ratio: 4.467054e-01	ci left: 6.882744e-05	ci right 1.093383e-04	k: 76	n:870000
MAPK1   870000 perm   485 sec   (1795 perm/sec)   p_kst 8.735632e-05   p_cons 1.453126e-01   p_joint 8.735632e-05

Joint ci ratio: 4.410144e-01	ci left: 7.006398e-05	ci right 1.106210e-04	k: 78	n:880000
Cons ci ratio: 1.013205e-02	ci left: 1.446324e-01	ci right 1.461063e-01	k: 127924	n:880000
KS ci ratio: 4.410144e-01	ci left: 7.006398e-05	ci right 1.106210e-04	k: 78	n:880000
MAPK1   880000 perm   494 sec   (1781 perm/sec)   p_kst 8.863636e-05   p_cons 1.453682e-01   p_joint 8.863636e-05

Joint ci ratio: 4.410146e-01	ci left: 6.927674e-05	ci right 1.093781e-04	k: 78	n:890000
Cons ci ratio: 1.007819e-02	ci left: 1.445572e-01	ci right 1.460226e-01	k: 129307	n:890000
KS ci ratio: 4.410146e-01	ci left: 6.927674e-05	ci right 1.093781e-04	k: 78	n:890000
MAPK1   890000 perm   504 sec   (1766 perm/sec)   p_kst 8.764045e-05   p_cons 1.452888e-01   p_joint 8.764045e-05

Joint ci ratio: 4.410149e-01	ci left: 6.850699e-05	ci right 1.081628e-04	k: 78	n:900000
Cons ci ratio: 1.002617e-02	ci left: 1.444594e-01	ci right 1.459162e-01	k: 130668	n:900000
KS ci ratio: 4.410149e-01	ci left: 6.850699e-05	ci right 1.081628e-04	k: 78	n:900000
MAPK1   900000 perm   513 sec   (1753 perm/sec)   p_kst 8.666667e-05   p_cons 1.451867e-01   p_joint 8.666667e-05

Joint ci ratio: 4.382498e-01	ci left: 6.873140e-05	ci right 1.081940e-04	k: 79	n:910000
Cons ci ratio: 9.970171e-03	ci left: 1.444822e-01	ci right 1.459310e-01	k: 132137	n:910000
KS ci ratio: 4.382498e-01	ci left: 6.873140e-05	ci right 1.081940e-04	k: 79	n:910000
MAPK1   910000 perm   523 sec   (1739 perm/sec)   p_kst 8.681319e-05   p_cons 1.452055e-01   p_joint 8.681319e-05

Joint ci ratio: 4.302563e-01	ci left: 7.088869e-05	ci right 1.106332e-04	k: 82	n:920000
Cons ci ratio: 9.914148e-03	ci left: 1.445284e-01	ci right 1.459695e-01	k: 133628	n:920000
KS ci ratio: 4.302563e-01	ci left: 7.088869e-05	ci right 1.106332e-04	k: 82	n:920000
MAPK1   920000 perm   533 sec   (1726 perm/sec)   p_kst 8.913043e-05   p_cons 1.452478e-01   p_joint 8.913043e-05

Joint ci ratio: 4.302565e-01	ci left: 7.012644e-05	ci right 1.094436e-04	k: 82	n:930000
Cons ci ratio: 9.859741e-03	ci left: 1.445564e-01	ci right 1.459898e-01	k: 135103	n:930000
KS ci ratio: 4.302565e-01	ci left: 7.012644e-05	ci right 1.094436e-04	k: 82	n:930000
MAPK1   930000 perm   543 sec   (1713 perm/sec)   p_kst 8.817204e-05   p_cons 1.452720e-01   p_joint 8.817204e-05

Joint ci ratio: 4.302567e-01	ci left: 6.938041e-05	ci right 1.082793e-04	k: 82	n:940000
Cons ci ratio: 9.806682e-03	ci left: 1.445722e-01	ci right 1.459980e-01	k: 136567	n:940000
KS ci ratio: 4.302567e-01	ci left: 6.938041e-05	ci right 1.082793e-04	k: 82	n:940000
MAPK1   940000 perm   553 sec   (1700 perm/sec)   p_kst 8.723404e-05   p_cons 1.452840e-01   p_joint 8.723404e-05

Joint ci ratio: 4.302569e-01	ci left: 6.865008e-05	ci right 1.071395e-04	k: 82	n:950000
Cons ci ratio: 9.753271e-03	ci left: 1.446182e-01	ci right 1.460366e-01	k: 138060	n:950000
KS ci ratio: 4.302569e-01	ci left: 6.865008e-05	ci right 1.071395e-04	k: 82	n:950000
MAPK1   950000 perm   563 sec   (1687 perm/sec)   p_kst 8.631579e-05   p_cons 1.453263e-01   p_joint 8.631579e-05

Joint ci ratio: 4.302571e-01	ci left: 6.793497e-05	ci right 1.060235e-04	k: 82	n:960000
Cons ci ratio: 9.701782e-03	ci left: 1.446362e-01	ci right 1.460472e-01	k: 139527	n:960000
KS ci ratio: 4.302571e-01	ci left: 6.793497e-05	ci right 1.060235e-04	k: 82	n:960000
MAPK1   960000 perm   574 sec   (1674 perm/sec)   p_kst 8.541667e-05   p_cons 1.453406e-01   p_joint 8.541667e-05

Joint ci ratio: 4.276883e-01	ci left: 6.815420e-05	ci right 1.060721e-04	k: 83	n:970000
Cons ci ratio: 9.652381e-03	ci left: 1.446209e-01	ci right 1.460246e-01	k: 140962	n:970000
KS ci ratio: 4.276883e-01	ci left: 6.815420e-05	ci right 1.060721e-04	k: 83	n:970000
MAPK1   970000 perm   584 sec   (1662 perm/sec)   p_kst 8.556701e-05   p_cons 1.453216e-01   p_joint 8.556701e-05

Joint ci ratio: 4.251650e-01	ci left: 6.836963e-05	ci right 1.061190e-04	k: 84	n:980000
Cons ci ratio: 9.603845e-03	ci left: 1.446028e-01	ci right 1.459993e-01	k: 142394	n:980000
KS ci ratio: 4.251650e-01	ci left: 6.836963e-05	ci right 1.061190e-04	k: 84	n:980000
MAPK1   980000 perm   594 sec   (1650 perm/sec)   p_kst 8.571429e-05   p_cons 1.453000e-01   p_joint 8.571429e-05

Joint ci ratio: 4.178546e-01	ci left: 7.038789e-05	ci right 1.083970e-04	k: 87	n:990000
Cons ci ratio: 9.554324e-03	ci left: 1.446295e-01	ci right 1.460190e-01	k: 143870	n:990000
KS ci ratio: 4.178546e-01	ci left: 7.038789e-05	ci right 1.083970e-04	k: 87	n:990000
MAPK1   990000 perm   605 sec   (1638 perm/sec)   p_kst 8.787879e-05   p_cons 1.453232e-01   p_joint 8.787879e-05

Joint ci ratio: 4.155005e-01	ci left: 7.057915e-05	ci right 1.084174e-04	k: 88	n:1000000
Cons ci ratio: 9.508203e-03	ci left: 1.445869e-01	ci right 1.459692e-01	k: 145277	n:1000000
KS ci ratio: 4.155005e-01	ci left: 7.057915e-05	ci right 1.084174e-04	k: 88	n:1000000
MAPK1   1000000 perm   615 sec   (1625 perm/sec)   p_kst 8.800000e-05   p_cons 1.452770e-01   p_joint 8.800000e-05

Joint ci ratio: 4.131857e-01	ci left: 7.076722e-05	ci right 1.084367e-04	k: 89	n:1010000
Cons ci ratio: 9.461384e-03	ci left: 1.445806e-01	ci right 1.459560e-01	k: 146720	n:1010000
KS ci ratio: 4.131857e-01	ci left: 7.076722e-05	ci right 1.084367e-04	k: 89	n:1010000
MAPK1   1010000 perm   626 sec   (1614 perm/sec)   p_kst 8.811881e-05   p_cons 1.452673e-01   p_joint 8.811881e-05

Joint ci ratio: 4.131858e-01	ci left: 7.007342e-05	ci right 1.073736e-04	k: 89	n:1020000
Cons ci ratio: 9.412984e-03	ci left: 1.446342e-01	ci right 1.460031e-01	k: 148224	n:1020000
KS ci ratio: 4.131858e-01	ci left: 7.007342e-05	ci right 1.073736e-04	k: 89	n:1020000
MAPK1   1020000 perm   637 sec   (1602 perm/sec)   p_kst 8.725490e-05   p_cons 1.453176e-01   p_joint 8.725490e-05

Joint ci ratio: 4.131860e-01	ci left: 6.939309e-05	ci right 1.063311e-04	k: 89	n:1030000
Cons ci ratio: 9.367515e-03	ci left: 1.446287e-01	ci right 1.459908e-01	k: 149668	n:1030000
KS ci ratio: 4.131860e-01	ci left: 6.939309e-05	ci right 1.063311e-04	k: 89	n:1030000
MAPK1   1030000 perm   648 sec   (1591 perm/sec)   p_kst 8.640777e-05   p_cons 1.453087e-01   p_joint 8.640777e-05

Joint ci ratio: 4.131862e-01	ci left: 6.872584e-05	ci right 1.053087e-04	k: 89	n:1040000
Cons ci ratio: 9.323601e-03	ci left: 1.445992e-01	ci right 1.459547e-01	k: 151087	n:1040000
KS ci ratio: 4.131862e-01	ci left: 6.872584e-05	ci right 1.053087e-04	k: 89	n:1040000
MAPK1   1040000 perm   658 sec   (1580 perm/sec)   p_kst 8.557692e-05   p_cons 1.452760e-01   p_joint 8.557692e-05

Joint ci ratio: 4.131864e-01	ci left: 6.807131e-05	ci right 1.043058e-04	k: 89	n:1050000
Cons ci ratio: 9.281580e-03	ci left: 1.445361e-01	ci right 1.458849e-01	k: 152470	n:1050000
KS ci ratio: 4.131864e-01	ci left: 6.807131e-05	ci right 1.043058e-04	k: 89	n:1050000
MAPK1   1050000 perm   669 sec   (1570 perm/sec)   p_kst 8.476190e-05   p_cons 1.452095e-01   p_joint 8.476190e-05

Joint ci ratio: 4.109098e-01	ci left: 6.827471e-05	ci right 1.043625e-04	k: 90	n:1060000
Cons ci ratio: 9.236295e-03	ci left: 1.445769e-01	ci right 1.459194e-01	k: 153962	n:1060000
KS ci ratio: 4.109098e-01	ci left: 6.827471e-05	ci right 1.043625e-04	k: 90	n:1060000
MAPK1   1060000 perm   680 sec   (1559 perm/sec)   p_kst 8.490566e-05   p_cons 1.452472e-01   p_joint 8.490566e-05

Joint ci ratio: 4.109100e-01	ci left: 6.763663e-05	ci right 1.033871e-04	k: 90	n:1070000
Cons ci ratio: 9.192047e-03	ci left: 1.446067e-01	ci right 1.459429e-01	k: 155443	n:1070000
KS ci ratio: 4.109100e-01	ci left: 6.763663e-05	ci right 1.033871e-04	k: 90	n:1070000
MAPK1   1070000 perm   691 sec   (1549 perm/sec)   p_kst 8.411215e-05   p_cons 1.452738e-01   p_joint 8.411215e-05

Joint ci ratio: 4.042993e-01	ci left: 6.950333e-05	ci right 1.054909e-04	k: 93	n:1080000
Cons ci ratio: 9.151601e-03	ci left: 1.445499e-01	ci right 1.458798e-01	k: 156831	n:1080000
KS ci ratio: 4.042993e-01	ci left: 6.950333e-05	ci right 1.054909e-04	k: 93	n:1080000
MAPK1   1080000 perm   702 sec   (1538 perm/sec)   p_kst 8.611111e-05   p_cons 1.452139e-01   p_joint 8.611111e-05

Joint ci ratio: 4.042995e-01	ci left: 6.886568e-05	ci right 1.045231e-04	k: 93	n:1090000
Cons ci ratio: 9.109328e-03	ci left: 1.445583e-01	ci right 1.458821e-01	k: 158289	n:1090000
KS ci ratio: 4.042995e-01	ci left: 6.886568e-05	ci right 1.045231e-04	k: 93	n:1090000
MAPK1   1090000 perm   713 sec   (1528 perm/sec)   p_kst 8.532110e-05   p_cons 1.452193e-01   p_joint 8.532110e-05

Joint ci ratio: 4.042997e-01	ci left: 6.823962e-05	ci right 1.035729e-04	k: 93	n:1100000
Cons ci ratio: 9.069162e-03	ci left: 1.445249e-01	ci right 1.458424e-01	k: 159701	n:1100000
KS ci ratio: 4.042997e-01	ci left: 6.823962e-05	ci right 1.035729e-04	k: 93	n:1100000
MAPK1   1100000 perm   725 sec   (1518 perm/sec)   p_kst 8.454545e-05   p_cons 1.451827e-01   p_joint 8.454545e-05

Joint ci ratio: 4.042998e-01	ci left: 6.762484e-05	ci right 1.026398e-04	k: 93	n:1110000
Cons ci ratio: 9.029589e-03	ci left: 1.444902e-01	ci right 1.458017e-01	k: 161111	n:1110000
KS ci ratio: 4.042998e-01	ci left: 6.762484e-05	ci right 1.026398e-04	k: 93	n:1110000
MAPK1   1110000 perm   736 sec   (1508 perm/sec)   p_kst 8.378378e-05   p_cons 1.451450e-01   p_joint 8.378378e-05

Joint ci ratio: 3.979983e-01	ci left: 6.942938e-05	ci right 1.046708e-04	k: 96	n:1120000
Cons ci ratio: 8.990367e-03	ci left: 1.444607e-01	ci right 1.457662e-01	k: 162526	n:1120000
KS ci ratio: 3.979983e-01	ci left: 6.942938e-05	ci right 1.046708e-04	k: 96	n:1120000
MAPK1   1120000 perm   747 sec   (1499 perm/sec)   p_kst 8.571429e-05   p_cons 1.451125e-01   p_joint 8.571429e-05

Joint ci ratio: 3.979984e-01	ci left: 6.881496e-05	ci right 1.037445e-04	k: 96	n:1130000
Cons ci ratio: 8.950758e-03	ci left: 1.444564e-01	ci right 1.457561e-01	k: 163969	n:1130000
KS ci ratio: 3.979984e-01	ci left: 6.881496e-05	ci right 1.037445e-04	k: 96	n:1130000
MAPK1   1130000 perm   759 sec   (1489 perm/sec)   p_kst 8.495575e-05   p_cons 1.451053e-01   p_joint 8.495575e-05

Joint ci ratio: 3.959626e-01	ci left: 6.900093e-05	ci right 1.037988e-04	k: 97	n:1140000
Cons ci ratio: 8.911889e-03	ci left: 1.444461e-01	ci right 1.457400e-01	k: 165405	n:1140000
KS ci ratio: 3.959626e-01	ci left: 6.900093e-05	ci right 1.037988e-04	k: 97	n:1140000
MAPK1   1140000 perm   771 sec   (1479 perm/sec)   p_kst 8.508772e-05   p_cons 1.450921e-01   p_joint 8.508772e-05

Joint ci ratio: 3.939577e-01	ci left: 6.918412e-05	ci right 1.038517e-04	k: 98	n:1150000
Cons ci ratio: 8.872712e-03	ci left: 1.444585e-01	ci right 1.457468e-01	k: 166867	n:1150000
KS ci ratio: 3.939577e-01	ci left: 6.918412e-05	ci right 1.038517e-04	k: 98	n:1150000
MAPK1   1150000 perm   782 sec   (1470 perm/sec)   p_kst 8.521739e-05   p_cons 1.451017e-01   p_joint 8.521739e-05

Joint ci ratio: 3.919829e-01	ci left: 6.936459e-05	ci right 1.039033e-04	k: 99	n:1160000
Cons ci ratio: 8.835706e-03	ci left: 1.444242e-01	ci right 1.457068e-01	k: 168275	n:1160000
KS ci ratio: 3.919829e-01	ci left: 6.936459e-05	ci right 1.039033e-04	k: 99	n:1160000
MAPK1   1160000 perm   795 sec   (1460 perm/sec)   p_kst 8.534483e-05   p_cons 1.450647e-01   p_joint 8.534483e-05

Joint ci ratio: 3.919831e-01	ci left: 6.877172e-05	ci right 1.030152e-04	k: 99	n:1170000
Cons ci ratio: 8.798401e-03	ci left: 1.444119e-01	ci right 1.456890e-01	k: 169708	n:1170000
KS ci ratio: 3.919831e-01	ci left: 6.877172e-05	ci right 1.030152e-04	k: 99	n:1170000
MAPK1   1170000 perm   806 sec   (1451 perm/sec)   p_kst 8.461538e-05   p_cons 1.450496e-01   p_joint 8.461538e-05

Joint ci ratio: 3.881209e-01	ci left: 6.971761e-05	ci right 1.040026e-04	k: 101	n:1180000
Cons ci ratio: 8.760966e-03	ci left: 1.444168e-01	ci right 1.456884e-01	k: 171161	n:1180000
KS ci ratio: 3.881209e-01	ci left: 6.971761e-05	ci right 1.040026e-04	k: 101	n:1180000
MAPK1   1180000 perm   819 sec   (1441 perm/sec)   p_kst 8.559322e-05   p_cons 1.450517e-01   p_joint 8.559322e-05

Joint ci ratio: 3.862322e-01	ci left: 6.989028e-05	ci right 1.040503e-04	k: 102	n:1190000
Cons ci ratio: 8.725837e-03	ci left: 1.443695e-01	ci right 1.456356e-01	k: 172552	n:1190000
KS ci ratio: 3.862322e-01	ci left: 6.989028e-05	ci right 1.040503e-04	k: 102	n:1190000
MAPK1   1190000 perm   831 sec   (1433 perm/sec)   p_kst 8.571429e-05   p_cons 1.450017e-01   p_joint 8.571429e-05

Joint ci ratio: 3.843708e-01	ci left: 7.006047e-05	ci right 1.040969e-04	k: 103	n:1200000
Cons ci ratio: 8.689872e-03	ci left: 1.443588e-01	ci right 1.456196e-01	k: 173986	n:1200000
KS ci ratio: 3.843708e-01	ci left: 7.006047e-05	ci right 1.040969e-04	k: 103	n:1200000
MAPK1   1200000 perm   843 sec   (1423 perm/sec)   p_kst 8.583333e-05   p_cons 1.449883e-01   p_joint 8.583333e-05

Joint ci ratio: 3.825361e-01	ci left: 7.022824e-05	ci right 1.041424e-04	k: 104	n:1210000
Cons ci ratio: 8.652645e-03	ci left: 1.443970e-01	ci right 1.456526e-01	k: 175479	n:1210000
KS ci ratio: 3.825361e-01	ci left: 7.022824e-05	ci right 1.041424e-04	k: 104	n:1210000
MAPK1   1210000 perm   856 sec   (1414 perm/sec)   p_kst 8.595041e-05   p_cons 1.450240e-01   p_joint 8.595041e-05

Joint ci ratio: 3.825362e-01	ci left: 6.965259e-05	ci right 1.032887e-04	k: 104	n:1220000
Cons ci ratio: 8.618628e-03	ci left: 1.443560e-01	ci right 1.456063e-01	k: 176876	n:1220000
KS ci ratio: 3.825362e-01	ci left: 6.965259e-05	ci right 1.032887e-04	k: 104	n:1220000
MAPK1   1220000 perm   868 sec   (1406 perm/sec)   p_kst 8.524590e-05   p_cons 1.449803e-01   p_joint 8.524590e-05

Joint ci ratio: 3.789441e-01	ci left: 7.055671e-05	ci right 1.042299e-04	k: 106	n:1230000
Cons ci ratio: 8.583656e-03	ci left: 1.443546e-01	ci right 1.455999e-01	k: 178321	n:1230000
KS ci ratio: 3.789441e-01	ci left: 7.055671e-05	ci right 1.042299e-04	k: 106	n:1230000
MAPK1   1230000 perm   880 sec   (1397 perm/sec)   p_kst 8.617886e-05   p_cons 1.449764e-01   p_joint 8.617886e-05

Joint ci ratio: 3.754512e-01	ci left: 7.144770e-05	ci right 1.051545e-04	k: 108	n:1240000
Cons ci ratio: 8.549135e-03	ci left: 1.443525e-01	ci right 1.455927e-01	k: 179765	n:1240000
KS ci ratio: 3.754512e-01	ci left: 7.144770e-05	ci right 1.051545e-04	k: 108	n:1240000
MAPK1   1240000 perm   893 sec   (1389 perm/sec)   p_kst 8.709677e-05   p_cons 1.449718e-01   p_joint 8.709677e-05

Joint ci ratio: 3.754514e-01	ci left: 7.087612e-05	ci right 1.043132e-04	k: 108	n:1250000
Cons ci ratio: 8.512720e-03	ci left: 1.444175e-01	ci right 1.456529e-01	k: 181293	n:1250000
KS ci ratio: 3.754514e-01	ci left: 7.087612e-05	ci right 1.043132e-04	k: 108	n:1250000
MAPK1   1250000 perm   905 sec   (1381 perm/sec)   p_kst 8.640000e-05   p_cons 1.450344e-01   p_joint 8.640000e-05

Joint ci ratio: 3.754515e-01	ci left: 7.031360e-05	ci right 1.034854e-04	k: 108	n:1260000
Cons ci ratio: 8.478719e-03	ci left: 1.444244e-01	ci right 1.456550e-01	k: 182749	n:1260000
KS ci ratio: 3.754515e-01	ci left: 7.031360e-05	ci right 1.034854e-04	k: 108	n:1260000
MAPK1   1260000 perm   918 sec   (1372 perm/sec)   p_kst 8.571429e-05   p_cons 1.450389e-01   p_joint 8.571429e-05

Joint ci ratio: 3.754516e-01	ci left: 6.975995e-05	ci right 1.026705e-04	k: 108	n:1270000
Cons ci ratio: 8.444264e-03	ci left: 1.444564e-01	ci right 1.456822e-01	k: 184237	n:1270000
KS ci ratio: 3.754516e-01	ci left: 6.975995e-05	ci right 1.026705e-04	k: 108	n:1270000
MAPK1   1270000 perm   931 sec   (1364 perm/sec)   p_kst 8.503937e-05   p_cons 1.450685e-01   p_joint 8.503937e-05

Joint ci ratio: 3.737411e-01	ci left: 6.992265e-05	ci right 1.027229e-04	k: 109	n:1280000
Cons ci ratio: 8.411895e-03	ci left: 1.444388e-01	ci right 1.456597e-01	k: 185662	n:1280000
KS ci ratio: 3.737411e-01	ci left: 6.992265e-05	ci right 1.027229e-04	k: 109	n:1280000
MAPK1   1280000 perm   944 sec   (1356 perm/sec)   p_kst 8.515625e-05   p_cons 1.450484e-01   p_joint 8.515625e-05

Joint ci ratio: 3.703890e-01	ci left: 7.078604e-05	ci right 1.036213e-04	k: 111	n:1290000
Cons ci ratio: 8.379842e-03	ci left: 1.444230e-01	ci right 1.456391e-01	k: 187089	n:1290000
KS ci ratio: 3.703890e-01	ci left: 7.078604e-05	ci right 1.036213e-04	k: 111	n:1290000
MAPK1   1290000 perm   957 sec   (1348 perm/sec)   p_kst 8.604651e-05   p_cons 1.450302e-01   p_joint 8.604651e-05

Joint ci ratio: 3.687464e-01	ci left: 7.093932e-05	ci right 1.036646e-04	k: 112	n:1300000
Cons ci ratio: 8.348024e-03	ci left: 1.444113e-01	ci right 1.456226e-01	k: 188521	n:1300000
KS ci ratio: 3.687464e-01	ci left: 7.093932e-05	ci right 1.036646e-04	k: 112	n:1300000
MAPK1   1300000 perm   970 sec   (1340 perm/sec)   p_kst 8.615385e-05   p_cons 1.450162e-01   p_joint 8.615385e-05

Joint ci ratio: 3.687465e-01	ci left: 7.039780e-05	ci right 1.028732e-04	k: 112	n:1310000
Cons ci ratio: 8.317564e-03	ci left: 1.443700e-01	ci right 1.455766e-01	k: 189914	n:1310000
KS ci ratio: 3.687465e-01	ci left: 7.039780e-05	ci right 1.028732e-04	k: 112	n:1310000
MAPK1   1310000 perm   983 sec   (1333 perm/sec)   p_kst 8.549618e-05   p_cons 1.449725e-01   p_joint 8.549618e-05

Joint ci ratio: 3.687467e-01	ci left: 6.986448e-05	ci right 1.020939e-04	k: 112	n:1320000
Cons ci ratio: 8.284878e-03	ci left: 1.444058e-01	ci right 1.456079e-01	k: 191408	n:1320000
KS ci ratio: 3.687467e-01	ci left: 6.986448e-05	ci right 1.020939e-04	k: 112	n:1320000
MAPK1   1320000 perm   996 sec   (1325 perm/sec)   p_kst 8.484848e-05   p_cons 1.450061e-01   p_joint 8.484848e-05

Joint ci ratio: 3.687468e-01	ci left: 6.933918e-05	ci right 1.013263e-04	k: 112	n:1330000
Cons ci ratio: 8.254851e-03	ci left: 1.443727e-01	ci right 1.455702e-01	k: 192811	n:1330000
KS ci ratio: 3.687468e-01	ci left: 6.933918e-05	ci right 1.013263e-04	k: 112	n:1330000
MAPK1   1330000 perm   1009 sec   (1318 perm/sec)   p_kst 8.421053e-05   p_cons 1.449707e-01   p_joint 8.421053e-05

Joint ci ratio: 3.671259e-01	ci left: 6.949899e-05	ci right 1.013851e-04	k: 113	n:1340000
Cons ci ratio: 8.224059e-03	ci left: 1.443729e-01	ci right 1.455659e-01	k: 194258	n:1340000
KS ci ratio: 3.671259e-01	ci left: 6.949899e-05	ci right 1.013851e-04	k: 113	n:1340000
MAPK1   1340000 perm   1022 sec   (1311 perm/sec)   p_kst 8.432836e-05   p_cons 1.449687e-01   p_joint 8.432836e-05

Joint ci ratio: 3.671260e-01	ci left: 6.898418e-05	ci right 1.006341e-04	k: 113	n:1350000
Cons ci ratio: 8.194147e-03	ci left: 1.443569e-01	ci right 1.455454e-01	k: 195683	n:1350000
KS ci ratio: 3.671260e-01	ci left: 6.898418e-05	ci right 1.006341e-04	k: 113	n:1350000
MAPK1   1350000 perm   1035 sec   (1304 perm/sec)   p_kst 8.370370e-05   p_cons 1.449504e-01   p_joint 8.370370e-05

Joint ci ratio: 3.671261e-01	ci left: 6.847694e-05	ci right 9.989413e-05	k: 113	n:1360000
Cons ci ratio: 8.164051e-03	ci left: 1.443565e-01	ci right 1.455406e-01	k: 197129	n:1360000
KS ci ratio: 3.671261e-01	ci left: 6.847694e-05	ci right 9.989413e-05	k: 113	n:1360000
MAPK1   1360000 perm   1049 sec   (1296 perm/sec)   p_kst 8.308824e-05   p_cons 1.449478e-01   p_joint 8.308824e-05

Joint ci ratio: 3.655264e-01	ci left: 6.863985e-05	ci right 9.996181e-05	k: 114	n:1370000
Cons ci ratio: 8.134380e-03	ci left: 1.443532e-01	ci right 1.455330e-01	k: 198571	n:1370000
KS ci ratio: 3.655264e-01	ci left: 6.863985e-05	ci right 9.996181e-05	k: 114	n:1370000
MAPK1   1370000 perm   1063 sec   (1289 perm/sec)   p_kst 8.321168e-05   p_cons 1.449423e-01   p_joint 8.321168e-05

Joint ci ratio: 3.623886e-01	ci left: 6.945921e-05	ci right 1.008187e-04	k: 116	n:1380000
Cons ci ratio: 8.104841e-03	ci left: 1.443558e-01	ci right 1.455312e-01	k: 200021	n:1380000
KS ci ratio: 3.623886e-01	ci left: 6.945921e-05	ci right 1.008187e-04	k: 116	n:1380000
MAPK1   1380000 perm   1076 sec   (1282 perm/sec)   p_kst 8.405797e-05   p_cons 1.449428e-01   p_joint 8.405797e-05

Joint ci ratio: 3.593303e-01	ci left: 7.026791e-05	ci right 1.016621e-04	k: 118	n:1390000
Cons ci ratio: 8.075949e-03	ci left: 1.443482e-01	ci right 1.455194e-01	k: 201457	n:1390000
KS ci ratio: 3.593303e-01	ci left: 7.026791e-05	ci right 1.016621e-04	k: 118	n:1390000
MAPK1   1390000 perm   1090 sec   (1275 perm/sec)   p_kst 8.489209e-05   p_cons 1.449331e-01   p_joint 8.489209e-05

Joint ci ratio: 3.593304e-01	ci left: 6.976600e-05	ci right 1.009360e-04	k: 118	n:1400000
Cons ci ratio: 8.046645e-03	ci left: 1.443629e-01	ci right 1.455300e-01	k: 202924	n:1400000
KS ci ratio: 3.593304e-01	ci left: 6.976600e-05	ci right 1.009360e-04	k: 118	n:1400000
MAPK1   1400000 perm   1104 sec   (1268 perm/sec)   p_kst 8.428571e-05   p_cons 1.449457e-01   p_joint 8.428571e-05

Joint ci ratio: 3.578300e-01	ci left: 6.991653e-05	ci right 1.009930e-04	k: 119	n:1410000
Cons ci ratio: 8.017864e-03	ci left: 1.443711e-01	ci right 1.455339e-01	k: 204382	n:1410000
KS ci ratio: 3.578300e-01	ci left: 6.991653e-05	ci right 1.009930e-04	k: 119	n:1410000
MAPK1   1410000 perm   1117 sec   (1262 perm/sec)   p_kst 8.439716e-05   p_cons 1.449518e-01   p_joint 8.439716e-05

Joint ci ratio: 3.534391e-01	ci left: 7.134812e-05	ci right 1.025824e-04	k: 122	n:1420000
Cons ci ratio: 7.989572e-03	ci left: 1.443734e-01	ci right 1.455322e-01	k: 205832	n:1420000
KS ci ratio: 3.534391e-01	ci left: 7.134812e-05	ci right 1.025824e-04	k: 122	n:1420000
MAPK1   1420000 perm   1132 sec   (1255 perm/sec)   p_kst 8.591549e-05   p_cons 1.449521e-01   p_joint 8.591549e-05

Joint ci ratio: 3.520110e-01	ci left: 7.148653e-05	ci right 1.026260e-04	k: 123	n:1430000
Cons ci ratio: 7.960880e-03	ci left: 1.443974e-01	ci right 1.455522e-01	k: 207313	n:1430000
KS ci ratio: 3.520110e-01	ci left: 7.148653e-05	ci right 1.026260e-04	k: 123	n:1430000
MAPK1   1430000 perm   1146 sec   (1248 perm/sec)   p_kst 8.601399e-05   p_cons 1.449741e-01   p_joint 8.601399e-05

Joint ci ratio: 3.520111e-01	ci left: 7.099009e-05	ci right 1.019133e-04	k: 123	n:1440000
Cons ci ratio: 7.933629e-03	ci left: 1.443858e-01	ci right 1.455365e-01	k: 208743	n:1440000
KS ci ratio: 3.520111e-01	ci left: 7.099009e-05	ci right 1.019133e-04	k: 123	n:1440000
MAPK1   1440000 perm   1160 sec   (1242 perm/sec)   p_kst 8.541667e-05   p_cons 1.449604e-01   p_joint 8.541667e-05

Joint ci ratio: 3.520112e-01	ci left: 7.050050e-05	ci right 1.012105e-04	k: 123	n:1450000
Cons ci ratio: 7.906898e-03	ci left: 1.443667e-01	ci right 1.455134e-01	k: 210162	n:1450000
KS ci ratio: 3.520112e-01	ci left: 7.050050e-05	ci right 1.012105e-04	k: 123	n:1450000
MAPK1   1450000 perm   1174 sec   (1235 perm/sec)   p_kst 8.482759e-05   p_cons 1.449393e-01   p_joint 8.482759e-05

Joint ci ratio: 3.520113e-01	ci left: 7.001761e-05	ci right 1.005173e-04	k: 123	n:1460000
Cons ci ratio: 7.877844e-03	ci left: 1.444292e-01	ci right 1.455722e-01	k: 211700	n:1460000
KS ci ratio: 3.520113e-01	ci left: 7.001761e-05	ci right 1.005173e-04	k: 123	n:1460000
MAPK1   1460000 perm   1188 sec   (1229 perm/sec)   p_kst 8.424658e-05   p_cons 1.450000e-01   p_joint 8.424658e-05

Joint ci ratio: 3.478286e-01	ci left: 7.140278e-05	ci right 1.020529e-04	k: 126	n:1470000
Cons ci ratio: 7.850831e-03	ci left: 1.444366e-01	ci right 1.455757e-01	k: 213158	n:1470000
KS ci ratio: 3.478286e-01	ci left: 7.140278e-05	ci right 1.020529e-04	k: 126	n:1470000
MAPK1   1470000 perm   1203 sec   (1222 perm/sec)   p_kst 8.571429e-05   p_cons 1.450054e-01   p_joint 8.571429e-05

Joint ci ratio: 3.478287e-01	ci left: 7.092032e-05	ci right 1.013634e-04	k: 126	n:1480000
Cons ci ratio: 7.823412e-03	ci left: 1.444655e-01	ci right 1.456008e-01	k: 214648	n:1480000
KS ci ratio: 3.478287e-01	ci left: 7.092032e-05	ci right 1.013634e-04	k: 126	n:1480000
MAPK1   1480000 perm   1217 sec   (1216 perm/sec)   p_kst 8.513514e-05   p_cons 1.450324e-01   p_joint 8.513514e-05

Joint ci ratio: 3.464673e-01	ci left: 7.105698e-05	ci right 1.014125e-04	k: 127	n:1490000
Cons ci ratio: 7.797543e-03	ci left: 1.444538e-01	ci right 1.455852e-01	k: 216078	n:1490000
KS ci ratio: 3.464673e-01	ci left: 7.105698e-05	ci right 1.014125e-04	k: 127	n:1490000
MAPK1   1490000 perm   1232 sec   (1210 perm/sec)   p_kst 8.523490e-05   p_cons 1.450188e-01   p_joint 8.523490e-05

Joint ci ratio: 3.451218e-01	ci left: 7.119204e-05	ci right 1.014608e-04	k: 128	n:1500000
Cons ci ratio: 7.771847e-03	ci left: 1.444449e-01	ci right 1.455725e-01	k: 217512	n:1500000
KS ci ratio: 3.451218e-01	ci left: 7.119204e-05	ci right 1.014608e-04	k: 128	n:1500000
MAPK1   1500000 perm   1247 sec   (1203 perm/sec)   p_kst 8.533333e-05   p_cons 1.450080e-01   p_joint 8.533333e-05

Joint ci ratio: 3.451219e-01	ci left: 7.072056e-05	ci right 1.007889e-04	k: 128	n:1510000
Cons ci ratio: 7.745388e-03	ci left: 1.444685e-01	ci right 1.455925e-01	k: 218995	n:1510000
KS ci ratio: 3.451219e-01	ci left: 7.072056e-05	ci right 1.007889e-04	k: 128	n:1510000
MAPK1   1510000 perm   1261 sec   (1197 perm/sec)   p_kst 8.476821e-05   p_cons 1.450298e-01   p_joint 8.476821e-05

Joint ci ratio: 3.451220e-01	ci left: 7.025529e-05	ci right 1.001258e-04	k: 128	n:1520000
Cons ci ratio: 7.719547e-03	ci left: 1.444807e-01	ci right 1.456010e-01	k: 220461	n:1520000
KS ci ratio: 3.451220e-01	ci left: 7.025529e-05	ci right 1.001258e-04	k: 128	n:1520000
MAPK1   1520000 perm   1277 sec   (1191 perm/sec)   p_kst 8.421053e-05   p_cons 1.450401e-01   p_joint 8.421053e-05

Joint ci ratio: 3.424772e-01	ci left: 7.099045e-05	ci right 1.008910e-04	k: 130	n:1530000
Cons ci ratio: 7.693840e-03	ci left: 1.444966e-01	ci right 1.456133e-01	k: 221933	n:1530000
KS ci ratio: 3.424772e-01	ci left: 7.099045e-05	ci right 1.008910e-04	k: 130	n:1530000
MAPK1   1530000 perm   1292 sec   (1185 perm/sec)   p_kst 8.496732e-05   p_cons 1.450542e-01   p_joint 8.496732e-05

Joint ci ratio: 3.424773e-01	ci left: 7.052947e-05	ci right 1.002359e-04	k: 130	n:1540000
Cons ci ratio: 7.668710e-03	ci left: 1.445019e-01	ci right 1.456150e-01	k: 223389	n:1540000
KS ci ratio: 3.424773e-01	ci left: 7.052947e-05	ci right 1.002359e-04	k: 130	n:1540000
MAPK1   1540000 perm   1307 sec   (1178 perm/sec)   p_kst 8.441558e-05   p_cons 1.450578e-01   p_joint 8.441558e-05

Joint ci ratio: 3.424774e-01	ci left: 7.007443e-05	ci right 9.958918e-05	k: 130	n:1550000
Cons ci ratio: 7.643109e-03	ci left: 1.445304e-01	ci right 1.456399e-01	k: 224881	n:1550000
KS ci ratio: 3.424774e-01	ci left: 7.007443e-05	ci right 9.958918e-05	k: 130	n:1550000
MAPK1   1550000 perm   1322 sec   (1173 perm/sec)   p_kst 8.387097e-05   p_cons 1.450845e-01   p_joint 8.387097e-05

Joint ci ratio: 3.411777e-01	ci left: 7.021124e-05	ci right 9.964663e-05	k: 131	n:1560000
Cons ci ratio: 7.618373e-03	ci left: 1.445387e-01	ci right 1.456447e-01	k: 226342	n:1560000
KS ci ratio: 3.411777e-01	ci left: 7.021124e-05	ci right 9.964663e-05	k: 131	n:1560000
MAPK1   1560000 perm   1337 sec   (1166 perm/sec)   p_kst 8.397436e-05   p_cons 1.450910e-01   p_joint 8.397436e-05

Joint ci ratio: 3.398926e-01	ci left: 7.034652e-05	ci right 9.970314e-05	k: 132	n:1570000
Cons ci ratio: 7.592959e-03	ci left: 1.445768e-01	ci right 1.456793e-01	k: 227850	n:1570000
KS ci ratio: 3.398926e-01	ci left: 7.034652e-05	ci right 9.970314e-05	k: 132	n:1570000
MAPK1   1570000 perm   1353 sec   (1161 perm/sec)   p_kst 8.407643e-05   p_cons 1.451274e-01   p_joint 8.407643e-05

Joint ci ratio: 3.398927e-01	ci left: 6.990128e-05	ci right 9.907212e-05	k: 132	n:1580000
Cons ci ratio: 7.568415e-03	ci left: 1.445941e-01	ci right 1.456932e-01	k: 229326	n:1580000
KS ci ratio: 3.398927e-01	ci left: 6.990128e-05	ci right 9.907212e-05	k: 132	n:1580000
MAPK1   1580000 perm   1368 sec   (1155 perm/sec)   p_kst 8.354430e-05   p_cons 1.451430e-01   p_joint 8.354430e-05

Joint ci ratio: 3.386220e-01	ci left: 7.003701e-05	ci right 9.913133e-05	k: 133	n:1590000
Cons ci ratio: 7.545466e-03	ci left: 1.445667e-01	ci right 1.456623e-01	k: 230731	n:1590000
KS ci ratio: 3.386220e-01	ci left: 7.003701e-05	ci right 9.913133e-05	k: 133	n:1590000
MAPK1   1590000 perm   1383 sec   (1149 perm/sec)   p_kst 8.364780e-05   p_cons 1.451138e-01   p_joint 8.364780e-05

Joint ci ratio: 3.373655e-01	ci left: 7.017124e-05	ci right 9.918960e-05	k: 134	n:1600000
Cons ci ratio: 7.522079e-03	ci left: 1.445608e-01	ci right 1.456529e-01	k: 232170	n:1600000
KS ci ratio: 3.373655e-01	ci left: 7.017124e-05	ci right 9.918960e-05	k: 134	n:1600000
MAPK1   1600000 perm   1399 sec   (1143 perm/sec)   p_kst 8.375000e-05   p_cons 1.451062e-01   p_joint 8.375000e-05

Joint ci ratio: 3.373656e-01	ci left: 6.973539e-05	ci right 9.857352e-05	k: 134	n:1610000
Cons ci ratio: 7.498946e-03	ci left: 1.445538e-01	ci right 1.456425e-01	k: 233607	n:1610000
KS ci ratio: 3.373656e-01	ci left: 6.973539e-05	ci right 9.857352e-05	k: 134	n:1610000
MAPK1   1610000 perm   1415 sec   (1138 perm/sec)   p_kst 8.322981e-05   p_cons 1.450975e-01   p_joint 8.322981e-05

Joint ci ratio: 3.361230e-01	ci left: 6.987002e-05	ci right 9.863433e-05	k: 135	n:1620000
Cons ci ratio: 7.475170e-03	ci left: 1.445752e-01	ci right 1.456606e-01	k: 235090	n:1620000
KS ci ratio: 3.361230e-01	ci left: 6.987002e-05	ci right 9.863433e-05	k: 135	n:1620000
MAPK1   1620000 perm   1431 sec   (1132 perm/sec)   p_kst 8.333333e-05   p_cons 1.451173e-01   p_joint 8.333333e-05

Joint ci ratio: 3.348940e-01	ci left: 7.000319e-05	ci right 9.869420e-05	k: 136	n:1630000
Cons ci ratio: 7.452098e-03	ci left: 1.445805e-01	ci right 1.456625e-01	k: 236547	n:1630000
KS ci ratio: 3.348940e-01	ci left: 7.000319e-05	ci right 9.869420e-05	k: 136	n:1630000
MAPK1   1630000 perm   1446 sec   (1127 perm/sec)   p_kst 8.343558e-05   p_cons 1.451209e-01   p_joint 8.343558e-05

Joint ci ratio: 3.348941e-01	ci left: 6.957634e-05	ci right 9.809241e-05	k: 136	n:1640000
Cons ci ratio: 7.429329e-03	ci left: 1.445826e-01	ci right 1.456613e-01	k: 237999	n:1640000
KS ci ratio: 3.348941e-01	ci left: 6.957634e-05	ci right 9.809241e-05	k: 136	n:1640000
MAPK1   1640000 perm   1463 sec   (1121 perm/sec)   p_kst 8.292683e-05   p_cons 1.451213e-01   p_joint 8.292683e-05

Joint ci ratio: 3.324760e-01	ci left: 7.026524e-05	ci right 9.881121e-05	k: 138	n:1650000
Cons ci ratio: 7.406749e-03	ci left: 1.445853e-01	ci right 1.456608e-01	k: 239452	n:1650000
KS ci ratio: 3.324760e-01	ci left: 7.026524e-05	ci right 9.881121e-05	k: 138	n:1650000
MAPK1   1650000 perm   1479 sec   (1116 perm/sec)   p_kst 8.363636e-05   p_cons 1.451224e-01   p_joint 8.363636e-05

Joint ci ratio: 3.312864e-01	ci left: 7.039418e-05	ci right 9.886838e-05	k: 139	n:1660000
Cons ci ratio: 7.384159e-03	ci left: 1.445952e-01	ci right 1.456675e-01	k: 240917	n:1660000
KS ci ratio: 3.312864e-01	ci left: 7.039418e-05	ci right 9.886838e-05	k: 139	n:1660000
MAPK1   1660000 perm   1495 sec   (1111 perm/sec)   p_kst 8.373494e-05   p_cons 1.451307e-01   p_joint 8.373494e-05

Joint ci ratio: 3.301095e-01	ci left: 7.052175e-05	ci right 9.892470e-05	k: 140	n:1670000
Cons ci ratio: 7.361082e-03	ci left: 1.446283e-01	ci right 1.456975e-01	k: 242421	n:1670000
KS ci ratio: 3.301095e-01	ci left: 7.052175e-05	ci right 9.892470e-05	k: 140	n:1670000
MAPK1   1670000 perm   1511 sec   (1105 perm/sec)   p_kst 8.383234e-05   p_cons 1.451623e-01   p_joint 8.383234e-05

Joint ci ratio: 3.301096e-01	ci left: 7.010197e-05	ci right 9.833586e-05	k: 140	n:1680000
Cons ci ratio: 7.339117e-03	ci left: 1.446307e-01	ci right 1.456967e-01	k: 243874	n:1680000
KS ci ratio: 3.301096e-01	ci left: 7.010197e-05	ci right 9.833586e-05	k: 140	n:1680000
MAPK1   1680000 perm   1527 sec   (1100 perm/sec)   p_kst 8.333333e-05   p_cons 1.451631e-01   p_joint 8.333333e-05

Joint ci ratio: 3.289452e-01	ci left: 7.022994e-05	ci right 9.839449e-05	k: 141	n:1690000
Cons ci ratio: 7.317138e-03	ci left: 1.446402e-01	ci right 1.457030e-01	k: 245339	n:1690000
KS ci ratio: 3.289452e-01	ci left: 7.022994e-05	ci right 9.839449e-05	k: 141	n:1690000
MAPK1   1690000 perm   1543 sec   (1095 perm/sec)   p_kst 8.343195e-05   p_cons 1.451710e-01   p_joint 8.343195e-05

Joint ci ratio: 3.289453e-01	ci left: 6.981682e-05	ci right 9.781570e-05	k: 141	n:1700000
Cons ci ratio: 7.295581e-03	ci left: 1.446419e-01	ci right 1.457016e-01	k: 246791	n:1700000
KS ci ratio: 3.289453e-01	ci left: 6.981682e-05	ci right 9.781570e-05	k: 141	n:1700000
MAPK1   1700000 perm   1559 sec   (1090 perm/sec)   p_kst 8.294118e-05   p_cons 1.451712e-01   p_joint 8.294118e-05

Joint ci ratio: 3.277931e-01	ci left: 6.994513e-05	ci right 9.787651e-05	k: 142	n:1710000
Cons ci ratio: 7.273424e-03	ci left: 1.446705e-01	ci right 1.457272e-01	k: 248289	n:1710000
KS ci ratio: 3.277931e-01	ci left: 6.994513e-05	ci right 9.787651e-05	k: 142	n:1710000
MAPK1   1710000 perm   1576 sec   (1085 perm/sec)   p_kst 8.304094e-05   p_cons 1.451982e-01   p_joint 8.304094e-05

Joint ci ratio: 3.266529e-01	ci left: 7.007211e-05	ci right 9.793645e-05	k: 143	n:1720000
Cons ci ratio: 7.252369e-03	ci left: 1.446680e-01	ci right 1.457216e-01	k: 249734	n:1720000
KS ci ratio: 3.266529e-01	ci left: 7.007211e-05	ci right 9.793645e-05	k: 143	n:1720000
MAPK1   1720000 perm   1592 sec   (1080 perm/sec)   p_kst 8.313953e-05   p_cons 1.451942e-01   p_joint 8.313953e-05

Joint ci ratio: 3.255245e-01	ci left: 7.019779e-05	ci right 9.799553e-05	k: 144	n:1730000
Cons ci ratio: 7.231815e-03	ci left: 1.446545e-01	ci right 1.457050e-01	k: 251160	n:1730000
KS ci ratio: 3.255245e-01	ci left: 7.019779e-05	ci right 9.799553e-05	k: 144	n:1730000
MAPK1   1730000 perm   1609 sec   (1075 perm/sec)   p_kst 8.323699e-05   p_cons 1.451792e-01   p_joint 8.323699e-05

Joint ci ratio: 3.233024e-01	ci left: 7.085019e-05	ci right 9.867503e-05	k: 146	n:1740000
Cons ci ratio: 7.210816e-03	ci left: 1.446625e-01	ci right 1.457100e-01	k: 252623	n:1740000
KS ci ratio: 3.233024e-01	ci left: 7.085019e-05	ci right 9.867503e-05	k: 146	n:1740000
MAPK1   1740000 perm   1626 sec   (1070 perm/sec)   p_kst 8.390805e-05   p_cons 1.451856e-01   p_joint 8.390805e-05

Joint ci ratio: 3.233025e-01	ci left: 7.044533e-05	ci right 9.811118e-05	k: 146	n:1750000
Cons ci ratio: 7.189471e-03	ci left: 1.446886e-01	ci right 1.457331e-01	k: 254118	n:1750000
KS ci ratio: 3.233025e-01	ci left: 7.044533e-05	ci right 9.811118e-05	k: 146	n:1750000
MAPK1   1750000 perm   1643 sec   (1065 perm/sec)   p_kst 8.342857e-05   p_cons 1.452103e-01   p_joint 8.342857e-05

Joint ci ratio: 3.211252e-01	ci left: 7.108954e-05	ci right 9.878168e-05	k: 148	n:1760000
Cons ci ratio: 7.168543e-03	ci left: 1.447065e-01	ci right 1.457481e-01	k: 255599	n:1760000
KS ci ratio: 3.211252e-01	ci left: 7.108954e-05	ci right 9.878168e-05	k: 148	n:1760000
MAPK1   1760000 perm   1660 sec   (1060 perm/sec)   p_kst 8.409091e-05   p_cons 1.452267e-01   p_joint 8.409091e-05

Joint ci ratio: 3.189914e-01	ci left: 7.172709e-05	ci right 9.944400e-05	k: 150	n:1770000
Cons ci ratio: 7.148041e-03	ci left: 1.447157e-01	ci right 1.457544e-01	k: 257065	n:1770000
KS ci ratio: 3.189914e-01	ci left: 7.172709e-05	ci right 9.944400e-05	k: 150	n:1770000
MAPK1   1770000 perm   1678 sec   (1055 perm/sec)   p_kst 8.474576e-05   p_cons 1.452345e-01   p_joint 8.474576e-05

Joint ci ratio: 3.168995e-01	ci left: 7.235808e-05	ci right 1.000983e-04	k: 152	n:1780000
Cons ci ratio: 7.128230e-03	ci left: 1.447069e-01	ci right 1.457426e-01	k: 258499	n:1780000
KS ci ratio: 3.168995e-01	ci left: 7.235808e-05	ci right 1.000983e-04	k: 152	n:1780000
MAPK1   1780000 perm   1695 sec   (1050 perm/sec)   p_kst 8.539326e-05   p_cons 1.452242e-01   p_joint 8.539326e-05

Joint ci ratio: 3.158689e-01	ci left: 7.246815e-05	ci right 1.001419e-04	k: 153	n:1790000
Cons ci ratio: 7.109270e-03	ci left: 1.446742e-01	ci right 1.457069e-01	k: 259890	n:1790000
KS ci ratio: 3.158689e-01	ci left: 7.246815e-05	ci right 1.001419e-04	k: 153	n:1790000
MAPK1   1790000 perm   1713 sec   (1045 perm/sec)   p_kst 8.547486e-05   p_cons 1.451899e-01   p_joint 8.547486e-05

Joint ci ratio: 3.158690e-01	ci left: 7.206554e-05	ci right 9.958560e-05	k: 153	n:1800000
Cons ci ratio: 7.089573e-03	ci left: 1.446729e-01	ci right 1.457027e-01	k: 261337	n:1800000
KS ci ratio: 3.158690e-01	ci left: 7.206554e-05	ci right 9.958560e-05	k: 153	n:1800000
MAPK1   1800000 perm   1730 sec   (1041 perm/sec)   p_kst 8.500000e-05   p_cons 1.451872e-01   p_joint 8.500000e-05

Joint ci ratio: 3.128364e-01	ci left: 7.319411e-05	ci right 1.008232e-04	k: 156	n:1810000
Cons ci ratio: 7.070715e-03	ci left: 1.446479e-01	ci right 1.456748e-01	k: 262741	n:1810000
KS ci ratio: 3.128364e-01	ci left: 7.319411e-05	ci right 1.008232e-04	k: 156	n:1810000
MAPK1   1810000 perm   1747 sec   (1036 perm/sec)   p_kst 8.618785e-05   p_cons 1.451608e-01   p_joint 8.618785e-05

Joint ci ratio: 3.108626e-01	ci left: 7.380487e-05	ci right 1.014538e-04	k: 158	n:1820000
Cons ci ratio: 7.051163e-03	ci left: 1.446528e-01	ci right 1.456769e-01	k: 264199	n:1820000
KS ci ratio: 3.108626e-01	ci left: 7.380487e-05	ci right 1.014538e-04	k: 158	n:1820000
MAPK1   1820000 perm   1765 sec   (1031 perm/sec)   p_kst 8.681319e-05   p_cons 1.451643e-01   p_joint 8.681319e-05

Joint ci ratio: 3.089256e-01	ci left: 7.440948e-05	ci right 1.020770e-04	k: 160	n:1830000
Cons ci ratio: 7.032083e-03	ci left: 1.446467e-01	ci right 1.456680e-01	k: 265637	n:1830000
KS ci ratio: 3.089256e-01	ci left: 7.440948e-05	ci right 1.020770e-04	k: 160	n:1830000
MAPK1   1830000 perm   1783 sec   (1027 perm/sec)   p_kst 8.743169e-05   p_cons 1.451568e-01   p_joint 8.743169e-05

Joint ci ratio: 3.070244e-01	ci left: 7.500805e-05	ci right 1.026930e-04	k: 162	n:1840000
Cons ci ratio: 7.013433e-03	ci left: 1.446310e-01	ci right 1.456495e-01	k: 267057	n:1840000
KS ci ratio: 3.070244e-01	ci left: 7.500805e-05	ci right 1.026930e-04	k: 162	n:1840000
MAPK1   1840000 perm   1800 sec   (1022 perm/sec)   p_kst 8.804348e-05   p_cons 1.451397e-01   p_joint 8.804348e-05

Joint ci ratio: 3.070245e-01	ci left: 7.460260e-05	ci right 1.021379e-04	k: 162	n:1850000
Cons ci ratio: 6.994336e-03	ci left: 1.446365e-01	ci right 1.456522e-01	k: 268516	n:1850000
KS ci ratio: 3.070245e-01	ci left: 7.460260e-05	ci right 1.021379e-04	k: 162	n:1850000
MAPK1   1850000 perm   1818 sec   (1018 perm/sec)   p_kst 8.756757e-05   p_cons 1.451438e-01   p_joint 8.756757e-05

Joint ci ratio: 3.060870e-01	ci left: 7.469780e-05	ci right 1.021676e-04	k: 163	n:1860000
Cons ci ratio: 6.975969e-03	ci left: 1.446215e-01	ci right 1.456344e-01	k: 269937	n:1860000
KS ci ratio: 3.060870e-01	ci left: 7.469780e-05	ci right 1.021676e-04	k: 163	n:1860000
MAPK1   1860000 perm   1836 sec   (1013 perm/sec)   p_kst 8.763441e-05   p_cons 1.451274e-01   p_joint 8.763441e-05

Joint ci ratio: 3.060871e-01	ci left: 7.429834e-05	ci right 1.016212e-04	k: 163	n:1870000
Cons ci ratio: 6.957446e-03	ci left: 1.446174e-01	ci right 1.456276e-01	k: 271378	n:1870000
KS ci ratio: 3.060871e-01	ci left: 7.429834e-05	ci right 1.016212e-04	k: 163	n:1870000
MAPK1   1870000 perm   1853 sec   (1009 perm/sec)   p_kst 8.716578e-05   p_cons 1.451219e-01   p_joint 8.716578e-05

Joint ci ratio: 3.060871e-01	ci left: 7.390314e-05	ci right 1.010807e-04	k: 163	n:1880000
Cons ci ratio: 6.938980e-03	ci left: 1.446165e-01	ci right 1.456240e-01	k: 272825	n:1880000
KS ci ratio: 3.060871e-01	ci left: 7.390314e-05	ci right 1.010807e-04	k: 163	n:1880000
MAPK1   1880000 perm   1871 sec   (1005 perm/sec)   p_kst 8.670213e-05   p_cons 1.451197e-01   p_joint 8.670213e-05

Joint ci ratio: 3.042376e-01	ci left: 7.448930e-05	ci right 1.016849e-04	k: 165	n:1890000
Cons ci ratio: 6.920956e-03	ci left: 1.446050e-01	ci right 1.456098e-01	k: 274252	n:1890000
KS ci ratio: 3.042376e-01	ci left: 7.448930e-05	ci right 1.016849e-04	k: 165	n:1890000
MAPK1   1890000 perm   1889 sec   (1001 perm/sec)   p_kst 8.730159e-05   p_cons 1.451069e-01   p_joint 8.730159e-05

Joint ci ratio: 3.015250e-01	ci left: 7.555624e-05	ci right 1.028482e-04	k: 168	n:1900000
Cons ci ratio: 6.902354e-03	ci left: 1.446195e-01	ci right 1.456216e-01	k: 275728	n:1900000
KS ci ratio: 3.015250e-01	ci left: 7.555624e-05	ci right 1.028482e-04	k: 168	n:1900000
MAPK1   1900000 perm   1907 sec   (996 perm/sec)   p_kst 8.842105e-05   p_cons 1.451200e-01   p_joint 8.842105e-05

Joint ci ratio: 3.006368e-01	ci left: 7.564467e-05	ci right 1.028728e-04	k: 169	n:1910000
Cons ci ratio: 6.884032e-03	ci left: 1.446290e-01	ci right 1.456286e-01	k: 277195	n:1910000
KS ci ratio: 3.006368e-01	ci left: 7.564467e-05	ci right 1.028728e-04	k: 169	n:1910000
MAPK1   1910000 perm   1926 sec   (992 perm/sec)   p_kst 8.848168e-05   p_cons 1.451283e-01   p_joint 8.848168e-05

Joint ci ratio: 3.006369e-01	ci left: 7.525068e-05	ci right 1.023370e-04	k: 169	n:1920000
Cons ci ratio: 6.865394e-03	ci left: 1.446551e-01	ci right 1.456522e-01	k: 278694	n:1920000
KS ci ratio: 3.006369e-01	ci left: 7.525068e-05	ci right 1.023370e-04	k: 169	n:1920000
MAPK1   1920000 perm   1944 sec   (988 perm/sec)   p_kst 8.802083e-05   p_cons 1.451531e-01   p_joint 8.802083e-05

Joint ci ratio: 2.997565e-01	ci left: 7.533990e-05	ci right 1.023638e-04	k: 170	n:1930000
Cons ci ratio: 6.847964e-03	ci left: 1.446427e-01	ci right 1.456371e-01	k: 280119	n:1930000
KS ci ratio: 2.997565e-01	ci left: 7.533990e-05	ci right 1.023638e-04	k: 170	n:1930000
MAPK1   1930000 perm   1962 sec   (984 perm/sec)   p_kst 8.808290e-05   p_cons 1.451394e-01   p_joint 8.808290e-05

Joint ci ratio: 2.971610e-01	ci left: 7.638218e-05	ci right 1.034979e-04	k: 173	n:1940000
Cons ci ratio: 6.829858e-03	ci left: 1.446597e-01	ci right 1.456516e-01	k: 281601	n:1940000
KS ci ratio: 2.971610e-01	ci left: 7.638218e-05	ci right 1.034979e-04	k: 173	n:1940000
MAPK1   1940000 perm   1980 sec   (980 perm/sec)   p_kst 8.917526e-05   p_cons 1.451552e-01   p_joint 8.917526e-05

Joint ci ratio: 2.963108e-01	ci left: 7.646513e-05	ci right 1.035181e-04	k: 174	n:1950000
Cons ci ratio: 6.812260e-03	ci left: 1.446633e-01	ci right 1.456526e-01	k: 283057	n:1950000
KS ci ratio: 2.963108e-01	ci left: 7.646513e-05	ci right 1.035181e-04	k: 174	n:1950000
MAPK1   1950000 perm   1998 sec   (976 perm/sec)   p_kst 8.923077e-05   p_cons 1.451574e-01   p_joint 8.923077e-05

Joint ci ratio: 2.963108e-01	ci left: 7.607500e-05	ci right 1.029899e-04	k: 174	n:1960000
Cons ci ratio: 6.794938e-03	ci left: 1.446617e-01	ci right 1.456485e-01	k: 284503	n:1960000
KS ci ratio: 2.963108e-01	ci left: 7.607500e-05	ci right 1.029899e-04	k: 174	n:1960000
MAPK1   1960000 perm   2017 sec   (972 perm/sec)   p_kst 8.877551e-05   p_cons 1.451546e-01   p_joint 8.877551e-05

Joint ci ratio: 2.954678e-01	ci left: 7.615877e-05	ci right 1.030123e-04	k: 175	n:1970000
Cons ci ratio: 6.777164e-03	ci left: 1.446814e-01	ci right 1.456658e-01	k: 285991	n:1970000
KS ci ratio: 2.954678e-01	ci left: 7.615877e-05	ci right 1.030123e-04	k: 175	n:1970000
MAPK1   1970000 perm   2036 sec   (968 perm/sec)   p_kst 8.883249e-05   p_cons 1.451731e-01   p_joint 8.883249e-05

Joint ci ratio: 2.954679e-01	ci left: 7.577413e-05	ci right 1.024920e-04	k: 175	n:1980000
Cons ci ratio: 6.758925e-03	ci left: 1.447232e-01	ci right 1.457051e-01	k: 287523	n:1980000
KS ci ratio: 2.954679e-01	ci left: 7.577413e-05	ci right 1.024920e-04	k: 175	n:1980000
MAPK1   1980000 perm   2054 sec   (964 perm/sec)   p_kst 8.838384e-05   p_cons 1.452136e-01   p_joint 8.838384e-05

Joint ci ratio: 2.946321e-01	ci left: 7.585868e-05	ci right 1.025166e-04	k: 176	n:1990000
Cons ci ratio: 6.741445e-03	ci left: 1.447419e-01	ci right 1.457214e-01	k: 289010	n:1990000
KS ci ratio: 2.946321e-01	ci left: 7.585868e-05	ci right 1.025166e-04	k: 176	n:1990000
MAPK1   1990000 perm   2073 sec   (960 perm/sec)   p_kst 8.844221e-05   p_cons 1.452312e-01   p_joint 8.844221e-05

Joint ci ratio: 2.913580e-01	ci left: 7.733242e-05	ci right 1.041506e-04	k: 180	n:2000000
Cons ci ratio: 6.724426e-03	ci left: 1.447485e-01	ci right 1.457256e-01	k: 290473	n:2000000
KS ci ratio: 2.913580e-01	ci left: 7.733242e-05	ci right 1.041506e-04	k: 180	n:2000000
MAPK1   2000000 perm   2092 sec   (956 perm/sec)   p_kst 9.000000e-05   p_cons 1.452365e-01   p_joint 9.000000e-05

Joint ci ratio: 2.905565e-01	ci left: 7.740889e-05	ci right 1.041661e-04	k: 181	n:2010000
Cons ci ratio: 6.707898e-03	ci left: 1.447415e-01	ci right 1.457162e-01	k: 291909	n:2010000
KS ci ratio: 2.905565e-01	ci left: 7.740889e-05	ci right 1.041661e-04	k: 181	n:2010000
MAPK1   2010000 perm   2111 sec   (952 perm/sec)   p_kst 9.004975e-05   p_cons 1.452284e-01   p_joint 9.004975e-05

Joint ci ratio: 2.905566e-01	ci left: 7.702568e-05	ci right 1.036505e-04	k: 181	n:2020000
Cons ci ratio: 6.691104e-03	ci left: 1.447490e-01	ci right 1.457213e-01	k: 293374	n:2020000
KS ci ratio: 2.905566e-01	ci left: 7.702568e-05	ci right 1.036505e-04	k: 181	n:2020000
MAPK1   2020000 perm   2130 sec   (948 perm/sec)   p_kst 8.960396e-05   p_cons 1.452347e-01   p_joint 8.960396e-05

Joint ci ratio: 2.897616e-01	ci left: 7.710300e-05	ci right 1.036682e-04	k: 182	n:2030000
Cons ci ratio: 6.674369e-03	ci left: 1.447589e-01	ci right 1.457288e-01	k: 294844	n:2030000
KS ci ratio: 2.897616e-01	ci left: 7.710300e-05	ci right 1.036682e-04	k: 182	n:2030000
MAPK1   2030000 perm   2149 sec   (944 perm/sec)   p_kst 8.965517e-05   p_cons 1.452433e-01   p_joint 8.965517e-05

Joint ci ratio: 2.897617e-01	ci left: 7.672504e-05	ci right 1.031601e-04	k: 182	n:2040000
Cons ci ratio: 6.658443e-03	ci left: 1.447432e-01	ci right 1.457107e-01	k: 296262	n:2040000
KS ci ratio: 2.897617e-01	ci left: 7.672504e-05	ci right 1.031601e-04	k: 182	n:2040000
MAPK1   2040000 perm   2168 sec   (941 perm/sec)   p_kst 8.921569e-05   p_cons 1.452265e-01   p_joint 8.921569e-05

Joint ci ratio: 2.897617e-01	ci left: 7.635077e-05	ci right 1.026568e-04	k: 182	n:2050000
Cons ci ratio: 6.642552e-03	ci left: 1.447307e-01	ci right 1.456957e-01	k: 297686	n:2050000
KS ci ratio: 2.897617e-01	ci left: 7.635077e-05	ci right 1.026568e-04	k: 182	n:2050000
MAPK1   2050000 perm   2187 sec   (937 perm/sec)   p_kst 8.878049e-05   p_cons 1.452127e-01   p_joint 8.878049e-05

Joint ci ratio: 2.889733e-01	ci left: 7.643035e-05	ci right 1.026791e-04	k: 183	n:2060000
Cons ci ratio: 6.626399e-03	ci left: 1.447323e-01	ci right 1.456950e-01	k: 299139	n:2060000
KS ci ratio: 2.889733e-01	ci left: 7.643035e-05	ci right 1.026791e-04	k: 183	n:2060000
MAPK1   2060000 perm   2207 sec   (933 perm/sec)   p_kst 8.883495e-05   p_cons 1.452131e-01   p_joint 8.883495e-05

Joint ci ratio: 2.881912e-01	ci left: 7.650925e-05	ci right 1.027010e-04	k: 184	n:2070000
Cons ci ratio: 6.610530e-03	ci left: 1.447276e-01	ci right 1.456879e-01	k: 300579	n:2070000
KS ci ratio: 2.881912e-01	ci left: 7.650925e-05	ci right 1.027010e-04	k: 184	n:2070000
MAPK1   2070000 perm   2226 sec   (930 perm/sec)   p_kst 8.888889e-05   p_cons 1.452072e-01   p_joint 8.888889e-05

Joint ci ratio: 2.881912e-01	ci left: 7.614141e-05	ci right 1.022073e-04	k: 184	n:2080000
Cons ci ratio: 6.595285e-03	ci left: 1.447037e-01	ci right 1.456617e-01	k: 301979	n:2080000
KS ci ratio: 2.881912e-01	ci left: 7.614141e-05	ci right 1.022073e-04	k: 184	n:2080000
MAPK1   2080000 perm   2246 sec   (926 perm/sec)   p_kst 8.846154e-05   p_cons 1.451822e-01   p_joint 8.846154e-05

Joint ci ratio: 2.881913e-01	ci left: 7.577710e-05	ci right 1.017182e-04	k: 184	n:2090000
Cons ci ratio: 6.579853e-03	ci left: 1.446911e-01	ci right 1.456467e-01	k: 303402	n:2090000
KS ci ratio: 2.881913e-01	ci left: 7.577710e-05	ci right 1.017182e-04	k: 184	n:2090000
MAPK1   2090000 perm   2266 sec   (922 perm/sec)   p_kst 8.803828e-05   p_cons 1.451684e-01   p_joint 8.803828e-05

Joint ci ratio: 2.874155e-01	ci left: 7.585808e-05	ci right 1.017443e-04	k: 185	n:2100000
Cons ci ratio: 6.564845e-03	ci left: 1.446667e-01	ci right 1.456200e-01	k: 304800	n:2100000
KS ci ratio: 2.874155e-01	ci left: 7.585808e-05	ci right 1.017443e-04	k: 185	n:2100000
MAPK1   2100000 perm   2286 sec   (919 perm/sec)   p_kst 8.809524e-05   p_cons 1.451429e-01   p_joint 8.809524e-05

Joint ci ratio: 2.866460e-01	ci left: 7.593838e-05	ci right 1.017701e-04	k: 186	n:2110000
Cons ci ratio: 6.549225e-03	ci left: 1.446695e-01	ci right 1.456206e-01	k: 306255	n:2110000
KS ci ratio: 2.866460e-01	ci left: 7.593838e-05	ci right 1.017701e-04	k: 186	n:2110000
MAPK1   2110000 perm   2306 sec   (915 perm/sec)   p_kst 8.815166e-05   p_cons 1.451445e-01   p_joint 8.815166e-05

Joint ci ratio: 2.866461e-01	ci left: 7.558018e-05	ci right 1.012900e-04	k: 186	n:2120000
Cons ci ratio: 6.533617e-03	ci left: 1.446761e-01	ci right 1.456249e-01	k: 307718	n:2120000
KS ci ratio: 2.866461e-01	ci left: 7.558018e-05	ci right 1.012900e-04	k: 186	n:2120000
MAPK1   2120000 perm   2326 sec   (911 perm/sec)   p_kst 8.773585e-05   p_cons 1.451500e-01   p_joint 8.773585e-05

Joint ci ratio: 2.858827e-01	ci left: 7.566112e-05	ci right 1.013176e-04	k: 187	n:2130000
Cons ci ratio: 6.518367e-03	ci left: 1.446732e-01	ci right 1.456198e-01	k: 309161	n:2130000
KS ci ratio: 2.858827e-01	ci left: 7.566112e-05	ci right 1.013176e-04	k: 187	n:2130000
MAPK1   2130000 perm   2346 sec   (908 perm/sec)   p_kst 8.779343e-05   p_cons 1.451460e-01   p_joint 8.779343e-05

Joint ci ratio: 2.858828e-01	ci left: 7.530756e-05	ci right 1.008442e-04	k: 187	n:2140000
Cons ci ratio: 6.503162e-03	ci left: 1.446727e-01	ci right 1.456170e-01	k: 310609	n:2140000
KS ci ratio: 2.858828e-01	ci left: 7.530756e-05	ci right 1.008442e-04	k: 187	n:2140000
MAPK1   2140000 perm   2366 sec   (904 perm/sec)   p_kst 8.738318e-05   p_cons 1.451444e-01   p_joint 8.738318e-05

Joint ci ratio: 2.858828e-01	ci left: 7.495729e-05	ci right 1.003751e-04	k: 187	n:2150000
Cons ci ratio: 6.487685e-03	ci left: 1.446866e-01	ci right 1.456288e-01	k: 312088	n:2150000
KS ci ratio: 2.858828e-01	ci left: 7.495729e-05	ci right 1.003751e-04	k: 187	n:2150000
MAPK1   2150000 perm   2387 sec   (901 perm/sec)   p_kst 8.697674e-05   p_cons 1.451572e-01   p_joint 8.697674e-05

Joint ci ratio: 2.851255e-01	ci left: 7.504008e-05	ci right 1.004064e-04	k: 188	n:2160000
Cons ci ratio: 6.472814e-03	ci left: 1.446814e-01	ci right 1.456214e-01	k: 313526	n:2160000
KS ci ratio: 2.851255e-01	ci left: 7.504008e-05	ci right 1.004064e-04	k: 188	n:2160000
MAPK1   2160000 perm   2408 sec   (897 perm/sec)   p_kst 8.703704e-05   p_cons 1.451509e-01   p_joint 8.703704e-05

Joint ci ratio: 2.836287e-01	ci left: 7.555021e-05	ci right 1.009309e-04	k: 190	n:2170000
Cons ci ratio: 6.456690e-03	ci left: 1.447283e-01	ci right 1.456662e-01	k: 315077	n:2170000
KS ci ratio: 2.836287e-01	ci left: 7.555021e-05	ci right 1.009309e-04	k: 190	n:2170000
MAPK1   2170000 perm   2429 sec   (893 perm/sec)   p_kst 8.755760e-05   p_cons 1.451968e-01   p_joint 8.755760e-05

Joint ci ratio: 2.836288e-01	ci left: 7.520365e-05	ci right 1.004680e-04	k: 190	n:2180000
Cons ci ratio: 6.441709e-03	ci left: 1.447353e-01	ci right 1.456711e-01	k: 316542	n:2180000
KS ci ratio: 2.836288e-01	ci left: 7.520365e-05	ci right 1.004680e-04	k: 190	n:2180000
MAPK1   2180000 perm   2449 sec   (890 perm/sec)   p_kst 8.715596e-05   p_cons 1.452028e-01   p_joint 8.715596e-05

Joint ci ratio: 2.828892e-01	ci left: 7.528444e-05	ci right 1.004982e-04	k: 191	n:2190000
Cons ci ratio: 6.426962e-03	ci left: 1.447373e-01	ci right 1.456710e-01	k: 317996	n:2190000
KS ci ratio: 2.828892e-01	ci left: 7.528444e-05	ci right 1.004982e-04	k: 191	n:2190000
MAPK1   2190000 perm   2470 sec   (887 perm/sec)   p_kst 8.721461e-05   p_cons 1.452037e-01   p_joint 8.721461e-05

Joint ci ratio: 2.828892e-01	ci left: 7.494224e-05	ci right 1.000414e-04	k: 191	n:2200000
Cons ci ratio: 6.412855e-03	ci left: 1.447184e-01	ci right 1.456498e-01	k: 319404	n:2200000
KS ci ratio: 2.828892e-01	ci left: 7.494224e-05	ci right 1.000414e-04	k: 191	n:2200000
MAPK1   2200000 perm   2491 sec   (883 perm/sec)   p_kst 8.681818e-05   p_cons 1.451836e-01   p_joint 8.681818e-05

Joint ci ratio: 2.828893e-01	ci left: 7.460313e-05	ci right 9.958869e-05	k: 191	n:2210000
Cons ci ratio: 6.397815e-03	ci left: 1.447394e-01	ci right 1.456688e-01	k: 320900	n:2210000
KS ci ratio: 2.828893e-01	ci left: 7.460313e-05	ci right 9.958869e-05	k: 191	n:2210000
MAPK1   2210000 perm   2512 sec   (880 perm/sec)   p_kst 8.642534e-05   p_cons 1.452036e-01   p_joint 8.642534e-05

Joint ci ratio: 2.821554e-01	ci left: 7.468562e-05	ci right 9.962237e-05	k: 192	n:2220000
Cons ci ratio: 6.383170e-03	ci left: 1.447490e-01	ci right 1.456763e-01	k: 322371	n:2220000
KS ci ratio: 2.821554e-01	ci left: 7.468562e-05	ci right 9.962237e-05	k: 192	n:2220000
MAPK1   2220000 perm   2534 sec   (876 perm/sec)   p_kst 8.648649e-05   p_cons 1.452122e-01   p_joint 8.648649e-05

Joint ci ratio: 2.814273e-01	ci left: 7.476745e-05	ci right 9.965567e-05	k: 193	n:2230000
Cons ci ratio: 6.368797e-03	ci left: 1.447517e-01	ci right 1.456770e-01	k: 323827	n:2230000
KS ci ratio: 2.814273e-01	ci left: 7.476745e-05	ci right 9.965567e-05	k: 193	n:2230000
MAPK1   2230000 perm   2555 sec   (873 perm/sec)   p_kst 8.654709e-05   p_cons 1.452139e-01   p_joint 8.654709e-05

Joint ci ratio: 2.799877e-01	ci left: 7.526368e-05	ci right 1.001663e-04	k: 195	n:2240000
Cons ci ratio: 6.354807e-03	ci left: 1.447433e-01	ci right 1.456665e-01	k: 325258	n:2240000
KS ci ratio: 2.799877e-01	ci left: 7.526368e-05	ci right 1.001663e-04	k: 195	n:2240000
MAPK1   2240000 perm   2576 sec   (870 perm/sec)   p_kst 8.705357e-05   p_cons 1.452045e-01   p_joint 8.705357e-05

Joint ci ratio: 2.785699e-01	ci left: 7.575583e-05	ci right 1.006721e-04	k: 197	n:2250000
Cons ci ratio: 6.340658e-03	ci left: 1.447448e-01	ci right 1.456659e-01	k: 326711	n:2250000
KS ci ratio: 2.785699e-01	ci left: 7.575583e-05	ci right 1.006721e-04	k: 197	n:2250000
MAPK1   2250000 perm   2598 sec   (866 perm/sec)   p_kst 8.755556e-05   p_cons 1.452049e-01   p_joint 8.755556e-05

Joint ci ratio: 2.785700e-01	ci left: 7.542062e-05	ci right 1.002267e-04	k: 197	n:2260000
Cons ci ratio: 6.326740e-03	ci left: 1.447409e-01	ci right 1.456600e-01	k: 328152	n:2260000
KS ci ratio: 2.785700e-01	ci left: 7.542062e-05	ci right 1.002267e-04	k: 197	n:2260000
MAPK1   2260000 perm   2619 sec   (863 perm/sec)   p_kst 8.716814e-05   p_cons 1.452000e-01   p_joint 8.716814e-05

Joint ci ratio: 2.785701e-01	ci left: 7.508837e-05	ci right 9.978514e-05	k: 197	n:2270000
Cons ci ratio: 6.312834e-03	ci left: 1.447402e-01	ci right 1.456572e-01	k: 329600	n:2270000
KS ci ratio: 2.785701e-01	ci left: 7.508837e-05	ci right 9.978514e-05	k: 197	n:2270000
MAPK1   2270000 perm   2641 sec   (860 perm/sec)   p_kst 8.678414e-05   p_cons 1.451982e-01   p_joint 8.678414e-05

Joint ci ratio: 2.785701e-01	ci left: 7.475903e-05	ci right 9.934749e-05	k: 197	n:2280000
Cons ci ratio: 6.299008e-03	ci left: 1.447399e-01	ci right 1.456549e-01	k: 331049	n:2280000
KS ci ratio: 2.785701e-01	ci left: 7.475903e-05	ci right 9.934749e-05	k: 197	n:2280000
MAPK1   2280000 perm   2663 sec   (856 perm/sec)   p_kst 8.640351e-05   p_cons 1.451969e-01   p_joint 8.640351e-05

Joint ci ratio: 2.771737e-01	ci left: 7.524509e-05	ci right 9.984771e-05	k: 199	n:2290000
Cons ci ratio: 6.284896e-03	ci left: 1.447544e-01	ci right 1.456675e-01	k: 332532	n:2290000
KS ci ratio: 2.771737e-01	ci left: 7.524509e-05	ci right 9.984771e-05	k: 199	n:2290000
MAPK1   2290000 perm   2684 sec   (853 perm/sec)   p_kst 8.689956e-05   p_cons 1.452105e-01   p_joint 8.689956e-05

Joint ci ratio: 2.764833e-01	ci left: 7.532254e-05	ci right 9.987848e-05	k: 200	n:2300000
Cons ci ratio: 6.271143e-03	ci left: 1.447584e-01	ci right 1.456695e-01	k: 333991	n:2300000
KS ci ratio: 2.764833e-01	ci left: 7.532254e-05	ci right 9.987848e-05	k: 200	n:2300000
MAPK1   2300000 perm   2706 sec   (850 perm/sec)   p_kst 8.695652e-05   p_cons 1.452135e-01   p_joint 8.695652e-05

Joint ci ratio: 2.764834e-01	ci left: 7.499647e-05	ci right 9.944611e-05	k: 200	n:2310000
Cons ci ratio: 6.257698e-03	ci left: 1.447537e-01	ci right 1.456628e-01	k: 335430	n:2310000
KS ci ratio: 2.764834e-01	ci left: 7.499647e-05	ci right 9.944611e-05	k: 200	n:2310000
MAPK1   2310000 perm   2728 sec   (847 perm/sec)   p_kst 8.658009e-05   p_cons 1.452078e-01   p_joint 8.658009e-05

Joint ci ratio: 2.757982e-01	ci left: 7.507440e-05	ci right 9.947826e-05	k: 201	n:2320000
Cons ci ratio: 6.244208e-03	ci left: 1.447542e-01	ci right 1.456613e-01	k: 336881	n:2320000
KS ci ratio: 2.757982e-01	ci left: 7.507440e-05	ci right 9.947826e-05	k: 201	n:2320000
MAPK1   2320000 perm   2750 sec   (844 perm/sec)   p_kst 8.663793e-05   p_cons 1.452073e-01   p_joint 8.663793e-05

Joint ci ratio: 2.751180e-01	ci left: 7.515174e-05	ci right 9.951007e-05	k: 202	n:2330000
Cons ci ratio: 6.230871e-03	ci left: 1.447522e-01	ci right 1.456573e-01	k: 338326	n:2330000
KS ci ratio: 2.751180e-01	ci left: 7.515174e-05	ci right 9.951007e-05	k: 202	n:2330000
MAPK1   2330000 perm   2772 sec   (841 perm/sec)   p_kst 8.669528e-05   p_cons 1.452043e-01   p_joint 8.669528e-05

Joint ci ratio: 2.751181e-01	ci left: 7.483058e-05	ci right 9.908482e-05	k: 202	n:2340000
Cons ci ratio: 6.217564e-03	ci left: 1.447522e-01	ci right 1.456555e-01	k: 339776	n:2340000
KS ci ratio: 2.751181e-01	ci left: 7.483058e-05	ci right 9.908482e-05	k: 202	n:2340000
MAPK1   2340000 perm   2794 sec   (838 perm/sec)   p_kst 8.632479e-05   p_cons 1.452034e-01   p_joint 8.632479e-05

Joint ci ratio: 2.737727e-01	ci left: 7.530466e-05	ci right 9.957266e-05	k: 204	n:2350000
Cons ci ratio: 6.204567e-03	ci left: 1.447434e-01	ci right 1.456447e-01	k: 341205	n:2350000
KS ci ratio: 2.737727e-01	ci left: 7.530466e-05	ci right 9.957266e-05	k: 204	n:2350000
MAPK1   2350000 perm   2816 sec   (835 perm/sec)   p_kst 8.680851e-05   p_cons 1.451936e-01   p_joint 8.680851e-05

Joint ci ratio: 2.731074e-01	ci left: 7.538025e-05	ci right 9.960345e-05	k: 205	n:2360000
Cons ci ratio: 6.192125e-03	ci left: 1.447156e-01	ci right 1.456149e-01	k: 342589	n:2360000
KS ci ratio: 2.731074e-01	ci left: 7.538025e-05	ci right 9.960345e-05	k: 205	n:2360000
MAPK1   2360000 perm   2838 sec   (832 perm/sec)   p_kst 8.686441e-05   p_cons 1.451648e-01   p_joint 8.686441e-05

Joint ci ratio: 2.724469e-01	ci left: 7.545528e-05	ci right 9.963390e-05	k: 206	n:2370000
Cons ci ratio: 6.178551e-03	ci left: 1.447365e-01	ci right 1.456340e-01	k: 344088	n:2370000
KS ci ratio: 2.724469e-01	ci left: 7.545528e-05	ci right 9.963390e-05	k: 206	n:2370000
MAPK1   2370000 perm   2860 sec   (829 perm/sec)   p_kst 8.691983e-05   p_cons 1.451848e-01   p_joint 8.691983e-05

Joint ci ratio: 2.724469e-01	ci left: 7.513823e-05	ci right 9.921528e-05	k: 206	n:2380000
Cons ci ratio: 6.165722e-03	ci left: 1.447308e-01	ci right 1.456263e-01	k: 345524	n:2380000
KS ci ratio: 2.724469e-01	ci left: 7.513823e-05	ci right 9.921528e-05	k: 206	n:2380000
MAPK1   2380000 perm   2883 sec   (826 perm/sec)   p_kst 8.655462e-05   p_cons 1.451782e-01   p_joint 8.655462e-05

Joint ci ratio: 2.724470e-01	ci left: 7.482385e-05	ci right 9.880015e-05	k: 206	n:2390000
Cons ci ratio: 6.152465e-03	ci left: 1.447456e-01	ci right 1.456393e-01	k: 347009	n:2390000
KS ci ratio: 2.724470e-01	ci left: 7.482385e-05	ci right 9.880015e-05	k: 206	n:2390000
MAPK1   2390000 perm   2905 sec   (823 perm/sec)   p_kst 8.619247e-05   p_cons 1.451921e-01   p_joint 8.619247e-05

Joint ci ratio: 2.717913e-01	ci left: 7.490032e-05	ci right 9.883351e-05	k: 207	n:2400000
Cons ci ratio: 6.139902e-03	ci left: 1.447358e-01	ci right 1.456276e-01	k: 348435	n:2400000
KS ci ratio: 2.717913e-01	ci left: 7.490032e-05	ci right 9.883351e-05	k: 207	n:2400000
MAPK1   2400000 perm   2927 sec   (820 perm/sec)   p_kst 8.625000e-05   p_cons 1.451813e-01   p_joint 8.625000e-05

Joint ci ratio: 2.717913e-01	ci left: 7.458953e-05	ci right 9.842341e-05	k: 207	n:2410000
Cons ci ratio: 6.126769e-03	ci left: 1.447521e-01	ci right 1.456421e-01	k: 349924	n:2410000
KS ci ratio: 2.717913e-01	ci left: 7.458953e-05	ci right 9.842341e-05	k: 207	n:2410000
MAPK1   2410000 perm   2950 sec   (817 perm/sec)   p_kst 8.589212e-05   p_cons 1.451967e-01   p_joint 8.589212e-05

Joint ci ratio: 2.711403e-01	ci left: 7.466641e-05	ci right 9.845798e-05	k: 208	n:2420000
Cons ci ratio: 6.113904e-03	ci left: 1.447609e-01	ci right 1.456491e-01	k: 351395	n:2420000
KS ci ratio: 2.711403e-01	ci left: 7.466641e-05	ci right 9.845798e-05	k: 208	n:2420000
MAPK1   2420000 perm   2972 sec   (814 perm/sec)   p_kst 8.595041e-05   p_cons 1.452045e-01   p_joint 8.595041e-05

Joint ci ratio: 2.698522e-01	ci left: 7.512638e-05	ci right 9.893153e-05	k: 210	n:2430000
Cons ci ratio: 6.101847e-03	ci left: 1.447400e-01	ci right 1.456263e-01	k: 352794	n:2430000
KS ci ratio: 2.698522e-01	ci left: 7.512638e-05	ci right 9.893153e-05	k: 210	n:2430000
MAPK1   2430000 perm   2995 sec   (811 perm/sec)   p_kst 8.641975e-05   p_cons 1.451827e-01   p_joint 8.641975e-05

Joint ci ratio: 2.692150e-01	ci left: 7.520063e-05	ci right 9.896354e-05	k: 211	n:2440000
Cons ci ratio: 6.089862e-03	ci left: 1.447193e-01	ci right 1.456037e-01	k: 354193	n:2440000
KS ci ratio: 2.692150e-01	ci left: 7.520063e-05	ci right 9.896354e-05	k: 211	n:2440000
MAPK1   2440000 perm   3018 sec   (809 perm/sec)   p_kst 8.647541e-05   p_cons 1.451611e-01   p_joint 8.647541e-05

Joint ci ratio: 2.692150e-01	ci left: 7.489368e-05	ci right 9.855961e-05	k: 211	n:2450000
Cons ci ratio: 6.077307e-03	ci left: 1.447248e-01	ci right 1.456074e-01	k: 355656	n:2450000
KS ci ratio: 2.692150e-01	ci left: 7.489368e-05	ci right 9.855961e-05	k: 211	n:2450000
MAPK1   2450000 perm   3040 sec   (806 perm/sec)   p_kst 8.612245e-05   p_cons 1.451657e-01   p_joint 8.612245e-05

Joint ci ratio: 2.685823e-01	ci left: 7.496834e-05	ci right 9.859280e-05	k: 212	n:2460000
Cons ci ratio: 6.065158e-03	ci left: 1.447169e-01	ci right 1.455977e-01	k: 357086	n:2460000
KS ci ratio: 2.685823e-01	ci left: 7.496834e-05	ci right 9.859280e-05	k: 212	n:2460000
MAPK1   2460000 perm   3063 sec   (803 perm/sec)   p_kst 8.617886e-05   p_cons 1.451569e-01   p_joint 8.617886e-05

Joint ci ratio: 2.679540e-01	ci left: 7.504246e-05	ci right 9.862566e-05	k: 213	n:2470000
Cons ci ratio: 6.052893e-03	ci left: 1.447168e-01	ci right 1.455958e-01	k: 358535	n:2470000
KS ci ratio: 2.679540e-01	ci left: 7.504246e-05	ci right 9.862566e-05	k: 213	n:2470000
MAPK1   2470000 perm   3087 sec   (800 perm/sec)   p_kst 8.623482e-05   p_cons 1.451559e-01   p_joint 8.623482e-05

Joint ci ratio: 2.673301e-01	ci left: 7.511604e-05	ci right 9.865819e-05	k: 214	n:2480000
Cons ci ratio: 6.041252e-03	ci left: 1.446941e-01	ci right 1.455713e-01	k: 359928	n:2480000
KS ci ratio: 2.673301e-01	ci left: 7.511604e-05	ci right 9.865819e-05	k: 214	n:2480000
MAPK1   2480000 perm   3109 sec   (798 perm/sec)   p_kst 8.629032e-05   p_cons 1.451323e-01   p_joint 8.629032e-05

Joint ci ratio: 2.667106e-01	ci left: 7.518909e-05	ci right 9.869040e-05	k: 215	n:2490000
Cons ci ratio: 6.028917e-03	ci left: 1.447029e-01	ci right 1.455783e-01	k: 361399	n:2490000
KS ci ratio: 2.667106e-01	ci left: 7.518909e-05	ci right 9.869040e-05	k: 215	n:2490000
MAPK1   2490000 perm   3133 sec   (795 perm/sec)   p_kst 8.634538e-05   p_cons 1.451402e-01   p_joint 8.634538e-05

Joint ci ratio: 2.667106e-01	ci left: 7.488834e-05	ci right 9.829564e-05	k: 215	n:2500000
Cons ci ratio: 6.016463e-03	ci left: 1.447196e-01	ci right 1.455933e-01	k: 362890	n:2500000
KS ci ratio: 2.667106e-01	ci left: 7.488834e-05	ci right 9.829564e-05	k: 215	n:2500000
MAPK1   2500000 perm   3156 sec   (792 perm/sec)   p_kst 8.600000e-05   p_cons 1.451560e-01   p_joint 8.600000e-05

Joint ci ratio: 2.660954e-01	ci left: 7.496178e-05	ci right 9.832898e-05	k: 216	n:2510000
Cons ci ratio: 6.004423e-03	ci left: 1.447222e-01	ci right 1.455942e-01	k: 364346	n:2510000
KS ci ratio: 2.660954e-01	ci left: 7.496178e-05	ci right 9.832898e-05	k: 216	n:2510000
MAPK1   2510000 perm   3179 sec   (790 perm/sec)   p_kst 8.605578e-05   p_cons 1.451578e-01   p_joint 8.605578e-05

Joint ci ratio: 2.660954e-01	ci left: 7.466431e-05	ci right 9.793879e-05	k: 216	n:2520000
Cons ci ratio: 5.992005e-03	ci left: 1.447434e-01	ci right 1.456137e-01	k: 365849	n:2520000
KS ci ratio: 2.660954e-01	ci left: 7.466431e-05	ci right 9.793879e-05	k: 216	n:2520000
MAPK1   2520000 perm   3203 sec   (787 perm/sec)   p_kst 8.571429e-05   p_cons 1.451782e-01   p_joint 8.571429e-05

Joint ci ratio: 2.654844e-01	ci left: 7.473812e-05	ci right 9.797321e-05	k: 217	n:2530000
Cons ci ratio: 5.980931e-03	ci left: 1.447120e-01	ci right 1.455805e-01	k: 367219	n:2530000
KS ci ratio: 2.654844e-01	ci left: 7.473812e-05	ci right 9.797321e-05	k: 217	n:2530000
MAPK1   2530000 perm   3226 sec   (784 perm/sec)   p_kst 8.577075e-05   p_cons 1.451458e-01   p_joint 8.577075e-05

Joint ci ratio: 2.648776e-01	ci left: 7.481140e-05	ci right 9.800730e-05	k: 218	n:2540000
Cons ci ratio: 5.968733e-03	ci left: 1.447300e-01	ci right 1.455968e-01	k: 368714	n:2540000
KS ci ratio: 2.648776e-01	ci left: 7.481140e-05	ci right 9.800730e-05	k: 218	n:2540000
MAPK1   2540000 perm   3250 sec   (781 perm/sec)   p_kst 8.582677e-05   p_cons 1.451630e-01   p_joint 8.582677e-05

Joint ci ratio: 2.648776e-01	ci left: 7.451802e-05	ci right 9.762296e-05	k: 218	n:2550000
Cons ci ratio: 5.956732e-03	ci left: 1.447427e-01	ci right 1.456079e-01	k: 370196	n:2550000
KS ci ratio: 2.648776e-01	ci left: 7.451802e-05	ci right 9.762296e-05	k: 218	n:2550000
MAPK1   2550000 perm   3274 sec   (779 perm/sec)   p_kst 8.549020e-05   p_cons 1.451749e-01   p_joint 8.549020e-05

Joint ci ratio: 2.642749e-01	ci left: 7.459166e-05	ci right 9.765809e-05	k: 219	n:2560000
Cons ci ratio: 5.945524e-03	ci left: 1.447253e-01	ci right 1.455887e-01	k: 371601	n:2560000
KS ci ratio: 2.642749e-01	ci left: 7.459166e-05	ci right 9.765809e-05	k: 219	n:2560000
MAPK1   2560000 perm   3299 sec   (776 perm/sec)   p_kst 8.554687e-05   p_cons 1.451566e-01   p_joint 8.554687e-05

Joint ci ratio: 2.636763e-01	ci left: 7.466478e-05	ci right 9.769289e-05	k: 220	n:2570000
Cons ci ratio: 5.933486e-03	ci left: 1.447454e-01	ci right 1.456072e-01	k: 373102	n:2570000
KS ci ratio: 2.636763e-01	ci left: 7.466478e-05	ci right 9.769289e-05	k: 220	n:2570000
MAPK1   2570000 perm   3323 sec   (773 perm/sec)   p_kst 8.560311e-05   p_cons 1.451759e-01   p_joint 8.560311e-05

Joint ci ratio: 2.630818e-01	ci left: 7.473739e-05	ci right 9.772736e-05	k: 221	n:2580000
Cons ci ratio: 5.921853e-03	ci left: 1.447513e-01	ci right 1.456115e-01	k: 374567	n:2580000
KS ci ratio: 2.630818e-01	ci left: 7.473739e-05	ci right 9.772736e-05	k: 221	n:2580000
MAPK1   2580000 perm   3347 sec   (771 perm/sec)   p_kst 8.565891e-05   p_cons 1.451810e-01   p_joint 8.565891e-05

Joint ci ratio: 2.630818e-01	ci left: 7.444882e-05	ci right 9.735004e-05	k: 221	n:2590000
Cons ci ratio: 5.910767e-03	ci left: 1.447372e-01	ci right 1.455956e-01	k: 375980	n:2590000
KS ci ratio: 2.630818e-01	ci left: 7.444882e-05	ci right 9.735004e-05	k: 221	n:2590000
MAPK1   2590000 perm   3371 sec   (768 perm/sec)   p_kst 8.532819e-05   p_cons 1.451660e-01   p_joint 8.532819e-05

Joint ci ratio: 2.630819e-01	ci left: 7.416248e-05	ci right 9.697562e-05	k: 221	n:2600000
Cons ci ratio: 5.899533e-03	ci left: 1.447320e-01	ci right 1.455888e-01	k: 377416	n:2600000
KS ci ratio: 2.630819e-01	ci left: 7.416248e-05	ci right 9.697562e-05	k: 221	n:2600000
MAPK1   2600000 perm   3394 sec   (766 perm/sec)   p_kst 8.500000e-05   p_cons 1.451600e-01   p_joint 8.500000e-05

Joint ci ratio: 2.624914e-01	ci left: 7.423624e-05	ci right 9.701239e-05	k: 222	n:2610000
Cons ci ratio: 5.888735e-03	ci left: 1.447112e-01	ci right 1.455662e-01	k: 378811	n:2610000
KS ci ratio: 2.624914e-01	ci left: 7.423624e-05	ci right 9.701239e-05	k: 222	n:2610000
MAPK1   2610000 perm   3418 sec   (763 perm/sec)   p_kst 8.505747e-05   p_cons 1.451383e-01   p_joint 8.505747e-05

Joint ci ratio: 2.613221e-01	ci left: 7.466614e-05	ci right 9.745547e-05	k: 224	n:2620000
Cons ci ratio: 5.877806e-03	ci left: 1.446985e-01	ci right 1.455519e-01	k: 380227	n:2620000
KS ci ratio: 2.613221e-01	ci left: 7.466614e-05	ci right 9.745547e-05	k: 224	n:2620000
MAPK1   2620000 perm   3444 sec   (761 perm/sec)   p_kst 8.549618e-05   p_cons 1.451248e-01   p_joint 8.549618e-05

Joint ci ratio: 2.607433e-01	ci left: 7.473759e-05	ci right 9.748997e-05	k: 225	n:2630000
Cons ci ratio: 5.866623e-03	ci left: 1.446992e-01	ci right 1.455510e-01	k: 381678	n:2630000
KS ci ratio: 2.607433e-01	ci left: 7.473759e-05	ci right 9.748997e-05	k: 225	n:2630000
MAPK1   2630000 perm   3469 sec   (758 perm/sec)   p_kst 8.555133e-05   p_cons 1.451247e-01   p_joint 8.555133e-05

Joint ci ratio: 2.595971e-01	ci left: 7.516267e-05	ci right 9.792755e-05	k: 227	n:2640000
Cons ci ratio: 5.855673e-03	ci left: 1.446928e-01	ci right 1.455429e-01	k: 383110	n:2640000
KS ci ratio: 2.595971e-01	ci left: 7.516267e-05	ci right 9.792755e-05	k: 227	n:2640000
MAPK1   2640000 perm   3494 sec   (756 perm/sec)   p_kst 8.598485e-05   p_cons 1.451174e-01   p_joint 8.598485e-05

Joint ci ratio: 2.595971e-01	ci left: 7.487904e-05	ci right 9.755802e-05	k: 227	n:2650000
Cons ci ratio: 5.844812e-03	ci left: 1.446852e-01	ci right 1.455337e-01	k: 384539	n:2650000
KS ci ratio: 2.595971e-01	ci left: 7.487904e-05	ci right 9.755802e-05	k: 227	n:2650000
MAPK1   2650000 perm   3519 sec   (753 perm/sec)   p_kst 8.566038e-05   p_cons 1.451091e-01   p_joint 8.566038e-05

Joint ci ratio: 2.595972e-01	ci left: 7.459754e-05	ci right 9.719126e-05	k: 227	n:2660000
Cons ci ratio: 5.834222e-03	ci left: 1.446687e-01	ci right 1.455155e-01	k: 385944	n:2660000
KS ci ratio: 2.595972e-01	ci left: 7.459754e-05	ci right 9.719126e-05	k: 227	n:2660000
MAPK1   2660000 perm   3543 sec   (751 perm/sec)   p_kst 8.533835e-05   p_cons 1.450917e-01   p_joint 8.533835e-05

Joint ci ratio: 2.584660e-01	ci left: 7.501858e-05	ci right 9.762483e-05	k: 229	n:2670000
Cons ci ratio: 5.823136e-03	ci left: 1.446759e-01	ci right 1.455212e-01	k: 387412	n:2670000
KS ci ratio: 2.584660e-01	ci left: 7.501858e-05	ci right 9.762483e-05	k: 229	n:2670000
MAPK1   2670000 perm   3568 sec   (748 perm/sec)   p_kst 8.576779e-05   p_cons 1.450981e-01   p_joint 8.576779e-05

Joint ci ratio: 2.562472e-01	ci left: 7.613494e-05	ci right 9.884916e-05	k: 233	n:2680000
Cons ci ratio: 5.812166e-03	ci left: 1.446808e-01	ci right 1.455245e-01	k: 388874	n:2680000
KS ci ratio: 2.562472e-01	ci left: 7.613494e-05	ci right 9.884916e-05	k: 233	n:2680000
MAPK1   2680000 perm   3593 sec   (746 perm/sec)   p_kst 8.694030e-05   p_cons 1.451022e-01   p_joint 8.694030e-05

Joint ci ratio: 2.557014e-01	ci left: 7.619981e-05	ci right 9.887723e-05	k: 234	n:2690000
Cons ci ratio: 5.801848e-03	ci left: 1.446604e-01	ci right 1.455025e-01	k: 390268	n:2690000
KS ci ratio: 2.557014e-01	ci left: 7.619981e-05	ci right 9.887723e-05	k: 234	n:2690000
MAPK1   2690000 perm   3618 sec   (744 perm/sec)   p_kst 8.698885e-05   p_cons 1.450810e-01   p_joint 8.698885e-05

Joint ci ratio: 2.551591e-01	ci left: 7.626425e-05	ci right 9.890505e-05	k: 235	n:2700000
Cons ci ratio: 5.790591e-03	ci left: 1.446827e-01	ci right 1.455233e-01	k: 391777	n:2700000
KS ci ratio: 2.551591e-01	ci left: 7.626425e-05	ci right 9.890505e-05	k: 235	n:2700000
MAPK1   2700000 perm   3643 sec   (741 perm/sec)   p_kst 8.703704e-05   p_cons 1.451026e-01   p_joint 8.703704e-05

Joint ci ratio: 2.551591e-01	ci left: 7.598283e-05	ci right 9.854009e-05	k: 235	n:2710000
Cons ci ratio: 5.779717e-03	ci left: 1.446912e-01	ci right 1.455302e-01	k: 393249	n:2710000
KS ci ratio: 2.551591e-01	ci left: 7.598283e-05	ci right 9.854009e-05	k: 235	n:2710000
MAPK1   2710000 perm   3668 sec   (739 perm/sec)   p_kst 8.671587e-05   p_cons 1.451103e-01   p_joint 8.671587e-05

Joint ci ratio: 2.551591e-01	ci left: 7.570348e-05	ci right 9.817781e-05	k: 235	n:2720000
Cons ci ratio: 5.769118e-03	ci left: 1.446904e-01	ci right 1.455280e-01	k: 394696	n:2720000
KS ci ratio: 2.551591e-01	ci left: 7.570348e-05	ci right 9.817781e-05	k: 235	n:2720000
MAPK1   2720000 perm   3693 sec   (737 perm/sec)   p_kst 8.639706e-05   p_cons 1.451088e-01   p_joint 8.639706e-05

Joint ci ratio: 2.551592e-01	ci left: 7.542617e-05	ci right 9.781819e-05	k: 235	n:2730000
Cons ci ratio: 5.757999e-03	ci left: 1.447146e-01	ci right 1.455506e-01	k: 396211	n:2730000
KS ci ratio: 2.551592e-01	ci left: 7.542617e-05	ci right 9.781819e-05	k: 235	n:2730000
MAPK1   2730000 perm   3718 sec   (734 perm/sec)   p_kst 8.608059e-05   p_cons 1.451322e-01   p_joint 8.608059e-05

Joint ci ratio: 2.546203e-01	ci left: 7.549254e-05	ci right 9.784941e-05	k: 236	n:2740000
Cons ci ratio: 5.748026e-03	ci left: 1.446919e-01	ci right 1.455264e-01	k: 397598	n:2740000
KS ci ratio: 2.546203e-01	ci left: 7.549254e-05	ci right 9.784941e-05	k: 236	n:2740000
MAPK1   2740000 perm   3744 sec   (732 perm/sec)   p_kst 8.613139e-05   p_cons 1.451088e-01   p_joint 8.613139e-05

Joint ci ratio: 2.546203e-01	ci left: 7.521803e-05	ci right 9.749360e-05	k: 236	n:2750000
Cons ci ratio: 5.736868e-03	ci left: 1.447228e-01	ci right 1.455558e-01	k: 399132	n:2750000
KS ci ratio: 2.546203e-01	ci left: 7.521803e-05	ci right 9.749360e-05	k: 236	n:2750000
MAPK1   2750000 perm   3769 sec   (730 perm/sec)   p_kst 8.581818e-05   p_cons 1.451389e-01   p_joint 8.581818e-05

Joint ci ratio: 2.530239e-01	ci left: 7.596332e-05	ci right 9.829631e-05	k: 239	n:2760000
Cons ci ratio: 5.726503e-03	ci left: 1.447220e-01	ci right 1.455534e-01	k: 400579	n:2760000
KS ci ratio: 2.530239e-01	ci left: 7.596332e-05	ci right 9.829631e-05	k: 239	n:2760000
MAPK1   2760000 perm   3794 sec   (727 perm/sec)   p_kst 8.659420e-05   p_cons 1.451373e-01   p_joint 8.659420e-05

Joint ci ratio: 2.524984e-01	ci left: 7.602722e-05	ci right 9.832528e-05	k: 240	n:2770000
Cons ci ratio: 5.716235e-03	ci left: 1.447193e-01	ci right 1.455493e-01	k: 402021	n:2770000
KS ci ratio: 2.524984e-01	ci left: 7.602722e-05	ci right 9.832528e-05	k: 240	n:2770000
MAPK1   2770000 perm   3820 sec   (725 perm/sec)   p_kst 8.664260e-05   p_cons 1.451339e-01   p_joint 8.664260e-05

Joint ci ratio: 2.524984e-01	ci left: 7.575374e-05	ci right 9.797160e-05	k: 240	n:2780000
Cons ci ratio: 5.705641e-03	ci left: 1.447332e-01	ci right 1.455617e-01	k: 403509	n:2780000
KS ci ratio: 2.524984e-01	ci left: 7.575374e-05	ci right 9.797160e-05	k: 240	n:2780000
MAPK1   2780000 perm   3846 sec   (723 perm/sec)   p_kst 8.633094e-05   p_cons 1.451471e-01   p_joint 8.633094e-05

Joint ci ratio: 2.524984e-01	ci left: 7.548222e-05	ci right 9.762045e-05	k: 240	n:2790000
Cons ci ratio: 5.695263e-03	ci left: 1.447403e-01	ci right 1.455673e-01	k: 404978	n:2790000
KS ci ratio: 2.524984e-01	ci left: 7.548222e-05	ci right 9.762045e-05	k: 240	n:2790000
MAPK1   2790000 perm   3872 sec   (721 perm/sec)   p_kst 8.602151e-05   p_cons 1.451534e-01   p_joint 8.602151e-05

Joint ci ratio: 2.524985e-01	ci left: 7.521264e-05	ci right 9.727180e-05	k: 240	n:2800000
Cons ci ratio: 5.684311e-03	ci left: 1.447747e-01	ci right 1.456003e-01	k: 406524	n:2800000
KS ci ratio: 2.524985e-01	ci left: 7.521264e-05	ci right 9.727180e-05	k: 240	n:2800000
MAPK1   2800000 perm   3897 sec   (718 perm/sec)   p_kst 8.571429e-05   p_cons 1.451871e-01   p_joint 8.571429e-05

Joint ci ratio: 2.519762e-01	ci left: 7.527836e-05	ci right 9.730396e-05	k: 241	n:2810000
Cons ci ratio: 5.673877e-03	ci left: 1.447890e-01	ci right 1.456132e-01	k: 408014	n:2810000
KS ci ratio: 2.519762e-01	ci left: 7.527836e-05	ci right 9.730396e-05	k: 241	n:2810000
MAPK1   2810000 perm   3923 sec   (716 perm/sec)   p_kst 8.576512e-05   p_cons 1.452007e-01   p_joint 8.576512e-05

Joint ci ratio: 2.514572e-01	ci left: 7.534365e-05	ci right 9.733585e-05	k: 242	n:2820000
Cons ci ratio: 5.664197e-03	ci left: 1.447727e-01	ci right 1.455954e-01	k: 409418	n:2820000
KS ci ratio: 2.514572e-01	ci left: 7.534365e-05	ci right 9.733585e-05	k: 242	n:2820000
MAPK1   2820000 perm   3949 sec   (714 perm/sec)   p_kst 8.581560e-05   p_cons 1.451837e-01   p_joint 8.581560e-05

Joint ci ratio: 2.509414e-01	ci left: 7.540854e-05	ci right 9.736746e-05	k: 243	n:2830000
Cons ci ratio: 5.654163e-03	ci left: 1.447742e-01	ci right 1.455954e-01	k: 410872	n:2830000
KS ci ratio: 2.509414e-01	ci left: 7.540854e-05	ci right 9.736746e-05	k: 243	n:2830000
MAPK1   2830000 perm   3976 sec   (712 perm/sec)   p_kst 8.586572e-05   p_cons 1.451845e-01   p_joint 8.586572e-05

Joint ci ratio: 2.504288e-01	ci left: 7.547301e-05	ci right 9.739880e-05	k: 244	n:2840000
Cons ci ratio: 5.644103e-03	ci left: 1.447792e-01	ci right 1.455990e-01	k: 412336	n:2840000
KS ci ratio: 2.504288e-01	ci left: 7.547301e-05	ci right 9.739880e-05	k: 244	n:2840000
MAPK1   2840000 perm   4002 sec   (710 perm/sec)   p_kst 8.591549e-05   p_cons 1.451887e-01   p_joint 8.591549e-05

Joint ci ratio: 2.504288e-01	ci left: 7.520819e-05	ci right 9.705705e-05	k: 244	n:2850000
Cons ci ratio: 5.634191e-03	ci left: 1.447800e-01	ci right 1.455983e-01	k: 413788	n:2850000
KS ci ratio: 2.504288e-01	ci left: 7.520819e-05	ci right 9.705705e-05	k: 244	n:2850000
MAPK1   2850000 perm   4028 sec   (708 perm/sec)   p_kst 8.561404e-05   p_cons 1.451888e-01   p_joint 8.561404e-05

Joint ci ratio: 2.504288e-01	ci left: 7.494522e-05	ci right 9.671770e-05	k: 244	n:2860000
Cons ci ratio: 5.624886e-03	ci left: 1.447563e-01	ci right 1.455731e-01	k: 415170	n:2860000
KS ci ratio: 2.504288e-01	ci left: 7.494522e-05	ci right 9.671770e-05	k: 244	n:2860000
MAPK1   2860000 perm   4054 sec   (705 perm/sec)   p_kst 8.531469e-05   p_cons 1.451643e-01   p_joint 8.531469e-05

Joint ci ratio: 2.494129e-01	ci left: 7.533731e-05	ci right 9.712112e-05	k: 246	n:2870000
Cons ci ratio: 5.615399e-03	ci left: 1.447428e-01	ci right 1.455582e-01	k: 416581	n:2870000
KS ci ratio: 2.494129e-01	ci left: 7.533731e-05	ci right 9.712112e-05	k: 246	n:2870000
MAPK1   2870000 perm   4080 sec   (703 perm/sec)   p_kst 8.571429e-05   p_cons 1.451502e-01   p_joint 8.571429e-05

Joint ci ratio: 2.494129e-01	ci left: 7.507572e-05	ci right 9.678389e-05	k: 246	n:2880000
Cons ci ratio: 5.605873e-03	ci left: 1.447333e-01	ci right 1.455473e-01	k: 418003	n:2880000
KS ci ratio: 2.494129e-01	ci left: 7.507572e-05	ci right 9.678389e-05	k: 246	n:2880000
MAPK1   2880000 perm   4107 sec   (701 perm/sec)   p_kst 8.541667e-05   p_cons 1.451399e-01   p_joint 8.541667e-05

Joint ci ratio: 2.489095e-01	ci left: 7.514036e-05	ci right 9.681658e-05	k: 247	n:2890000
Cons ci ratio: 5.596738e-03	ci left: 1.447086e-01	ci right 1.455211e-01	k: 419381	n:2890000
KS ci ratio: 2.489095e-01	ci left: 7.514036e-05	ci right 9.681658e-05	k: 247	n:2890000
MAPK1   2890000 perm   4134 sec   (699 perm/sec)   p_kst 8.546713e-05   p_cons 1.451145e-01   p_joint 8.546713e-05

Joint ci ratio: 2.489096e-01	ci left: 7.488125e-05	ci right 9.648273e-05	k: 247	n:2900000
Cons ci ratio: 5.586880e-03	ci left: 1.447182e-01	ci right 1.455294e-01	k: 420858	n:2900000
KS ci ratio: 2.489096e-01	ci left: 7.488125e-05	ci right 9.648273e-05	k: 247	n:2900000
MAPK1   2900000 perm   4160 sec   (697 perm/sec)   p_kst 8.517241e-05   p_cons 1.451234e-01   p_joint 8.517241e-05

Joint ci ratio: 2.489096e-01	ci left: 7.462393e-05	ci right 9.615118e-05	k: 247	n:2910000
Cons ci ratio: 5.577328e-03	ci left: 1.447165e-01	ci right 1.455262e-01	k: 422302	n:2910000
KS ci ratio: 2.489096e-01	ci left: 7.462393e-05	ci right 9.615118e-05	k: 247	n:2910000
MAPK1   2910000 perm   4187 sec   (695 perm/sec)   p_kst 8.487973e-05   p_cons 1.451210e-01   p_joint 8.487973e-05

Joint ci ratio: 2.489096e-01	ci left: 7.436837e-05	ci right 9.582190e-05	k: 247	n:2920000
Cons ci ratio: 5.567994e-03	ci left: 1.447072e-01	ci right 1.455155e-01	k: 423724	n:2920000
KS ci ratio: 2.489096e-01	ci left: 7.436837e-05	ci right 9.582190e-05	k: 247	n:2920000
MAPK1   2920000 perm   4214 sec   (693 perm/sec)   p_kst 8.458904e-05   p_cons 1.451110e-01   p_joint 8.458904e-05

Joint ci ratio: 2.479119e-01	ci left: 7.475466e-05	ci right 9.621986e-05	k: 249	n:2930000
Cons ci ratio: 5.558737e-03	ci left: 1.446966e-01	ci right 1.455035e-01	k: 425142	n:2930000
KS ci ratio: 2.479119e-01	ci left: 7.475466e-05	ci right 9.621986e-05	k: 249	n:2930000
MAPK1   2930000 perm   4241 sec   (691 perm/sec)   p_kst 8.498294e-05   p_cons 1.450997e-01   p_joint 8.498294e-05

Joint ci ratio: 2.469262e-01	ci left: 7.513849e-05	ci right 9.661494e-05	k: 251	n:2940000
Cons ci ratio: 5.549025e-03	ci left: 1.447085e-01	ci right 1.455140e-01	k: 426626	n:2940000
KS ci ratio: 2.469262e-01	ci left: 7.513849e-05	ci right 9.661494e-05	k: 251	n:2940000
MAPK1   2940000 perm   4269 sec   (689 perm/sec)   p_kst 8.537415e-05   p_cons 1.451109e-01   p_joint 8.537415e-05

Joint ci ratio: 2.469262e-01	ci left: 7.488378e-05	ci right 9.628743e-05	k: 251	n:2950000
Cons ci ratio: 5.539688e-03	ci left: 1.447057e-01	ci right 1.455099e-01	k: 428067	n:2950000
KS ci ratio: 2.469262e-01	ci left: 7.488378e-05	ci right 9.628743e-05	k: 251	n:2950000
MAPK1   2950000 perm   4296 sec   (687 perm/sec)   p_kst 8.508475e-05   p_cons 1.451075e-01   p_joint 8.508475e-05

Joint ci ratio: 2.469262e-01	ci left: 7.463079e-05	ci right 9.596214e-05	k: 251	n:2960000
Cons ci ratio: 5.530466e-03	ci left: 1.447000e-01	ci right 1.455028e-01	k: 429499	n:2960000
KS ci ratio: 2.469262e-01	ci left: 7.463079e-05	ci right 9.596214e-05	k: 251	n:2960000
MAPK1   2960000 perm   4324 sec   (685 perm/sec)   p_kst 8.479730e-05   p_cons 1.451010e-01   p_joint 8.479730e-05

Joint ci ratio: 2.464377e-01	ci left: 7.469540e-05	ci right 9.599651e-05	k: 252	n:2970000
Cons ci ratio: 5.520991e-03	ci left: 1.447077e-01	ci right 1.455092e-01	k: 430971	n:2970000
KS ci ratio: 2.464377e-01	ci left: 7.469540e-05	ci right 9.599651e-05	k: 252	n:2970000
MAPK1   2970000 perm   4351 sec   (683 perm/sec)   p_kst 8.484848e-05   p_cons 1.451081e-01   p_joint 8.484848e-05

Joint ci ratio: 2.464378e-01	ci left: 7.444474e-05	ci right 9.567437e-05	k: 252	n:2980000
Cons ci ratio: 5.511467e-03	ci left: 1.447197e-01	ci right 1.455199e-01	k: 432456	n:2980000
KS ci ratio: 2.464378e-01	ci left: 7.444474e-05	ci right 9.567437e-05	k: 252	n:2980000
MAPK1   2980000 perm   4378 sec   (681 perm/sec)   p_kst 8.456376e-05   p_cons 1.451195e-01   p_joint 8.456376e-05

Joint ci ratio: 2.459522e-01	ci left: 7.450958e-05	ci right 9.570943e-05	k: 253	n:2990000
Cons ci ratio: 5.501918e-03	ci left: 1.447350e-01	ci right 1.455339e-01	k: 433951	n:2990000
KS ci ratio: 2.459522e-01	ci left: 7.450958e-05	ci right 9.570943e-05	k: 253	n:2990000
MAPK1   2990000 perm   4406 sec   (679 perm/sec)   p_kst 8.461538e-05   p_cons 1.451341e-01   p_joint 8.461538e-05

Joint ci ratio: 2.449895e-01	ci left: 7.488688e-05	ci right 9.609799e-05	k: 255	n:3000000
Cons ci ratio: 5.492706e-03	ci left: 1.447373e-01	ci right 1.455348e-01	k: 435407	n:3000000
KS ci ratio: 2.449895e-01	ci left: 7.488688e-05	ci right 9.609799e-05	k: 255	n:3000000
MAPK1   3000000 perm   4433 sec   (677 perm/sec)   p_kst 8.500000e-05   p_cons 1.451357e-01   p_joint 8.500000e-05

Joint ci ratio: 2.449895e-01	ci left: 7.463808e-05	ci right 9.577873e-05	k: 255	n:3010000
Cons ci ratio: 5.483621e-03	ci left: 1.447358e-01	ci right 1.455320e-01	k: 436852	n:3010000
KS ci ratio: 2.449895e-01	ci left: 7.463808e-05	ci right 9.577873e-05	k: 255	n:3010000
MAPK1   3010000 perm   4461 sec   (675 perm/sec)   p_kst 8.471761e-05   p_cons 1.451336e-01   p_joint 8.471761e-05

Joint ci ratio: 2.445124e-01	ci left: 7.470176e-05	ci right 9.581297e-05	k: 256	n:3020000
Cons ci ratio: 5.474551e-03	ci left: 1.447357e-01	ci right 1.455305e-01	k: 438301	n:3020000
KS ci ratio: 2.445124e-01	ci left: 7.470176e-05	ci right 9.581297e-05	k: 256	n:3020000
MAPK1   3020000 perm   4489 sec   (673 perm/sec)   p_kst 8.476821e-05   p_cons 1.451328e-01   p_joint 8.476821e-05

Joint ci ratio: 2.445125e-01	ci left: 7.445521e-05	ci right 9.549676e-05	k: 256	n:3030000
Cons ci ratio: 5.465571e-03	ci left: 1.447336e-01	ci right 1.455271e-01	k: 439744	n:3030000
KS ci ratio: 2.445125e-01	ci left: 7.445521e-05	ci right 9.549676e-05	k: 256	n:3030000
MAPK1   3030000 perm   4517 sec   (671 perm/sec)   p_kst 8.448845e-05   p_cons 1.451300e-01   p_joint 8.448845e-05

Joint ci ratio: 2.445125e-01	ci left: 7.421029e-05	ci right 9.518263e-05	k: 256	n:3040000
Cons ci ratio: 5.456706e-03	ci left: 1.447282e-01	ci right 1.455205e-01	k: 441177	n:3040000
KS ci ratio: 2.445125e-01	ci left: 7.421029e-05	ci right 9.518263e-05	k: 256	n:3040000
MAPK1   3040000 perm   4545 sec   (669 perm/sec)   p_kst 8.421053e-05   p_cons 1.451240e-01   p_joint 8.421053e-05

Joint ci ratio: 2.440382e-01	ci left: 7.427478e-05	ci right 9.521845e-05	k: 257	n:3050000
Cons ci ratio: 5.447676e-03	ci left: 1.447324e-01	ci right 1.455233e-01	k: 442639	n:3050000
KS ci ratio: 2.440382e-01	ci left: 7.427478e-05	ci right 9.521845e-05	k: 257	n:3050000
MAPK1   3050000 perm   4573 sec   (667 perm/sec)   p_kst 8.426230e-05   p_cons 1.451275e-01   p_joint 8.426230e-05

Joint ci ratio: 2.440382e-01	ci left: 7.403205e-05	ci right 9.490728e-05	k: 257	n:3060000
Cons ci ratio: 5.439149e-03	ci left: 1.447157e-01	ci right 1.455053e-01	k: 444037	n:3060000
KS ci ratio: 2.440382e-01	ci left: 7.403205e-05	ci right 9.490728e-05	k: 257	n:3060000
MAPK1   3060000 perm   4601 sec   (665 perm/sec)   p_kst 8.398693e-05   p_cons 1.451101e-01   p_joint 8.398693e-05

Joint ci ratio: 2.440382e-01	ci left: 7.379091e-05	ci right 9.459814e-05	k: 257	n:3070000
Cons ci ratio: 5.430213e-03	ci left: 1.447195e-01	ci right 1.455078e-01	k: 445498	n:3070000
KS ci ratio: 2.440382e-01	ci left: 7.379091e-05	ci right 9.459814e-05	k: 257	n:3070000
MAPK1   3070000 perm   4630 sec   (663 perm/sec)   p_kst 8.371336e-05   p_cons 1.451134e-01   p_joint 8.371336e-05

Joint ci ratio: 2.435667e-01	ci left: 7.385617e-05	ci right 9.463548e-05	k: 258	n:3080000
Cons ci ratio: 5.421391e-03	ci left: 1.447201e-01	ci right 1.455072e-01	k: 446949	n:3080000
KS ci ratio: 2.435667e-01	ci left: 7.385617e-05	ci right 9.463548e-05	k: 258	n:3080000
MAPK1   3080000 perm   4659 sec   (661 perm/sec)   p_kst 8.376623e-05   p_cons 1.451133e-01   p_joint 8.376623e-05

Joint ci ratio: 2.435667e-01	ci left: 7.361715e-05	ci right 9.432921e-05	k: 258	n:3090000
Cons ci ratio: 5.412584e-03	ci left: 1.447220e-01	ci right 1.455078e-01	k: 448404	n:3090000
KS ci ratio: 2.435667e-01	ci left: 7.361715e-05	ci right 9.432921e-05	k: 258	n:3090000
MAPK1   3090000 perm   4687 sec   (659 perm/sec)   p_kst 8.349515e-05   p_cons 1.451146e-01   p_joint 8.349515e-05

Joint ci ratio: 2.435667e-01	ci left: 7.337967e-05	ci right 9.402493e-05	k: 258	n:3100000
Cons ci ratio: 5.404186e-03	ci left: 1.447071e-01	ci right 1.454916e-01	k: 449807	n:3100000
KS ci ratio: 2.435667e-01	ci left: 7.337967e-05	ci right 9.402493e-05	k: 258	n:3100000
MAPK1   3100000 perm   4716 sec   (657 perm/sec)   p_kst 8.322581e-05   p_cons 1.450990e-01   p_joint 8.322581e-05

Joint ci ratio: 2.421682e-01	ci left: 7.404966e-05	ci right 9.474581e-05	k: 261	n:3110000
Cons ci ratio: 5.395637e-03	ci left: 1.447010e-01	ci right 1.454842e-01	k: 451237	n:3110000
KS ci ratio: 2.421682e-01	ci left: 7.404966e-05	ci right 9.474581e-05	k: 261	n:3110000
MAPK1   3110000 perm   4745 sec   (655 perm/sec)   p_kst 8.392283e-05   p_cons 1.450923e-01   p_joint 8.392283e-05

Joint ci ratio: 2.421682e-01	ci left: 7.381232e-05	ci right 9.444214e-05	k: 261	n:3120000
Cons ci ratio: 5.386809e-03	ci left: 1.447097e-01	ci right 1.454916e-01	k: 452713	n:3120000
KS ci ratio: 2.421682e-01	ci left: 7.381232e-05	ci right 9.444214e-05	k: 261	n:3120000
MAPK1   3120000 perm   4774 sec   (654 perm/sec)   p_kst 8.365385e-05   p_cons 1.451003e-01   p_joint 8.365385e-05

Joint ci ratio: 2.417074e-01	ci left: 7.387662e-05	ci right 9.447923e-05	k: 262	n:3130000
Cons ci ratio: 5.377934e-03	ci left: 1.447224e-01	ci right 1.455031e-01	k: 454202	n:3130000
KS ci ratio: 2.417074e-01	ci left: 7.387662e-05	ci right 9.447923e-05	k: 262	n:3130000
MAPK1   3130000 perm   4803 sec   (652 perm/sec)   p_kst 8.370607e-05   p_cons 1.451125e-01   p_joint 8.370607e-05

Joint ci ratio: 2.412491e-01	ci left: 7.394055e-05	ci right 9.451604e-05	k: 263	n:3140000
Cons ci ratio: 5.369316e-03	ci left: 1.447252e-01	ci right 1.455047e-01	k: 455660	n:3140000
KS ci ratio: 2.412491e-01	ci left: 7.394055e-05	ci right 9.451604e-05	k: 263	n:3140000
MAPK1   3140000 perm   4833 sec   (650 perm/sec)   p_kst 8.375796e-05   p_cons 1.451146e-01   p_joint 8.375796e-05

Joint ci ratio: 2.412492e-01	ci left: 7.370581e-05	ci right 9.421599e-05	k: 263	n:3150000
Cons ci ratio: 5.360904e-03	ci left: 1.447204e-01	ci right 1.454986e-01	k: 457094	n:3150000
KS ci ratio: 2.412492e-01	ci left: 7.370581e-05	ci right 9.421599e-05	k: 263	n:3150000
MAPK1   3150000 perm   4862 sec   (648 perm/sec)   p_kst 8.349206e-05   p_cons 1.451092e-01   p_joint 8.349206e-05

Joint ci ratio: 2.403405e-01	ci left: 7.406730e-05	ci right 9.458886e-05	k: 265	n:3160000
Cons ci ratio: 5.352122e-03	ci left: 1.447346e-01	ci right 1.455116e-01	k: 458588	n:3160000
KS ci ratio: 2.403405e-01	ci left: 7.406730e-05	ci right 9.458886e-05	k: 265	n:3160000
MAPK1   3160000 perm   4891 sec   (646 perm/sec)   p_kst 8.386076e-05   p_cons 1.451228e-01   p_joint 8.386076e-05

Joint ci ratio: 2.403405e-01	ci left: 7.383365e-05	ci right 9.429048e-05	k: 265	n:3170000
Cons ci ratio: 5.343926e-03	ci left: 1.447235e-01	ci right 1.454992e-01	k: 460002	n:3170000
KS ci ratio: 2.403405e-01	ci left: 7.383365e-05	ci right 9.429048e-05	k: 265	n:3170000
MAPK1   3170000 perm   4920 sec   (644 perm/sec)   p_kst 8.359621e-05   p_cons 1.451110e-01   p_joint 8.359621e-05

Joint ci ratio: 2.403405e-01	ci left: 7.360146e-05	ci right 9.399397e-05	k: 265	n:3180000
Cons ci ratio: 5.335396e-03	ci left: 1.447297e-01	ci right 1.455043e-01	k: 461471	n:3180000
KS ci ratio: 2.403405e-01	ci left: 7.360146e-05	ci right 9.399397e-05	k: 265	n:3180000
MAPK1   3180000 perm   4950 sec   (642 perm/sec)   p_kst 8.333333e-05   p_cons 1.451167e-01   p_joint 8.333333e-05

Joint ci ratio: 2.394420e-01	ci left: 7.396002e-05	ci right 9.436388e-05	k: 267	n:3190000
Cons ci ratio: 5.327116e-03	ci left: 1.447262e-01	ci right 1.454995e-01	k: 462909	n:3190000
KS ci ratio: 2.394420e-01	ci left: 7.396002e-05	ci right 9.436388e-05	k: 267	n:3190000
MAPK1   3190000 perm   4979 sec   (641 perm/sec)   p_kst 8.369906e-05   p_cons 1.451125e-01   p_joint 8.369906e-05

Joint ci ratio: 2.394420e-01	ci left: 7.372889e-05	ci right 9.406900e-05	k: 267	n:3200000
Cons ci ratio: 5.318847e-03	ci left: 1.447240e-01	ci right 1.454961e-01	k: 464351	n:3200000
KS ci ratio: 2.394420e-01	ci left: 7.372889e-05	ci right 9.406900e-05	k: 267	n:3200000
MAPK1   3200000 perm   5009 sec   (639 perm/sec)   p_kst 8.343750e-05   p_cons 1.451097e-01   p_joint 8.343750e-05

Joint ci ratio: 2.389966e-01	ci left: 7.379206e-05	ci right 9.410611e-05	k: 268	n:3210000
Cons ci ratio: 5.310703e-03	ci left: 1.447177e-01	ci right 1.454886e-01	k: 465780	n:3210000
KS ci ratio: 2.389966e-01	ci left: 7.379206e-05	ci right 9.410611e-05	k: 268	n:3210000
MAPK1   3210000 perm   5039 sec   (637 perm/sec)   p_kst 8.348910e-05   p_cons 1.451028e-01   p_joint 8.348910e-05

Joint ci ratio: 2.385536e-01	ci left: 7.385487e-05	ci right 9.414296e-05	k: 269	n:3220000
Cons ci ratio: 5.302882e-03	ci left: 1.446981e-01	ci right 1.454678e-01	k: 467166	n:3220000
KS ci ratio: 2.385536e-01	ci left: 7.385487e-05	ci right 9.414296e-05	k: 269	n:3220000
MAPK1   3220000 perm   5068 sec   (635 perm/sec)   p_kst 8.354037e-05   p_cons 1.450826e-01   p_joint 8.354037e-05

Joint ci ratio: 2.376749e-01	ci left: 7.420848e-05	ci right 9.450756e-05	k: 271	n:3230000
Cons ci ratio: 5.294692e-03	ci left: 1.446975e-01	ci right 1.454660e-01	k: 468613	n:3230000
KS ci ratio: 2.376749e-01	ci left: 7.420848e-05	ci right 9.450756e-05	k: 271	n:3230000
MAPK1   3230000 perm   5098 sec   (634 perm/sec)   p_kst 8.390093e-05   p_cons 1.450814e-01   p_joint 8.390093e-05

Joint ci ratio: 2.372392e-01	ci left: 7.426972e-05	ci right 9.454284e-05	k: 272	n:3240000
Cons ci ratio: 5.286507e-03	ci left: 1.446985e-01	ci right 1.454657e-01	k: 470065	n:3240000
KS ci ratio: 2.372392e-01	ci left: 7.426972e-05	ci right 9.454284e-05	k: 272	n:3240000
MAPK1   3240000 perm   5129 sec   (632 perm/sec)   p_kst 8.395062e-05   p_cons 1.450818e-01   p_joint 8.395062e-05

Joint ci ratio: 2.368058e-01	ci left: 7.433062e-05	ci right 9.457787e-05	k: 273	n:3250000
Cons ci ratio: 5.278452e-03	ci left: 1.446951e-01	ci right 1.454612e-01	k: 471503	n:3250000
KS ci ratio: 2.368058e-01	ci left: 7.433062e-05	ci right 9.457787e-05	k: 273	n:3250000
MAPK1   3250000 perm   5159 sec   (630 perm/sec)   p_kst 8.400000e-05   p_cons 1.450778e-01   p_joint 8.400000e-05

Joint ci ratio: 2.368059e-01	ci left: 7.410261e-05	ci right 9.428775e-05	k: 273	n:3260000
Cons ci ratio: 5.270452e-03	ci left: 1.446909e-01	ci right 1.454558e-01	k: 472938	n:3260000
KS ci ratio: 2.368059e-01	ci left: 7.410261e-05	ci right 9.428775e-05	k: 273	n:3260000
MAPK1   3260000 perm   5189 sec   (628 perm/sec)   p_kst 8.374233e-05   p_cons 1.450730e-01   p_joint 8.374233e-05

Joint ci ratio: 2.363749e-01	ci left: 7.416368e-05	ci right 9.432332e-05	k: 274	n:3270000
Cons ci ratio: 5.262548e-03	ci left: 1.446839e-01	ci right 1.454476e-01	k: 474364	n:3270000
KS ci ratio: 2.363749e-01	ci left: 7.416368e-05	ci right 9.432332e-05	k: 274	n:3270000
MAPK1   3270000 perm   5219 sec   (627 perm/sec)   p_kst 8.379205e-05   p_cons 1.450654e-01   p_joint 8.379205e-05

Joint ci ratio: 2.363749e-01	ci left: 7.393757e-05	ci right 9.403575e-05	k: 274	n:3280000
Cons ci ratio: 5.254627e-03	ci left: 1.446794e-01	ci right 1.454419e-01	k: 475798	n:3280000
KS ci ratio: 2.363749e-01	ci left: 7.393757e-05	ci right 9.403575e-05	k: 274	n:3280000
MAPK1   3280000 perm   5249 sec   (625 perm/sec)   p_kst 8.353659e-05   p_cons 1.450604e-01   p_joint 8.353659e-05

Joint ci ratio: 2.363750e-01	ci left: 7.371284e-05	ci right 9.374993e-05	k: 274	n:3290000
Cons ci ratio: 5.246768e-03	ci left: 1.446737e-01	ci right 1.454351e-01	k: 477228	n:3290000
KS ci ratio: 2.363750e-01	ci left: 7.371284e-05	ci right 9.374993e-05	k: 274	n:3290000
MAPK1   3290000 perm   5279 sec   (623 perm/sec)   p_kst 8.328267e-05   p_cons 1.450541e-01   p_joint 8.328267e-05

Joint ci ratio: 2.363750e-01	ci left: 7.348946e-05	ci right 9.346584e-05	k: 274	n:3300000
Cons ci ratio: 5.238995e-03	ci left: 1.446657e-01	ci right 1.454259e-01	k: 478650	n:3300000
KS ci ratio: 2.363750e-01	ci left: 7.348946e-05	ci right 9.346584e-05	k: 274	n:3300000
MAPK1   3300000 perm   5309 sec   (622 perm/sec)   p_kst 8.303030e-05   p_cons 1.450455e-01   p_joint 8.303030e-05

Joint ci ratio: 2.363750e-01	ci left: 7.326744e-05	ci right 9.318346e-05	k: 274	n:3310000
Cons ci ratio: 5.231123e-03	ci left: 1.446640e-01	ci right 1.454230e-01	k: 480093	n:3310000
KS ci ratio: 2.363750e-01	ci left: 7.326744e-05	ci right 9.318346e-05	k: 274	n:3310000
MAPK1   3310000 perm   5339 sec   (620 perm/sec)   p_kst 8.277946e-05   p_cons 1.450432e-01   p_joint 8.277946e-05

Joint ci ratio: 2.359464e-01	ci left: 7.333014e-05	ci right 9.322178e-05	k: 275	n:3320000
Cons ci ratio: 5.223013e-03	ci left: 1.446753e-01	ci right 1.454332e-01	k: 481579	n:3320000
KS ci ratio: 2.359464e-01	ci left: 7.333014e-05	ci right 9.322178e-05	k: 275	n:3320000
MAPK1   3320000 perm   5369 sec   (618 perm/sec)   p_kst 8.283133e-05   p_cons 1.450539e-01   p_joint 8.283133e-05

Joint ci ratio: 2.359465e-01	ci left: 7.310993e-05	ci right 9.294184e-05	k: 275	n:3330000
Cons ci ratio: 5.215294e-03	ci left: 1.446697e-01	ci right 1.454264e-01	k: 483009	n:3330000
KS ci ratio: 2.359465e-01	ci left: 7.310993e-05	ci right 9.294184e-05	k: 275	n:3330000
MAPK1   3330000 perm   5400 sec   (617 perm/sec)   p_kst 8.258258e-05   p_cons 1.450477e-01   p_joint 8.258258e-05

Joint ci ratio: 2.359465e-01	ci left: 7.289103e-05	ci right 9.266357e-05	k: 275	n:3340000
Cons ci ratio: 5.207503e-03	ci left: 1.446692e-01	ci right 1.454248e-01	k: 484456	n:3340000
KS ci ratio: 2.359465e-01	ci left: 7.289103e-05	ci right 9.266357e-05	k: 275	n:3340000
MAPK1   3340000 perm   5430 sec   (615 perm/sec)   p_kst 8.233533e-05   p_cons 1.450467e-01   p_joint 8.233533e-05

Joint ci ratio: 2.359465e-01	ci left: 7.267345e-05	ci right 9.238697e-05	k: 275	n:3350000
Cons ci ratio: 5.199928e-03	ci left: 1.446601e-01	ci right 1.454146e-01	k: 485874	n:3350000
KS ci ratio: 2.359465e-01	ci left: 7.267345e-05	ci right 9.238697e-05	k: 275	n:3350000
MAPK1   3350000 perm   5460 sec   (614 perm/sec)   p_kst 8.208955e-05   p_cons 1.450370e-01   p_joint 8.208955e-05

Joint ci ratio: 2.346745e-01	ci left: 7.329738e-05	ci right 9.305740e-05	k: 278	n:3360000
Cons ci ratio: 5.192448e-03	ci left: 1.446481e-01	ci right 1.454014e-01	k: 487282	n:3360000
KS ci ratio: 2.346745e-01	ci left: 7.329738e-05	ci right 9.305740e-05	k: 278	n:3360000
MAPK1   3360000 perm   5491 sec   (612 perm/sec)   p_kst 8.273810e-05   p_cons 1.450244e-01   p_joint 8.273810e-05

Joint ci ratio: 2.346745e-01	ci left: 7.307988e-05	ci right 9.278127e-05	k: 278	n:3370000
Cons ci ratio: 5.184988e-03	ci left: 1.446367e-01	ci right 1.453889e-01	k: 488692	n:3370000
KS ci ratio: 2.346745e-01	ci left: 7.307988e-05	ci right 9.278127e-05	k: 278	n:3370000
MAPK1   3370000 perm   5521 sec   (610 perm/sec)   p_kst 8.249258e-05   p_cons 1.450125e-01   p_joint 8.249258e-05

Joint ci ratio: 2.334228e-01	ci left: 7.369921e-05	ci right 9.344628e-05	k: 281	n:3380000
Cons ci ratio: 5.177208e-03	ci left: 1.446422e-01	ci right 1.453933e-01	k: 490159	n:3380000
KS ci ratio: 2.334228e-01	ci left: 7.369921e-05	ci right 9.344628e-05	k: 281	n:3380000
MAPK1   3380000 perm   5552 sec   (609 perm/sec)   p_kst 8.313609e-05   p_cons 1.450175e-01   p_joint 8.313609e-05

Joint ci ratio: 2.330101e-01	ci left: 7.375956e-05	ci right 9.348282e-05	k: 282	n:3390000
Cons ci ratio: 5.169623e-03	ci left: 1.446401e-01	ci right 1.453900e-01	k: 491600	n:3390000
KS ci ratio: 2.330101e-01	ci left: 7.375956e-05	ci right 9.348282e-05	k: 282	n:3390000
MAPK1   3390000 perm   5583 sec   (607 perm/sec)   p_kst 8.318584e-05   p_cons 1.450147e-01   p_joint 8.318584e-05

Joint ci ratio: 2.330101e-01	ci left: 7.354261e-05	ci right 9.320787e-05	k: 282	n:3400000
Cons ci ratio: 5.161845e-03	ci left: 1.446488e-01	ci right 1.453977e-01	k: 493078	n:3400000
KS ci ratio: 2.330101e-01	ci left: 7.354261e-05	ci right 9.320787e-05	k: 282	n:3400000
MAPK1   3400000 perm   5614 sec   (606 perm/sec)   p_kst 8.294118e-05   p_cons 1.450229e-01   p_joint 8.294118e-05

Joint ci ratio: 2.325995e-01	ci left: 7.360310e-05	ci right 9.324486e-05	k: 283	n:3410000
Cons ci ratio: 5.154132e-03	ci left: 1.446560e-01	ci right 1.454038e-01	k: 494551	n:3410000
KS ci ratio: 2.325995e-01	ci left: 7.360310e-05	ci right 9.324486e-05	k: 283	n:3410000
MAPK1   3410000 perm   5645 sec   (604 perm/sec)   p_kst 8.299120e-05   p_cons 1.450296e-01   p_joint 8.299120e-05

Joint ci ratio: 2.317847e-01	ci left: 7.393867e-05	ci right 9.359097e-05	k: 285	n:3420000
Cons ci ratio: 5.146738e-03	ci left: 1.446495e-01	ci right 1.453962e-01	k: 495977	n:3420000
KS ci ratio: 2.317847e-01	ci left: 7.393867e-05	ci right 9.359097e-05	k: 285	n:3420000
MAPK1   3420000 perm   5676 sec   (603 perm/sec)   p_kst 8.333333e-05   p_cons 1.450225e-01   p_joint 8.333333e-05

Joint ci ratio: 2.313806e-01	ci left: 7.399774e-05	ci right 9.362654e-05	k: 286	n:3430000
Cons ci ratio: 5.139141e-03	ci left: 1.446543e-01	ci right 1.453999e-01	k: 497442	n:3430000
KS ci ratio: 2.313806e-01	ci left: 7.399774e-05	ci right 9.362654e-05	k: 286	n:3430000
MAPK1   3430000 perm   5707 sec   (601 perm/sec)   p_kst 8.338192e-05   p_cons 1.450268e-01   p_joint 8.338192e-05

Joint ci ratio: 2.309785e-01	ci left: 7.405649e-05	ci right 9.366187e-05	k: 287	n:3440000
Cons ci ratio: 5.131391e-03	ci left: 1.446681e-01	ci right 1.454127e-01	k: 498938	n:3440000
KS ci ratio: 2.309785e-01	ci left: 7.405649e-05	ci right 9.366187e-05	k: 287	n:3440000
MAPK1   3440000 perm   5738 sec   (599 perm/sec)   p_kst 8.343023e-05   p_cons 1.450401e-01   p_joint 8.343023e-05

Joint ci ratio: 2.309785e-01	ci left: 7.384183e-05	ci right 9.339039e-05	k: 287	n:3450000
Cons ci ratio: 5.124035e-03	ci left: 1.446645e-01	ci right 1.454080e-01	k: 500374	n:3450000
KS ci ratio: 2.309785e-01	ci left: 7.384183e-05	ci right 9.339039e-05	k: 287	n:3450000
MAPK1   3450000 perm   5770 sec   (598 perm/sec)   p_kst 8.318841e-05   p_cons 1.450359e-01   p_joint 8.318841e-05

Joint ci ratio: 2.309786e-01	ci left: 7.362841e-05	ci right 9.312047e-05	k: 287	n:3460000
Cons ci ratio: 5.116961e-03	ci left: 1.446488e-01	ci right 1.453911e-01	k: 501768	n:3460000
KS ci ratio: 2.309786e-01	ci left: 7.362841e-05	ci right 9.312047e-05	k: 287	n:3460000
MAPK1   3460000 perm   5801 sec   (596 perm/sec)   p_kst 8.294798e-05   p_cons 1.450197e-01   p_joint 8.294798e-05

Joint ci ratio: 2.305786e-01	ci left: 7.368775e-05	ci right 9.315693e-05	k: 288	n:3470000
Cons ci ratio: 5.109566e-03	ci left: 1.446501e-01	ci right 1.453914e-01	k: 503221	n:3470000
KS ci ratio: 2.305786e-01	ci left: 7.368775e-05	ci right 9.315693e-05	k: 288	n:3470000
MAPK1   3470000 perm   5832 sec   (595 perm/sec)   p_kst 8.299712e-05   p_cons 1.450205e-01   p_joint 8.299712e-05

Joint ci ratio: 2.305786e-01	ci left: 7.347601e-05	ci right 9.288924e-05	k: 288	n:3480000
Cons ci ratio: 5.102120e-03	ci left: 1.446555e-01	ci right 1.453957e-01	k: 504688	n:3480000
KS ci ratio: 2.305786e-01	ci left: 7.347601e-05	ci right 9.288924e-05	k: 288	n:3480000
MAPK1   3480000 perm   5864 sec   (593 perm/sec)   p_kst 8.275862e-05   p_cons 1.450253e-01   p_joint 8.275862e-05

Joint ci ratio: 2.301807e-01	ci left: 7.353547e-05	ci right 9.292612e-05	k: 289	n:3490000
Cons ci ratio: 5.094595e-03	ci left: 1.446662e-01	ci right 1.454054e-01	k: 506174	n:3490000
KS ci ratio: 2.301807e-01	ci left: 7.353547e-05	ci right 9.292612e-05	k: 289	n:3490000
MAPK1   3490000 perm   5896 sec   (592 perm/sec)   p_kst 8.280802e-05   p_cons 1.450355e-01   p_joint 8.280802e-05

Joint ci ratio: 2.301808e-01	ci left: 7.332537e-05	ci right 9.266062e-05	k: 289	n:3500000
Cons ci ratio: 5.087536e-03	ci left: 1.446558e-01	ci right 1.453939e-01	k: 507586	n:3500000
KS ci ratio: 2.301808e-01	ci left: 7.332537e-05	ci right 9.266062e-05	k: 289	n:3500000
MAPK1   3500000 perm   5927 sec   (590 perm/sec)   p_kst 8.257143e-05   p_cons 1.450246e-01   p_joint 8.257143e-05

Joint ci ratio: 2.297849e-01	ci left: 7.338495e-05	ci right 9.269792e-05	k: 290	n:3510000
Cons ci ratio: 5.080525e-03	ci left: 1.446446e-01	ci right 1.453816e-01	k: 508995	n:3510000
KS ci ratio: 2.297849e-01	ci left: 7.338495e-05	ci right 9.269792e-05	k: 290	n:3510000
MAPK1   3510000 perm   5959 sec   (589 perm/sec)   p_kst 8.262108e-05   p_cons 1.450128e-01   p_joint 8.262108e-05

Joint ci ratio: 2.297849e-01	ci left: 7.317647e-05	ci right 9.243457e-05	k: 290	n:3520000
Cons ci ratio: 5.073676e-03	ci left: 1.446269e-01	ci right 1.453629e-01	k: 510381	n:3520000
KS ci ratio: 2.297849e-01	ci left: 7.317647e-05	ci right 9.243457e-05	k: 290	n:3520000
MAPK1   3520000 perm   5991 sec   (588 perm/sec)   p_kst 8.238636e-05   p_cons 1.449946e-01   p_joint 8.238636e-05

Joint ci ratio: 2.293911e-01	ci left: 7.323617e-05	ci right 9.247227e-05	k: 291	n:3530000
Cons ci ratio: 5.066704e-03	ci left: 1.446167e-01	ci right 1.453516e-01	k: 511793	n:3530000
KS ci ratio: 2.293911e-01	ci left: 7.323617e-05	ci right 9.247227e-05	k: 291	n:3530000
MAPK1   3530000 perm   6023 sec   (586 perm/sec)   p_kst 8.243626e-05   p_cons 1.449839e-01   p_joint 8.243626e-05

Joint ci ratio: 2.286095e-01	ci left: 7.356185e-05	ci right 9.280837e-05	k: 293	n:3540000
Cons ci ratio: 5.059657e-03	ci left: 1.446116e-01	ci right 1.453454e-01	k: 513223	n:3540000
KS ci ratio: 2.286095e-01	ci left: 7.356185e-05	ci right 9.280837e-05	k: 293	n:3540000
MAPK1   3540000 perm   6055 sec   (585 perm/sec)   p_kst 8.276836e-05   p_cons 1.449782e-01   p_joint 8.276836e-05

Joint ci ratio: 2.282217e-01	ci left: 7.362020e-05	ci right 9.284472e-05	k: 294	n:3550000
Cons ci ratio: 5.052145e-03	ci left: 1.446308e-01	ci right 1.453636e-01	k: 514739	n:3550000
KS ci ratio: 2.282217e-01	ci left: 7.362020e-05	ci right 9.284472e-05	k: 294	n:3550000
MAPK1   3550000 perm   6087 sec   (583 perm/sec)   p_kst 8.281690e-05   p_cons 1.449969e-01   p_joint 8.281690e-05

Joint ci ratio: 2.282217e-01	ci left: 7.341341e-05	ci right 9.258392e-05	k: 294	n:3560000
Cons ci ratio: 5.044982e-03	ci left: 1.446344e-01	ci right 1.453662e-01	k: 516200	n:3560000
KS ci ratio: 2.282217e-01	ci left: 7.341341e-05	ci right 9.258392e-05	k: 294	n:3560000
MAPK1   3560000 perm   6120 sec   (582 perm/sec)   p_kst 8.258427e-05   p_cons 1.450000e-01   p_joint 8.258427e-05

Joint ci ratio: 2.282218e-01	ci left: 7.320776e-05	ci right 9.232458e-05	k: 294	n:3570000
Cons ci ratio: 5.038070e-03	ci left: 1.446271e-01	ci right 1.453578e-01	k: 517622	n:3570000
KS ci ratio: 2.282218e-01	ci left: 7.320776e-05	ci right 9.232458e-05	k: 294	n:3570000
MAPK1   3570000 perm   6152 sec   (580 perm/sec)   p_kst 8.235294e-05   p_cons 1.449922e-01   p_joint 8.235294e-05

Joint ci ratio: 2.282218e-01	ci left: 7.300327e-05	ci right 9.206669e-05	k: 294	n:3580000
Cons ci ratio: 5.030978e-03	ci left: 1.446301e-01	ci right 1.453598e-01	k: 519081	n:3580000
KS ci ratio: 2.282218e-01	ci left: 7.300327e-05	ci right 9.206669e-05	k: 294	n:3580000
MAPK1   3580000 perm   6185 sec   (579 perm/sec)   p_kst 8.212291e-05   p_cons 1.449947e-01   p_joint 8.212291e-05

Joint ci ratio: 2.274520e-01	ci left: 7.332523e-05	ci right 9.239908e-05	k: 296	n:3590000
Cons ci ratio: 5.023926e-03	ci left: 1.446326e-01	ci right 1.453613e-01	k: 520538	n:3590000
KS ci ratio: 2.274520e-01	ci left: 7.332523e-05	ci right 9.239908e-05	k: 296	n:3590000
MAPK1   3590000 perm   6217 sec   (577 perm/sec)   p_kst 8.245125e-05   p_cons 1.449967e-01   p_joint 8.245125e-05

Joint ci ratio: 2.274521e-01	ci left: 7.312155e-05	ci right 9.214242e-05	k: 296	n:3600000
Cons ci ratio: 5.016870e-03	ci left: 1.446367e-01	ci right 1.453644e-01	k: 522001	n:3600000
KS ci ratio: 2.274521e-01	ci left: 7.312155e-05	ci right 9.214242e-05	k: 296	n:3600000
MAPK1   3600000 perm   6250 sec   (576 perm/sec)   p_kst 8.222222e-05   p_cons 1.450003e-01   p_joint 8.222222e-05

Joint ci ratio: 2.270701e-01	ci left: 7.318024e-05	ci right 9.217993e-05	k: 297	n:3610000
Cons ci ratio: 5.010202e-03	ci left: 1.446231e-01	ci right 1.453498e-01	k: 523400	n:3610000
KS ci ratio: 2.270701e-01	ci left: 7.318024e-05	ci right 9.217993e-05	k: 297	n:3610000
MAPK1   3610000 perm   6283 sec   (575 perm/sec)   p_kst 8.227147e-05   p_cons 1.449861e-01   p_joint 8.227147e-05

Joint ci ratio: 2.270701e-01	ci left: 7.297808e-05	ci right 9.192529e-05	k: 297	n:3620000
Cons ci ratio: 5.003193e-03	ci left: 1.446278e-01	ci right 1.453535e-01	k: 524865	n:3620000
KS ci ratio: 2.270701e-01	ci left: 7.297808e-05	ci right 9.192529e-05	k: 297	n:3620000
MAPK1   3620000 perm   6316 sec   (573 perm/sec)   p_kst 8.204420e-05   p_cons 1.449903e-01   p_joint 8.204420e-05

Joint ci ratio: 2.266901e-01	ci left: 7.303686e-05	ci right 9.196316e-05	k: 298	n:3630000
Cons ci ratio: 4.996779e-03	ci left: 1.446044e-01	ci right 1.453290e-01	k: 526228	n:3630000
KS ci ratio: 2.266901e-01	ci left: 7.303686e-05	ci right 9.196316e-05	k: 298	n:3630000
MAPK1   3630000 perm   6350 sec   (572 perm/sec)   p_kst 8.209366e-05   p_cons 1.449664e-01   p_joint 8.209366e-05

Joint ci ratio: 2.263119e-01	ci left: 7.309535e-05	ci right 9.200080e-05	k: 299	n:3640000
Cons ci ratio: 4.990069e-03	ci left: 1.445970e-01	ci right 1.453206e-01	k: 527649	n:3640000
KS ci ratio: 2.263119e-01	ci left: 7.309535e-05	ci right 9.200080e-05	k: 299	n:3640000
MAPK1   3640000 perm   6384 sec   (570 perm/sec)   p_kst 8.214286e-05   p_cons 1.449585e-01   p_joint 8.214286e-05

Joint ci ratio: 2.259357e-01	ci left: 7.315355e-05	ci right 9.203821e-05	k: 300	n:3650000
Cons ci ratio: 4.983452e-03	ci left: 1.445864e-01	ci right 1.453090e-01	k: 529058	n:3650000
KS ci ratio: 2.259357e-01	ci left: 7.315355e-05	ci right 9.203821e-05	k: 300	n:3650000
MAPK1   3650000 perm   6417 sec   (569 perm/sec)   p_kst 8.219178e-05   p_cons 1.449474e-01   p_joint 8.219178e-05

Joint ci ratio: 2.259357e-01	ci left: 7.295367e-05	ci right 9.178674e-05	k: 300	n:3660000
Cons ci ratio: 4.976538e-03	ci left: 1.445919e-01	ci right 1.453136e-01	k: 530526	n:3660000
KS ci ratio: 2.259357e-01	ci left: 7.295367e-05	ci right 9.178674e-05	k: 300	n:3660000
MAPK1   3660000 perm   6450 sec   (567 perm/sec)   p_kst 8.196721e-05   p_cons 1.449525e-01   p_joint 8.196721e-05

Joint ci ratio: 2.255613e-01	ci left: 7.301196e-05	ci right 9.182450e-05	k: 301	n:3670000
Cons ci ratio: 4.969429e-03	ci left: 1.446086e-01	ci right 1.453293e-01	k: 532035	n:3670000
KS ci ratio: 2.255613e-01	ci left: 7.301196e-05	ci right 9.182450e-05	k: 301	n:3670000
MAPK1   3670000 perm   6483 sec   (566 perm/sec)   p_kst 8.201635e-05   p_cons 1.449687e-01   p_joint 8.201635e-05

Joint ci ratio: 2.251888e-01	ci left: 7.306996e-05	ci right 9.186203e-05	k: 302	n:3680000
Cons ci ratio: 4.962670e-03	ci left: 1.446092e-01	ci right 1.453289e-01	k: 533485	n:3680000
KS ci ratio: 2.251888e-01	ci left: 7.306996e-05	ci right 9.186203e-05	k: 302	n:3680000
MAPK1   3680000 perm   6516 sec   (565 perm/sec)   p_kst 8.206522e-05   p_cons 1.449688e-01   p_joint 8.206522e-05

Joint ci ratio: 2.251888e-01	ci left: 7.287194e-05	ci right 9.161309e-05	k: 302	n:3690000
Cons ci ratio: 4.956417e-03	ci left: 1.445859e-01	ci right 1.453046e-01	k: 534847	n:3690000
KS ci ratio: 2.251888e-01	ci left: 7.287194e-05	ci right 9.161309e-05	k: 302	n:3690000
MAPK1   3690000 perm   6549 sec   (563 perm/sec)   p_kst 8.184282e-05   p_cons 1.449450e-01   p_joint 8.184282e-05

Joint ci ratio: 2.251889e-01	ci left: 7.267498e-05	ci right 9.136549e-05	k: 302	n:3700000
Cons ci ratio: 4.949425e-03	ci left: 1.446009e-01	ci right 1.453186e-01	k: 536350	n:3700000
KS ci ratio: 2.251889e-01	ci left: 7.267498e-05	ci right 9.136549e-05	k: 302	n:3700000
MAPK1   3700000 perm   6583 sec   (562 perm/sec)   p_kst 8.162162e-05   p_cons 1.449595e-01   p_joint 8.162162e-05

Joint ci ratio: 2.251889e-01	ci left: 7.247909e-05	ci right 9.111922e-05	k: 302	n:3710000
Cons ci ratio: 4.942759e-03	ci left: 1.446009e-01	ci right 1.453177e-01	k: 537798	n:3710000
KS ci ratio: 2.251889e-01	ci left: 7.247909e-05	ci right 9.111922e-05	k: 302	n:3710000
MAPK1   3710000 perm   6617 sec   (561 perm/sec)   p_kst 8.140162e-05   p_cons 1.449590e-01   p_joint 8.140162e-05

Joint ci ratio: 2.240822e-01	ci left: 7.304534e-05	ci right 9.172602e-05	k: 305	n:3720000
Cons ci ratio: 4.935852e-03	ci left: 1.446144e-01	ci right 1.453302e-01	k: 539296	n:3720000
KS ci ratio: 2.240822e-01	ci left: 7.304534e-05	ci right 9.172602e-05	k: 305	n:3720000
MAPK1   3720000 perm   6650 sec   (559 perm/sec)   p_kst 8.198925e-05   p_cons 1.449720e-01   p_joint 8.198925e-05

Joint ci ratio: 2.237170e-01	ci left: 7.310257e-05	ci right 9.176322e-05	k: 306	n:3730000
Cons ci ratio: 4.929112e-03	ci left: 1.446209e-01	ci right 1.453357e-01	k: 540768	n:3730000
KS ci ratio: 2.237170e-01	ci left: 7.310257e-05	ci right 9.176322e-05	k: 306	n:3730000
MAPK1   3730000 perm   6683 sec   (558 perm/sec)   p_kst 8.203753e-05   p_cons 1.449780e-01   p_joint 8.203753e-05

Joint ci ratio: 2.233535e-01	ci left: 7.315951e-05	ci right 9.180019e-05	k: 307	n:3740000
Cons ci ratio: 4.922798e-03	ci left: 1.446072e-01	ci right 1.453211e-01	k: 542165	n:3740000
KS ci ratio: 2.233535e-01	ci left: 7.315951e-05	ci right 9.180019e-05	k: 307	n:3740000
MAPK1   3740000 perm   6717 sec   (557 perm/sec)   p_kst 8.208556e-05   p_cons 1.449639e-01   p_joint 8.208556e-05

Joint ci ratio: 2.229918e-01	ci left: 7.321618e-05	ci right 9.183694e-05	k: 308	n:3750000
Cons ci ratio: 4.916392e-03	ci left: 1.445996e-01	ci right 1.453125e-01	k: 543584	n:3750000
KS ci ratio: 2.229918e-01	ci left: 7.321618e-05	ci right 9.183694e-05	k: 308	n:3750000
MAPK1   3750000 perm   6752 sec   (555 perm/sec)   p_kst 8.213333e-05   p_cons 1.449557e-01   p_joint 8.213333e-05

Joint ci ratio: 2.229918e-01	ci left: 7.302146e-05	ci right 9.159269e-05	k: 308	n:3760000
Cons ci ratio: 4.909679e-03	ci left: 1.446086e-01	ci right 1.453206e-01	k: 545066	n:3760000
KS ci ratio: 2.229918e-01	ci left: 7.302146e-05	ci right 9.159269e-05	k: 308	n:3760000
MAPK1   3760000 perm   6785 sec   (554 perm/sec)   p_kst 8.191489e-05   p_cons 1.449644e-01   p_joint 8.191489e-05

Joint ci ratio: 2.226319e-01	ci left: 7.307822e-05	ci right 9.162977e-05	k: 309	n:3770000
Cons ci ratio: 4.903009e-03	ci left: 1.446169e-01	ci right 1.453279e-01	k: 546545	n:3770000
KS ci ratio: 2.226319e-01	ci left: 7.307822e-05	ci right 9.162977e-05	k: 309	n:3770000
MAPK1   3770000 perm   6819 sec   (553 perm/sec)   p_kst 8.196286e-05   p_cons 1.449721e-01   p_joint 8.196286e-05

Joint ci ratio: 2.226319e-01	ci left: 7.288489e-05	ci right 9.138736e-05	k: 309	n:3780000
Cons ci ratio: 4.896759e-03	ci left: 1.446053e-01	ci right 1.453154e-01	k: 547949	n:3780000
KS ci ratio: 2.226319e-01	ci left: 7.288489e-05	ci right 9.138736e-05	k: 309	n:3780000
MAPK1   3780000 perm   6853 sec   (552 perm/sec)   p_kst 8.174603e-05   p_cons 1.449601e-01   p_joint 8.174603e-05

Joint ci ratio: 2.226319e-01	ci left: 7.269258e-05	ci right 9.114624e-05	k: 309	n:3790000
Cons ci ratio: 4.890292e-03	ci left: 1.446059e-01	ci right 1.453150e-01	k: 549399	n:3790000
KS ci ratio: 2.226319e-01	ci left: 7.269258e-05	ci right 9.114624e-05	k: 309	n:3790000
MAPK1   3790000 perm   6887 sec   (550 perm/sec)   p_kst 8.153034e-05   p_cons 1.449602e-01   p_joint 8.153034e-05

Joint ci ratio: 2.226319e-01	ci left: 7.250128e-05	ci right 9.090638e-05	k: 309	n:3800000
Cons ci ratio: 4.884074e-03	ci left: 1.445951e-01	ci right 1.453033e-01	k: 550806	n:3800000
KS ci ratio: 2.226319e-01	ci left: 7.250128e-05	ci right 9.090638e-05	k: 309	n:3800000
MAPK1   3800000 perm   6921 sec   (549 perm/sec)   p_kst 8.131579e-05   p_cons 1.449489e-01   p_joint 8.131579e-05

Joint ci ratio: 2.226320e-01	ci left: 7.231099e-05	ci right 9.066778e-05	k: 309	n:3810000
Cons ci ratio: 4.877539e-03	ci left: 1.446018e-01	ci right 1.453090e-01	k: 552279	n:3810000
KS ci ratio: 2.226320e-01	ci left: 7.231099e-05	ci right 9.066778e-05	k: 309	n:3810000
MAPK1   3810000 perm   6955 sec   (548 perm/sec)   p_kst 8.110236e-05   p_cons 1.449551e-01   p_joint 8.110236e-05

Joint ci ratio: 2.226320e-01	ci left: 7.212169e-05	ci right 9.043043e-05	k: 309	n:3820000
Cons ci ratio: 4.871082e-03	ci left: 1.446057e-01	ci right 1.453121e-01	k: 553742	n:3820000
KS ci ratio: 2.226320e-01	ci left: 7.212169e-05	ci right 9.043043e-05	k: 309	n:3820000
MAPK1   3820000 perm   6988 sec   (547 perm/sec)   p_kst 8.089005e-05   p_cons 1.449586e-01   p_joint 8.089005e-05

Joint ci ratio: 2.226320e-01	ci left: 7.193338e-05	ci right 9.019432e-05	k: 309	n:3830000
Cons ci ratio: 4.864347e-03	ci left: 1.446251e-01	ci right 1.453305e-01	k: 555264	n:3830000
KS ci ratio: 2.226320e-01	ci left: 7.193338e-05	ci right 9.019432e-05	k: 309	n:3830000
MAPK1   3830000 perm   7022 sec   (545 perm/sec)   p_kst 8.067885e-05   p_cons 1.449775e-01   p_joint 8.067885e-05

Joint ci ratio: 2.226320e-01	ci left: 7.174606e-05	ci right 8.995944e-05	k: 309	n:3840000
Cons ci ratio: 4.857983e-03	ci left: 1.446269e-01	ci right 1.453315e-01	k: 556719	n:3840000
KS ci ratio: 2.226320e-01	ci left: 7.174606e-05	ci right 8.995944e-05	k: 309	n:3840000
MAPK1   3840000 perm   7057 sec   (544 perm/sec)   p_kst 8.046875e-05   p_cons 1.449789e-01   p_joint 8.046875e-05

Joint ci ratio: 2.219173e-01	ci left: 7.205026e-05	ci right 9.027414e-05	k: 311	n:3850000
Cons ci ratio: 4.851907e-03	ci left: 1.446152e-01	ci right 1.453188e-01	k: 558122	n:3850000
KS ci ratio: 2.219173e-01	ci left: 7.205026e-05	ci right 9.027414e-05	k: 311	n:3850000
MAPK1   3850000 perm   7091 sec   (543 perm/sec)   p_kst 8.077922e-05   p_cons 1.449668e-01   p_joint 8.077922e-05

Joint ci ratio: 2.215625e-01	ci left: 7.210828e-05	ci right 9.031370e-05	k: 312	n:3860000
Cons ci ratio: 4.845267e-03	ci left: 1.446336e-01	ci right 1.453363e-01	k: 559641	n:3860000
KS ci ratio: 2.215625e-01	ci left: 7.210828e-05	ci right 9.031370e-05	k: 312	n:3860000
MAPK1   3860000 perm   7126 sec   (542 perm/sec)   p_kst 8.082902e-05   p_cons 1.449847e-01   p_joint 8.082902e-05

Joint ci ratio: 2.215625e-01	ci left: 7.192196e-05	ci right 9.008033e-05	k: 312	n:3870000
Cons ci ratio: 4.839033e-03	ci left: 1.446326e-01	ci right 1.453344e-01	k: 561085	n:3870000
KS ci ratio: 2.215625e-01	ci left: 7.192196e-05	ci right 9.008033e-05	k: 312	n:3870000
MAPK1   3870000 perm   7160 sec   (540 perm/sec)   p_kst 8.062016e-05   p_cons 1.449832e-01   p_joint 8.062016e-05

Joint ci ratio: 2.215625e-01	ci left: 7.173659e-05	ci right 8.984816e-05	k: 312	n:3880000
Cons ci ratio: 4.832802e-03	ci left: 1.446325e-01	ci right 1.453335e-01	k: 562533	n:3880000
KS ci ratio: 2.215625e-01	ci left: 7.173659e-05	ci right 8.984816e-05	k: 312	n:3880000
MAPK1   3880000 perm   7194 sec   (539 perm/sec)   p_kst 8.041237e-05   p_cons 1.449827e-01   p_joint 8.041237e-05

Joint ci ratio: 2.208580e-01	ci left: 7.203783e-05	ci right 9.015977e-05	k: 314	n:3890000
Cons ci ratio: 4.826726e-03	ci left: 1.446258e-01	ci right 1.453258e-01	k: 563955	n:3890000
KS ci ratio: 2.208580e-01	ci left: 7.203783e-05	ci right 9.015977e-05	k: 314	n:3890000
MAPK1   3890000 perm   7229 sec   (538 perm/sec)   p_kst 8.071979e-05   p_cons 1.449756e-01   p_joint 8.071979e-05

Joint ci ratio: 2.205083e-01	ci left: 7.209536e-05	ci right 9.019915e-05	k: 315	n:3900000
Cons ci ratio: 4.820507e-03	ci left: 1.446276e-01	ci right 1.453267e-01	k: 565410	n:3900000
KS ci ratio: 2.205083e-01	ci left: 7.209536e-05	ci right 9.019915e-05	k: 315	n:3900000
MAPK1   3900000 perm   7265 sec   (537 perm/sec)   p_kst 8.076923e-05   p_cons 1.449769e-01   p_joint 8.076923e-05

Joint ci ratio: 2.201602e-01	ci left: 7.215261e-05	ci right 9.023831e-05	k: 316	n:3910000
Cons ci ratio: 4.814174e-03	ci left: 1.446366e-01	ci right 1.453348e-01	k: 566893	n:3910000
KS ci ratio: 2.201602e-01	ci left: 7.215261e-05	ci right 9.023831e-05	k: 316	n:3910000
MAPK1   3910000 perm   7300 sec   (536 perm/sec)   p_kst 8.081841e-05   p_cons 1.449854e-01   p_joint 8.081841e-05

Joint ci ratio: 2.201602e-01	ci left: 7.196855e-05	ci right 9.000811e-05	k: 316	n:3920000
Cons ci ratio: 4.807890e-03	ci left: 1.446442e-01	ci right 1.453415e-01	k: 568371	n:3920000
KS ci ratio: 2.201602e-01	ci left: 7.196855e-05	ci right 9.000811e-05	k: 316	n:3920000
MAPK1   3920000 perm   7335 sec   (534 perm/sec)   p_kst 8.061224e-05   p_cons 1.449926e-01   p_joint 8.061224e-05

Joint ci ratio: 2.198138e-01	ci left: 7.202585e-05	ci right 9.004753e-05	k: 317	n:3930000
Cons ci ratio: 4.801750e-03	ci left: 1.446457e-01	ci right 1.453421e-01	k: 569825	n:3930000
KS ci ratio: 2.198138e-01	ci left: 7.202585e-05	ci right 9.004753e-05	k: 317	n:3930000
MAPK1   3930000 perm   7370 sec   (533 perm/sec)   p_kst 8.066158e-05   p_cons 1.449936e-01   p_joint 8.066158e-05

Joint ci ratio: 2.198138e-01	ci left: 7.184305e-05	ci right 8.981899e-05	k: 317	n:3940000
Cons ci ratio: 4.795343e-03	ci left: 1.446621e-01	ci right 1.453577e-01	k: 571338	n:3940000
KS ci ratio: 2.198138e-01	ci left: 7.184305e-05	ci right 8.981899e-05	k: 317	n:3940000
MAPK1   3940000 perm   7405 sec   (532 perm/sec)   p_kst 8.045685e-05   p_cons 1.450096e-01   p_joint 8.045685e-05

Joint ci ratio: 2.194690e-01	ci left: 7.190040e-05	ci right 8.985867e-05	k: 318	n:3950000
Cons ci ratio: 4.789641e-03	ci left: 1.446433e-01	ci right 1.453380e-01	k: 572712	n:3950000
KS ci ratio: 2.194690e-01	ci left: 7.190040e-05	ci right 8.985867e-05	k: 318	n:3950000
MAPK1   3950000 perm   7440 sec   (531 perm/sec)   p_kst 8.050633e-05   p_cons 1.449904e-01   p_joint 8.050633e-05

Joint ci ratio: 2.191258e-01	ci left: 7.195749e-05	ci right 8.989812e-05	k: 319	n:3960000
Cons ci ratio: 4.783570e-03	ci left: 1.446448e-01	ci right 1.453386e-01	k: 574166	n:3960000
KS ci ratio: 2.191258e-01	ci left: 7.195749e-05	ci right 8.989812e-05	k: 319	n:3960000
MAPK1   3960000 perm   7475 sec   (530 perm/sec)   p_kst 8.055556e-05   p_cons 1.449914e-01   p_joint 8.055556e-05

Joint ci ratio: 2.191258e-01	ci left: 7.177624e-05	ci right 8.967168e-05	k: 319	n:3970000
Cons ci ratio: 4.777521e-03	ci left: 1.446462e-01	ci right 1.453392e-01	k: 575620	n:3970000
KS ci ratio: 2.191258e-01	ci left: 7.177624e-05	ci right 8.967168e-05	k: 319	n:3970000
MAPK1   3970000 perm   7511 sec   (529 perm/sec)   p_kst 8.035264e-05   p_cons 1.449924e-01   p_joint 8.035264e-05

Joint ci ratio: 2.181058e-01	ci left: 7.230840e-05	ci right 9.024135e-05	k: 322	n:3980000
Cons ci ratio: 4.771356e-03	ci left: 1.446550e-01	ci right 1.453471e-01	k: 577103	n:3980000
KS ci ratio: 2.181058e-01	ci left: 7.230840e-05	ci right 9.024135e-05	k: 322	n:3980000
MAPK1   3980000 perm   7547 sec   (527 perm/sec)   p_kst 8.090452e-05   p_cons 1.450008e-01   p_joint 8.090452e-05

Joint ci ratio: 2.181058e-01	ci left: 7.212717e-05	ci right 9.001518e-05	k: 322	n:3990000
Cons ci ratio: 4.765493e-03	ci left: 1.446491e-01	ci right 1.453403e-01	k: 578528	n:3990000
KS ci ratio: 2.181058e-01	ci left: 7.212717e-05	ci right 9.001518e-05	k: 322	n:3990000
MAPK1   3990000 perm   7582 sec   (526 perm/sec)   p_kst 8.070175e-05   p_cons 1.449945e-01   p_joint 8.070175e-05

Joint ci ratio: 2.174336e-01	ci left: 7.241959e-05	ci right 9.031737e-05	k: 324	n:4000000
Cons ci ratio: 4.759398e-03	ci left: 1.446566e-01	ci right 1.453469e-01	k: 580006	n:4000000
KS ci ratio: 2.174336e-01	ci left: 7.241959e-05	ci right 9.031737e-05	k: 324	n:4000000
MAPK1   4000000 perm   7618 sec   (525 perm/sec)   p_kst 8.100000e-05   p_cons 1.450015e-01   p_joint 8.100000e-05

Joint ci ratio: 2.170999e-01	ci left: 7.247480e-05	ci right 9.035506e-05	k: 325	n:4010000
Cons ci ratio: 4.753321e-03	ci left: 1.446642e-01	ci right 1.453537e-01	k: 581485	n:4010000
KS ci ratio: 2.170999e-01	ci left: 7.247480e-05	ci right 9.035506e-05	k: 325	n:4010000
MAPK1   4010000 perm   7653 sec   (524 perm/sec)   p_kst 8.104738e-05   p_cons 1.450087e-01   p_joint 8.104738e-05

Joint ci ratio: 2.164369e-01	ci left: 7.276502e-05	ci right 9.065478e-05	k: 327	n:4020000
Cons ci ratio: 4.747506e-03	ci left: 1.446594e-01	ci right 1.453481e-01	k: 582914	n:4020000
KS ci ratio: 2.164369e-01	ci left: 7.276502e-05	ci right 9.065478e-05	k: 327	n:4020000
MAPK1   4020000 perm   7690 sec   (523 perm/sec)   p_kst 8.134328e-05   p_cons 1.450035e-01   p_joint 8.134328e-05

Joint ci ratio: 2.161077e-01	ci left: 7.281916e-05	ci right 9.069139e-05	k: 328	n:4030000
Cons ci ratio: 4.741622e-03	ci left: 1.446593e-01	ci right 1.453471e-01	k: 584362	n:4030000
KS ci ratio: 2.161077e-01	ci left: 7.281916e-05	ci right 9.069139e-05	k: 328	n:4030000
MAPK1   4030000 perm   7726 sec   (522 perm/sec)   p_kst 8.138958e-05   p_cons 1.450030e-01   p_joint 8.138958e-05

Joint ci ratio: 2.161078e-01	ci left: 7.263891e-05	ci right 9.046691e-05	k: 328	n:4040000
Cons ci ratio: 4.735897e-03	ci left: 1.446521e-01	ci right 1.453390e-01	k: 585781	n:4040000
KS ci ratio: 2.161078e-01	ci left: 7.263891e-05	ci right 9.046691e-05	k: 328	n:4040000
MAPK1   4040000 perm   7762 sec   (520 perm/sec)   p_kst 8.118812e-05   p_cons 1.449953e-01   p_joint 8.118812e-05

Joint ci ratio: 2.161078e-01	ci left: 7.245955e-05	ci right 9.024353e-05	k: 328	n:4050000
Cons ci ratio: 4.729914e-03	ci left: 1.446594e-01	ci right 1.453455e-01	k: 587259	n:4050000
KS ci ratio: 2.161078e-01	ci left: 7.245955e-05	ci right 9.024353e-05	k: 328	n:4050000
MAPK1   4050000 perm   7798 sec   (519 perm/sec)   p_kst 8.098765e-05   p_cons 1.450022e-01   p_joint 8.098765e-05

Joint ci ratio: 2.157801e-01	ci left: 7.251407e-05	ci right 9.028086e-05	k: 329	n:4060000
Cons ci ratio: 4.723893e-03	ci left: 1.446699e-01	ci right 1.453552e-01	k: 588750	n:4060000
KS ci ratio: 2.157801e-01	ci left: 7.251407e-05	ci right 9.028086e-05	k: 329	n:4060000
MAPK1   4060000 perm   7835 sec   (518 perm/sec)   p_kst 8.103448e-05   p_cons 1.450123e-01   p_joint 8.103448e-05

Joint ci ratio: 2.151291e-01	ci left: 7.280079e-05	ci right 9.057692e-05	k: 331	n:4070000
Cons ci ratio: 4.718115e-03	ci left: 1.446689e-01	ci right 1.453533e-01	k: 590194	n:4070000
KS ci ratio: 2.151291e-01	ci left: 7.280079e-05	ci right 9.057692e-05	k: 331	n:4070000
MAPK1   4070000 perm   7871 sec   (517 perm/sec)   p_kst 8.132678e-05   p_cons 1.450108e-01   p_joint 8.132678e-05

Joint ci ratio: 2.148059e-01	ci left: 7.285426e-05	ci right 9.061319e-05	k: 332	n:4080000
Cons ci ratio: 4.712381e-03	ci left: 1.446666e-01	ci right 1.453501e-01	k: 591633	n:4080000
KS ci ratio: 2.148059e-01	ci left: 7.285426e-05	ci right 9.061319e-05	k: 332	n:4080000
MAPK1   4080000 perm   7907 sec   (516 perm/sec)   p_kst 8.137255e-05   p_cons 1.450081e-01   p_joint 8.137255e-05

Joint ci ratio: 2.148059e-01	ci left: 7.267613e-05	ci right 9.039164e-05	k: 332	n:4090000
Cons ci ratio: 4.706956e-03	ci left: 1.446491e-01	ci right 1.453318e-01	k: 593010	n:4090000
KS ci ratio: 2.148059e-01	ci left: 7.267613e-05	ci right 9.039164e-05	k: 332	n:4090000
MAPK1   4090000 perm   7944 sec   (515 perm/sec)   p_kst 8.117359e-05   p_cons 1.449902e-01   p_joint 8.117359e-05

Joint ci ratio: 2.148059e-01	ci left: 7.249887e-05	ci right 9.017117e-05	k: 332	n:4100000
Cons ci ratio: 4.701073e-03	ci left: 1.446569e-01	ci right 1.453387e-01	k: 594490	n:4100000
KS ci ratio: 2.148059e-01	ci left: 7.249887e-05	ci right 9.017117e-05	k: 332	n:4100000
MAPK1   4100000 perm   7981 sec   (514 perm/sec)   p_kst 8.097561e-05   p_cons 1.449976e-01   p_joint 8.097561e-05

Joint ci ratio: 2.148059e-01	ci left: 7.232247e-05	ci right 8.995178e-05	k: 332	n:4110000
Cons ci ratio: 4.695166e-03	ci left: 1.446670e-01	ci right 1.453481e-01	k: 595980	n:4110000
KS ci ratio: 2.148059e-01	ci left: 7.232247e-05	ci right 8.995178e-05	k: 332	n:4110000
MAPK1   4110000 perm   8018 sec   (513 perm/sec)   p_kst 8.077859e-05   p_cons 1.450073e-01   p_joint 8.077859e-05

Joint ci ratio: 2.141637e-01	ci left: 7.260629e-05	ci right 9.024492e-05	k: 334	n:4120000
Cons ci ratio: 4.689382e-03	ci left: 1.446718e-01	ci right 1.453520e-01	k: 597448	n:4120000
KS ci ratio: 2.141637e-01	ci left: 7.260629e-05	ci right 9.024492e-05	k: 334	n:4120000
MAPK1   4120000 perm   8055 sec   (511 perm/sec)   p_kst 8.106796e-05   p_cons 1.450117e-01   p_joint 8.106796e-05

Joint ci ratio: 2.138448e-01	ci left: 7.265965e-05	ci right 9.028150e-05	k: 335	n:4130000
Cons ci ratio: 4.683634e-03	ci left: 1.446758e-01	ci right 1.453552e-01	k: 598913	n:4130000
KS ci ratio: 2.138448e-01	ci left: 7.265965e-05	ci right 9.028150e-05	k: 335	n:4130000
MAPK1   4130000 perm   8092 sec   (510 perm/sec)   p_kst 8.111380e-05   p_cons 1.450153e-01   p_joint 8.111380e-05

Joint ci ratio: 2.138448e-01	ci left: 7.248414e-05	ci right 9.006343e-05	k: 335	n:4140000
Cons ci ratio: 4.678143e-03	ci left: 1.446672e-01	ci right 1.453458e-01	k: 600326	n:4140000
KS ci ratio: 2.138448e-01	ci left: 7.248414e-05	ci right 9.006343e-05	k: 335	n:4140000
MAPK1   4140000 perm   8129 sec   (509 perm/sec)   p_kst 8.091787e-05   p_cons 1.450063e-01   p_joint 8.091787e-05

Joint ci ratio: 2.135273e-01	ci left: 7.253755e-05	ci right 9.010025e-05	k: 336	n:4150000
Cons ci ratio: 4.672426e-03	ci left: 1.446717e-01	ci right 1.453495e-01	k: 601793	n:4150000
KS ci ratio: 2.135273e-01	ci left: 7.253755e-05	ci right 9.010025e-05	k: 336	n:4150000
MAPK1   4150000 perm   8167 sec   (508 perm/sec)   p_kst 8.096386e-05   p_cons 1.450104e-01   p_joint 8.096386e-05

Joint ci ratio: 2.128965e-01	ci left: 7.281828e-05	ci right 9.039006e-05	k: 338	n:4160000
Cons ci ratio: 4.666817e-03	ci left: 1.446716e-01	ci right 1.453486e-01	k: 603241	n:4160000
KS ci ratio: 2.128965e-01	ci left: 7.281828e-05	ci right 9.039006e-05	k: 338	n:4160000
MAPK1   4160000 perm   8205 sec   (507 perm/sec)   p_kst 8.125000e-05   p_cons 1.450099e-01   p_joint 8.125000e-05

Joint ci ratio: 2.125832e-01	ci left: 7.287069e-05	ci right 9.042587e-05	k: 339	n:4170000
Cons ci ratio: 4.661277e-03	ci left: 1.446689e-01	ci right 1.453450e-01	k: 604678	n:4170000
KS ci ratio: 2.125832e-01	ci left: 7.287069e-05	ci right 9.042587e-05	k: 339	n:4170000
MAPK1   4170000 perm   8243 sec   (506 perm/sec)   p_kst 8.129496e-05   p_cons 1.450067e-01   p_joint 8.129496e-05

Joint ci ratio: 2.125832e-01	ci left: 7.269635e-05	ci right 9.020954e-05	k: 339	n:4180000
Cons ci ratio: 4.655698e-03	ci left: 1.446693e-01	ci right 1.453446e-01	k: 606128	n:4180000
KS ci ratio: 2.125832e-01	ci left: 7.269635e-05	ci right 9.020954e-05	k: 339	n:4180000
MAPK1   4180000 perm   8281 sec   (505 perm/sec)   p_kst 8.110048e-05   p_cons 1.450067e-01   p_joint 8.110048e-05

Joint ci ratio: 2.119606e-01	ci left: 7.297481e-05	ci right 9.049690e-05	k: 341	n:4190000
Cons ci ratio: 4.649956e-03	ci left: 1.446794e-01	ci right 1.453540e-01	k: 607619	n:4190000
KS ci ratio: 2.119606e-01	ci left: 7.297481e-05	ci right 9.049690e-05	k: 341	n:4190000
MAPK1   4190000 perm   8318 sec   (504 perm/sec)   p_kst 8.138425e-05   p_cons 1.450165e-01   p_joint 8.138425e-05

Joint ci ratio: 2.116514e-01	ci left: 7.302653e-05	ci right 9.053214e-05	k: 342	n:4200000
Cons ci ratio: 4.643931e-03	ci left: 1.447057e-01	ci right 1.453795e-01	k: 609178	n:4200000
KS ci ratio: 2.116514e-01	ci left: 7.302653e-05	ci right 9.053214e-05	k: 342	n:4200000
MAPK1   4200000 perm   8355 sec   (503 perm/sec)   p_kst 8.142857e-05   p_cons 1.450424e-01   p_joint 8.142857e-05

Joint ci ratio: 2.110370e-01	ci left: 7.330298e-05	ci right 9.081726e-05	k: 344	n:4210000
Cons ci ratio: 4.638193e-03	ci left: 1.447179e-01	ci right 1.453909e-01	k: 610678	n:4210000
KS ci ratio: 2.110370e-01	ci left: 7.330298e-05	ci right 9.081726e-05	k: 344	n:4210000
MAPK1   4210000 perm   8394 sec   (502 perm/sec)   p_kst 8.171021e-05   p_cons 1.450542e-01   p_joint 8.171021e-05

Joint ci ratio: 2.107318e-01	ci left: 7.335373e-05	ci right 9.085152e-05	k: 345	n:4220000
Cons ci ratio: 4.632479e-03	ci left: 1.447298e-01	ci right 1.454020e-01	k: 612177	n:4220000
KS ci ratio: 2.107318e-01	ci left: 7.335373e-05	ci right 9.085152e-05	k: 345	n:4220000
MAPK1   4220000 perm   8432 sec   (500 perm/sec)   p_kst 8.175355e-05   p_cons 1.450656e-01   p_joint 8.175355e-05

Joint ci ratio: 2.107319e-01	ci left: 7.318032e-05	ci right 9.063674e-05	k: 345	n:4230000
Cons ci ratio: 4.627043e-03	ci left: 1.447279e-01	ci right 1.453993e-01	k: 613618	n:4230000
KS ci ratio: 2.107319e-01	ci left: 7.318032e-05	ci right 9.063674e-05	k: 345	n:4230000
MAPK1   4230000 perm   8470 sec   (499 perm/sec)   p_kst 8.156028e-05   p_cons 1.450634e-01   p_joint 8.156028e-05

Joint ci ratio: 2.104280e-01	ci left: 7.323114e-05	ci right 9.067124e-05	k: 346	n:4240000
Cons ci ratio: 4.621700e-03	ci left: 1.447220e-01	ci right 1.453926e-01	k: 615042	n:4240000
KS ci ratio: 2.104280e-01	ci left: 7.323114e-05	ci right 9.067124e-05	k: 346	n:4240000
MAPK1   4240000 perm   8507 sec   (498 perm/sec)   p_kst 8.160377e-05   p_cons 1.450571e-01   p_joint 8.160377e-05

Joint ci ratio: 2.098241e-01	ci left: 7.350466e-05	ci right 9.095321e-05	k: 348	n:4250000
Cons ci ratio: 4.616372e-03	ci left: 1.447164e-01	ci right 1.453862e-01	k: 616467	n:4250000
KS ci ratio: 2.098241e-01	ci left: 7.350466e-05	ci right 9.095321e-05	k: 348	n:4250000
MAPK1   4250000 perm   8545 sec   (497 perm/sec)   p_kst 8.188235e-05   p_cons 1.450511e-01   p_joint 8.188235e-05

Joint ci ratio: 2.095242e-01	ci left: 7.355453e-05	ci right 9.098676e-05	k: 349	n:4260000
Cons ci ratio: 4.610721e-03	ci left: 1.447291e-01	ci right 1.453982e-01	k: 617970	n:4260000
KS ci ratio: 2.095242e-01	ci left: 7.355453e-05	ci right 9.098676e-05	k: 349	n:4260000
MAPK1   4260000 perm   8584 sec   (496 perm/sec)   p_kst 8.192488e-05   p_cons 1.450634e-01   p_joint 8.192488e-05

Joint ci ratio: 2.095242e-01	ci left: 7.338227e-05	ci right 9.077367e-05	k: 349	n:4270000
Cons ci ratio: 4.605670e-03	ci left: 1.447106e-01	ci right 1.453789e-01	k: 619340	n:4270000
KS ci ratio: 2.095242e-01	ci left: 7.338227e-05	ci right 9.077367e-05	k: 349	n:4270000
MAPK1   4270000 perm   8622 sec   (495 perm/sec)   p_kst 8.173302e-05   p_cons 1.450445e-01   p_joint 8.173302e-05

Joint ci ratio: 2.095242e-01	ci left: 7.321081e-05	ci right 9.056159e-05	k: 349	n:4280000
Cons ci ratio: 4.599963e-03	ci left: 1.447284e-01	ci right 1.453959e-01	k: 620865	n:4280000
KS ci ratio: 2.095242e-01	ci left: 7.321081e-05	ci right 9.056159e-05	k: 349	n:4280000
MAPK1   4280000 perm   8661 sec   (494 perm/sec)   p_kst 8.154206e-05   p_cons 1.450619e-01   p_joint 8.154206e-05

Joint ci ratio: 2.095242e-01	ci left: 7.304016e-05	ci right 9.035049e-05	k: 349	n:4290000
Cons ci ratio: 4.594697e-03	ci left: 1.447235e-01	ci right 1.453902e-01	k: 622293	n:4290000
KS ci ratio: 2.095242e-01	ci left: 7.304016e-05	ci right 9.035049e-05	k: 349	n:4290000
MAPK1   4290000 perm   8700 sec   (493 perm/sec)   p_kst 8.135198e-05   p_cons 1.450566e-01   p_joint 8.135198e-05

Joint ci ratio: 2.095243e-01	ci left: 7.287030e-05	ci right 9.014037e-05	k: 349	n:4300000
Cons ci ratio: 4.589396e-03	ci left: 1.447215e-01	ci right 1.453874e-01	k: 623733	n:4300000
KS ci ratio: 2.095243e-01	ci left: 7.287030e-05	ci right 9.014037e-05	k: 349	n:4300000
MAPK1   4300000 perm   8739 sec   (492 perm/sec)   p_kst 8.116279e-05   p_cons 1.450542e-01   p_joint 8.116279e-05

Joint ci ratio: 2.092256e-01	ci left: 7.292108e-05	ci right 9.017540e-05	k: 350	n:4310000
Cons ci ratio: 4.584239e-03	ci left: 1.447127e-01	ci right 1.453778e-01	k: 625144	n:4310000
KS ci ratio: 2.092256e-01	ci left: 7.292108e-05	ci right 9.017540e-05	k: 350	n:4310000
MAPK1   4310000 perm   8777 sec   (491 perm/sec)   p_kst 8.120650e-05   p_cons 1.450450e-01   p_joint 8.120650e-05

Joint ci ratio: 2.092256e-01	ci left: 7.275228e-05	ci right 8.996666e-05	k: 350	n:4320000
Cons ci ratio: 4.579081e-03	ci left: 1.447049e-01	ci right 1.453692e-01	k: 626559	n:4320000
KS ci ratio: 2.092256e-01	ci left: 7.275228e-05	ci right 8.996666e-05	k: 350	n:4320000
MAPK1   4320000 perm   8817 sec   (490 perm/sec)   p_kst 8.101852e-05   p_cons 1.450368e-01   p_joint 8.101852e-05

Joint ci ratio: 2.092256e-01	ci left: 7.258426e-05	ci right 8.975888e-05	k: 350	n:4330000
Cons ci ratio: 4.573767e-03	ci left: 1.447065e-01	ci right 1.453701e-01	k: 628015	n:4330000
KS ci ratio: 2.092256e-01	ci left: 7.258426e-05	ci right 8.975888e-05	k: 350	n:4330000
MAPK1   4330000 perm   8856 sec   (489 perm/sec)   p_kst 8.083141e-05   p_cons 1.450381e-01   p_joint 8.083141e-05

Joint ci ratio: 2.086320e-01	ci left: 7.285373e-05	ci right 9.003697e-05	k: 352	n:4340000
Cons ci ratio: 4.568449e-03	ci left: 1.447094e-01	ci right 1.453722e-01	k: 629476	n:4340000
KS ci ratio: 2.086320e-01	ci left: 7.285373e-05	ci right 9.003697e-05	k: 352	n:4340000
MAPK1   4340000 perm   8896 sec   (488 perm/sec)   p_kst 8.110599e-05   p_cons 1.450406e-01   p_joint 8.110599e-05

Joint ci ratio: 2.080435e-01	ci left: 7.312204e-05	ci right 9.031371e-05	k: 354	n:4350000
Cons ci ratio: 4.563176e-03	ci left: 1.447108e-01	ci right 1.453729e-01	k: 630931	n:4350000
KS ci ratio: 2.080435e-01	ci left: 7.312204e-05	ci right 9.031371e-05	k: 354	n:4350000
MAPK1   4350000 perm   8936 sec   (487 perm/sec)   p_kst 8.137931e-05   p_cons 1.450416e-01   p_joint 8.137931e-05

Joint ci ratio: 2.077511e-01	ci left: 7.317175e-05	ci right 9.034785e-05	k: 355	n:4360000
Cons ci ratio: 4.557916e-03	ci left: 1.447125e-01	ci right 1.453738e-01	k: 632387	n:4360000
KS ci ratio: 2.077511e-01	ci left: 7.317175e-05	ci right 9.034785e-05	k: 355	n:4360000
MAPK1   4360000 perm   8975 sec   (486 perm/sec)   p_kst 8.142202e-05   p_cons 1.450429e-01   p_joint 8.142202e-05

Joint ci ratio: 2.077511e-01	ci left: 7.300430e-05	ci right 9.014110e-05	k: 355	n:4370000
Cons ci ratio: 4.552679e-03	ci left: 1.447139e-01	ci right 1.453744e-01	k: 633842	n:4370000
KS ci ratio: 2.077511e-01	ci left: 7.300430e-05	ci right 9.014110e-05	k: 355	n:4370000
MAPK1   4370000 perm   9014 sec   (485 perm/sec)   p_kst 8.123570e-05   p_cons 1.450439e-01   p_joint 8.123570e-05

Joint ci ratio: 2.074599e-01	ci left: 7.305407e-05	ci right 9.017547e-05	k: 356	n:4380000
Cons ci ratio: 4.547636e-03	ci left: 1.447057e-01	ci right 1.453655e-01	k: 635255	n:4380000
KS ci ratio: 2.074599e-01	ci left: 7.305407e-05	ci right 9.017547e-05	k: 356	n:4380000
MAPK1   4380000 perm   9053 sec   (484 perm/sec)   p_kst 8.127854e-05   p_cons 1.450354e-01   p_joint 8.127854e-05

Joint ci ratio: 2.071700e-01	ci left: 7.310362e-05	ci right 9.020965e-05	k: 357	n:4390000
Cons ci ratio: 4.542797e-03	ci left: 1.446874e-01	ci right 1.453464e-01	k: 636623	n:4390000
KS ci ratio: 2.071700e-01	ci left: 7.310362e-05	ci right 9.020965e-05	k: 357	n:4390000
MAPK1   4390000 perm   9093 sec   (483 perm/sec)   p_kst 8.132118e-05   p_cons 1.450166e-01   p_joint 8.132118e-05

Joint ci ratio: 2.071700e-01	ci left: 7.293748e-05	ci right 9.000463e-05	k: 357	n:4400000
Cons ci ratio: 4.537466e-03	ci left: 1.446968e-01	ci right 1.453550e-01	k: 638113	n:4400000
KS ci ratio: 2.071700e-01	ci left: 7.293748e-05	ci right 9.000463e-05	k: 357	n:4400000
MAPK1   4400000 perm   9133 sec   (482 perm/sec)   p_kst 8.113636e-05   p_cons 1.450257e-01   p_joint 8.113636e-05

Joint ci ratio: 2.068812e-01	ci left: 7.298709e-05	ci right 9.003904e-05	k: 358	n:4410000
Cons ci ratio: 4.532390e-03	ci left: 1.446932e-01	ci right 1.453508e-01	k: 639546	n:4410000
KS ci ratio: 2.068812e-01	ci left: 7.298709e-05	ci right 9.003904e-05	k: 358	n:4410000
MAPK1   4410000 perm   9174 sec   (481 perm/sec)   p_kst 8.117914e-05   p_cons 1.450218e-01   p_joint 8.117914e-05

Joint ci ratio: 2.063073e-01	ci left: 7.325104e-05	ci right 9.031119e-05	k: 360	n:4420000
Cons ci ratio: 4.527331e-03	ci left: 1.446897e-01	ci right 1.453465e-01	k: 640979	n:4420000
KS ci ratio: 2.063073e-01	ci left: 7.325104e-05	ci right 9.031119e-05	k: 360	n:4420000
MAPK1   4420000 perm   9214 sec   (480 perm/sec)   p_kst 8.144796e-05   p_cons 1.450179e-01   p_joint 8.144796e-05

Joint ci ratio: 2.057382e-01	ci left: 7.351387e-05	ci right 9.058205e-05	k: 362	n:4430000
Cons ci ratio: 4.521812e-03	ci left: 1.447124e-01	ci right 1.453684e-01	k: 642528	n:4430000
KS ci ratio: 2.057382e-01	ci left: 7.351387e-05	ci right 9.058205e-05	k: 362	n:4430000
MAPK1   4430000 perm   9254 sec   (479 perm/sec)   p_kst 8.171558e-05   p_cons 1.450402e-01   p_joint 8.171558e-05

Joint ci ratio: 2.054554e-01	ci left: 7.356193e-05	ci right 9.061484e-05	k: 363	n:4440000
Cons ci ratio: 4.516841e-03	ci left: 1.447059e-01	ci right 1.453612e-01	k: 643948	n:4440000
KS ci ratio: 2.054554e-01	ci left: 7.356193e-05	ci right 9.061484e-05	k: 363	n:4440000
MAPK1   4440000 perm   9295 sec   (478 perm/sec)   p_kst 8.175676e-05   p_cons 1.450333e-01   p_joint 8.175676e-05

Joint ci ratio: 2.054554e-01	ci left: 7.339662e-05	ci right 9.041122e-05	k: 363	n:4450000
Cons ci ratio: 4.511863e-03	ci left: 1.447008e-01	ci right 1.453554e-01	k: 645374	n:4450000
KS ci ratio: 2.054554e-01	ci left: 7.339662e-05	ci right 9.041122e-05	k: 363	n:4450000
MAPK1   4450000 perm   9338 sec   (477 perm/sec)   p_kst 8.157303e-05   p_cons 1.450279e-01   p_joint 8.157303e-05

Joint ci ratio: 2.054554e-01	ci left: 7.323205e-05	ci right 9.020850e-05	k: 363	n:4460000
Cons ci ratio: 4.506628e-03	ci left: 1.447108e-01	ci right 1.453646e-01	k: 646867	n:4460000
KS ci ratio: 2.054554e-01	ci left: 7.323205e-05	ci right 9.020850e-05	k: 363	n:4460000
MAPK1   4460000 perm   9379 sec   (476 perm/sec)   p_kst 8.139013e-05   p_cons 1.450374e-01   p_joint 8.139013e-05

Joint ci ratio: 2.051738e-01	ci left: 7.328043e-05	ci right 9.024189e-05	k: 364	n:4470000
Cons ci ratio: 4.501476e-03	ci left: 1.447171e-01	ci right 1.453702e-01	k: 648344	n:4470000
KS ci ratio: 2.051738e-01	ci left: 7.328043e-05	ci right 9.024189e-05	k: 364	n:4470000
MAPK1   4470000 perm   9419 sec   (475 perm/sec)   p_kst 8.143177e-05   p_cons 1.450434e-01   p_joint 8.143177e-05

Joint ci ratio: 2.048933e-01	ci left: 7.332862e-05	ci right 9.027512e-05	k: 365	n:4480000
Cons ci ratio: 4.496398e-03	ci left: 1.447202e-01	ci right 1.453726e-01	k: 649807	n:4480000
KS ci ratio: 2.048933e-01	ci left: 7.332862e-05	ci right 9.027512e-05	k: 365	n:4480000
MAPK1   4480000 perm   9460 sec   (474 perm/sec)   p_kst 8.147321e-05   p_cons 1.450462e-01   p_joint 8.147321e-05

Joint ci ratio: 2.048933e-01	ci left: 7.316530e-05	ci right 9.007406e-05	k: 365	n:4490000
Cons ci ratio: 4.491443e-03	ci left: 1.447176e-01	ci right 1.453693e-01	k: 651244	n:4490000
KS ci ratio: 2.048933e-01	ci left: 7.316530e-05	ci right 9.007406e-05	k: 365	n:4490000
MAPK1   4490000 perm   9501 sec   (473 perm/sec)   p_kst 8.129176e-05   p_cons 1.450432e-01   p_joint 8.129176e-05

Joint ci ratio: 2.048933e-01	ci left: 7.300271e-05	ci right 8.987390e-05	k: 365	n:4500000
Cons ci ratio: 4.486584e-03	ci left: 1.447105e-01	ci right 1.453615e-01	k: 652661	n:4500000
KS ci ratio: 2.048933e-01	ci left: 7.300271e-05	ci right 8.987390e-05	k: 365	n:4500000
MAPK1   4500000 perm   9542 sec   (472 perm/sec)   p_kst 8.111111e-05   p_cons 1.450358e-01   p_joint 8.111111e-05

Joint ci ratio: 2.048933e-01	ci left: 7.284084e-05	ci right 8.967462e-05	k: 365	n:4510000
Cons ci ratio: 4.481548e-03	ci left: 1.447141e-01	ci right 1.453644e-01	k: 654126	n:4510000
KS ci ratio: 2.048933e-01	ci left: 7.284084e-05	ci right 8.967462e-05	k: 365	n:4510000
MAPK1   4510000 perm   9583 sec   (471 perm/sec)   p_kst 8.093126e-05   p_cons 1.450390e-01   p_joint 8.093126e-05

Joint ci ratio: 2.048934e-01	ci left: 7.267969e-05	ci right 8.947623e-05	k: 365	n:4520000
Cons ci ratio: 4.476510e-03	ci left: 1.447188e-01	ci right 1.453683e-01	k: 655596	n:4520000
KS ci ratio: 2.048934e-01	ci left: 7.267969e-05	ci right 8.947623e-05	k: 365	n:4520000
MAPK1   4520000 perm   9625 sec   (470 perm/sec)   p_kst 8.075221e-05   p_cons 1.450434e-01   p_joint 8.075221e-05

Joint ci ratio: 2.040587e-01	ci left: 7.314759e-05	ci right 8.997482e-05	k: 368	n:4530000
Cons ci ratio: 4.471727e-03	ci left: 1.447103e-01	ci right 1.453590e-01	k: 657006	n:4530000
KS ci ratio: 2.040587e-01	ci left: 7.314759e-05	ci right 8.997482e-05	k: 368	n:4530000
MAPK1   4530000 perm   9666 sec   (469 perm/sec)   p_kst 8.123620e-05   p_cons 1.450344e-01   p_joint 8.123620e-05

Joint ci ratio: 2.037828e-01	ci left: 7.319549e-05	ci right 9.000813e-05	k: 369	n:4540000
Cons ci ratio: 4.466634e-03	ci left: 1.447198e-01	ci right 1.453679e-01	k: 658498	n:4540000
KS ci ratio: 2.037828e-01	ci left: 7.319549e-05	ci right 9.000813e-05	k: 369	n:4540000
MAPK1   4540000 perm   9708 sec   (468 perm/sec)   p_kst 8.127753e-05   p_cons 1.450436e-01   p_joint 8.127753e-05

Joint ci ratio: 2.035079e-01	ci left: 7.324320e-05	ci right 9.004128e-05	k: 370	n:4550000
Cons ci ratio: 4.461832e-03	ci left: 1.447141e-01	ci right 1.453615e-01	k: 659921	n:4550000
KS ci ratio: 2.035079e-01	ci left: 7.324320e-05	ci right 9.004128e-05	k: 370	n:4550000
MAPK1   4550000 perm   9749 sec   (467 perm/sec)   p_kst 8.131868e-05   p_cons 1.450376e-01   p_joint 8.131868e-05

Joint ci ratio: 2.032342e-01	ci left: 7.329071e-05	ci right 9.007427e-05	k: 371	n:4560000
Cons ci ratio: 4.457159e-03	ci left: 1.447021e-01	ci right 1.453487e-01	k: 661315	n:4560000
KS ci ratio: 2.032342e-01	ci left: 7.329071e-05	ci right 9.007427e-05	k: 371	n:4560000
MAPK1   4560000 perm   9790 sec   (466 perm/sec)   p_kst 8.135965e-05   p_cons 1.450252e-01   p_joint 8.135965e-05

Joint ci ratio: 2.032342e-01	ci left: 7.313033e-05	ci right 8.987717e-05	k: 371	n:4570000
Cons ci ratio: 4.452332e-03	ci left: 1.446996e-01	ci right 1.453455e-01	k: 662752	n:4570000
KS ci ratio: 2.032342e-01	ci left: 7.313033e-05	ci right 8.987717e-05	k: 371	n:4570000
MAPK1   4570000 perm   9831 sec   (465 perm/sec)   p_kst 8.118162e-05   p_cons 1.450223e-01   p_joint 8.118162e-05

Joint ci ratio: 2.026901e-01	ci left: 7.338515e-05	ci right 9.013978e-05	k: 373	n:4580000
Cons ci ratio: 4.447462e-03	ci left: 1.447003e-01	ci right 1.453455e-01	k: 664204	n:4580000
KS ci ratio: 2.026901e-01	ci left: 7.338515e-05	ci right 9.013978e-05	k: 373	n:4580000
MAPK1   4580000 perm   9873 sec   (464 perm/sec)   p_kst 8.144105e-05   p_cons 1.450227e-01   p_joint 8.144105e-05

Joint ci ratio: 2.026901e-01	ci left: 7.322527e-05	ci right 8.994340e-05	k: 373	n:4590000
Cons ci ratio: 4.442830e-03	ci left: 1.446887e-01	ci right 1.453331e-01	k: 665599	n:4590000
KS ci ratio: 2.026901e-01	ci left: 7.322527e-05	ci right 8.994340e-05	k: 373	n:4590000
MAPK1   4590000 perm   9915 sec   (463 perm/sec)   p_kst 8.126362e-05   p_cons 1.450107e-01   p_joint 8.126362e-05

Joint ci ratio: 2.026901e-01	ci left: 7.306608e-05	ci right 8.974787e-05	k: 373	n:4600000
Cons ci ratio: 4.437847e-03	ci left: 1.446975e-01	ci right 1.453412e-01	k: 667088	n:4600000
KS ci ratio: 2.026901e-01	ci left: 7.306608e-05	ci right 8.974787e-05	k: 373	n:4600000
MAPK1   4600000 perm   9956 sec   (462 perm/sec)   p_kst 8.108696e-05   p_cons 1.450191e-01   p_joint 8.108696e-05

Joint ci ratio: 2.024197e-01	ci left: 7.311351e-05	ci right 8.978109e-05	k: 374	n:4610000
Cons ci ratio: 4.433330e-03	ci left: 1.446811e-01	ci right 1.453241e-01	k: 668461	n:4610000
KS ci ratio: 2.024197e-01	ci left: 7.311351e-05	ci right 8.978109e-05	k: 374	n:4610000
MAPK1   4610000 perm   9998 sec   (461 perm/sec)   p_kst 8.112798e-05   p_cons 1.450024e-01   p_joint 8.112798e-05

Joint ci ratio: 2.021503e-01	ci left: 7.316074e-05	ci right 8.981416e-05	k: 375	n:4620000
Cons ci ratio: 4.428959e-03	ci left: 1.446574e-01	ci right 1.452997e-01	k: 669800	n:4620000
KS ci ratio: 2.021503e-01	ci left: 7.316074e-05	ci right 8.981416e-05	k: 375	n:4620000
MAPK1   4620000 perm   10040 sec   (460 perm/sec)   p_kst 8.116883e-05   p_cons 1.449784e-01   p_joint 8.116883e-05

Joint ci ratio: 2.021503e-01	ci left: 7.300273e-05	ci right 8.962018e-05	k: 375	n:4630000
Cons ci ratio: 4.424223e-03	ci left: 1.446550e-01	ci right 1.452966e-01	k: 671237	n:4630000
KS ci ratio: 2.021503e-01	ci left: 7.300273e-05	ci right 8.962018e-05	k: 375	n:4630000
MAPK1   4630000 perm   10083 sec   (459 perm/sec)   p_kst 8.099352e-05   p_cons 1.449756e-01   p_joint 8.099352e-05

Joint ci ratio: 2.021504e-01	ci left: 7.284539e-05	ci right 8.942703e-05	k: 375	n:4640000
Cons ci ratio: 4.419340e-03	ci left: 1.446617e-01	ci right 1.453026e-01	k: 672716	n:4640000
KS ci ratio: 2.021504e-01	ci left: 7.284539e-05	ci right 8.942703e-05	k: 375	n:4640000
MAPK1   4640000 perm   10125 sec   (458 perm/sec)   p_kst 8.081897e-05   p_cons 1.449819e-01   p_joint 8.081897e-05

Joint ci ratio: 2.021504e-01	ci left: 7.268873e-05	ci right 8.923472e-05	k: 375	n:4650000
Cons ci ratio: 4.414642e-03	ci left: 1.446588e-01	ci right 1.452990e-01	k: 674151	n:4650000
KS ci ratio: 2.021504e-01	ci left: 7.268873e-05	ci right 8.923472e-05	k: 375	n:4650000
MAPK1   4650000 perm   10168 sec   (457 perm/sec)   p_kst 8.064516e-05   p_cons 1.449787e-01   p_joint 8.064516e-05

Joint ci ratio: 2.021504e-01	ci left: 7.253275e-05	ci right 8.904323e-05	k: 375	n:4660000
Cons ci ratio: 4.410086e-03	ci left: 1.446489e-01	ci right 1.452884e-01	k: 675553	n:4660000
KS ci ratio: 2.021504e-01	ci left: 7.253275e-05	ci right 8.904323e-05	k: 375	n:4660000
MAPK1   4660000 perm   10210 sec   (456 perm/sec)   p_kst 8.047210e-05   p_cons 1.449685e-01   p_joint 8.047210e-05

Joint ci ratio: 2.021504e-01	ci left: 7.237743e-05	ci right 8.885256e-05	k: 375	n:4670000
Cons ci ratio: 4.405246e-03	ci left: 1.446557e-01	ci right 1.452946e-01	k: 677033	n:4670000
KS ci ratio: 2.021504e-01	ci left: 7.237743e-05	ci right 8.885256e-05	k: 375	n:4670000
MAPK1   4670000 perm   10253 sec   (455 perm/sec)   p_kst 8.029979e-05   p_cons 1.449749e-01   p_joint 8.029979e-05

Joint ci ratio: 2.016149e-01	ci left: 7.262853e-05	ci right 8.911162e-05	k: 377	n:4680000
Cons ci ratio: 4.400544e-03	ci left: 1.446557e-01	ci right 1.452939e-01	k: 678481	n:4680000
KS ci ratio: 2.016149e-01	ci left: 7.262853e-05	ci right 8.911162e-05	k: 377	n:4680000
MAPK1   4680000 perm   10296 sec   (455 perm/sec)   p_kst 8.055556e-05   p_cons 1.449746e-01   p_joint 8.055556e-05

Joint ci ratio: 2.016149e-01	ci left: 7.247367e-05	ci right 8.892162e-05	k: 377	n:4690000
Cons ci ratio: 4.395902e-03	ci left: 1.446531e-01	ci right 1.452906e-01	k: 679917	n:4690000
KS ci ratio: 2.016149e-01	ci left: 7.247367e-05	ci right 8.892162e-05	k: 377	n:4690000
MAPK1   4690000 perm   10337 sec   (454 perm/sec)   p_kst 8.038380e-05   p_cons 1.449716e-01   p_joint 8.038380e-05

Joint ci ratio: 2.013487e-01	ci left: 7.252150e-05	ci right 8.895591e-05	k: 378	n:4700000
Cons ci ratio: 4.391161e-03	ci left: 1.446569e-01	ci right 1.452937e-01	k: 681383	n:4700000
KS ci ratio: 2.013487e-01	ci left: 7.252150e-05	ci right 8.895591e-05	k: 378	n:4700000
MAPK1   4700000 perm   10380 sec   (453 perm/sec)   p_kst 8.042553e-05   p_cons 1.449751e-01   p_joint 8.042553e-05

Joint ci ratio: 2.013488e-01	ci left: 7.236753e-05	ci right 8.876705e-05	k: 378	n:4710000
Cons ci ratio: 4.386534e-03	ci left: 1.446552e-01	ci right 1.452913e-01	k: 682823	n:4710000
KS ci ratio: 2.013488e-01	ci left: 7.236753e-05	ci right 8.876705e-05	k: 378	n:4710000
MAPK1   4710000 perm   10422 sec   (452 perm/sec)   p_kst 8.025478e-05   p_cons 1.449730e-01   p_joint 8.025478e-05

Joint ci ratio: 2.013488e-01	ci left: 7.221421e-05	ci right 8.857898e-05	k: 378	n:4720000
Cons ci ratio: 4.381884e-03	ci left: 1.446556e-01	ci right 1.452910e-01	k: 684273	n:4720000
KS ci ratio: 2.013488e-01	ci left: 7.221421e-05	ci right 8.857898e-05	k: 378	n:4720000
MAPK1   4720000 perm   10465 sec   (451 perm/sec)   p_kst 8.008475e-05   p_cons 1.449731e-01   p_joint 8.008475e-05

Joint ci ratio: 2.013488e-01	ci left: 7.206153e-05	ci right 8.839171e-05	k: 378	n:4730000
Cons ci ratio: 4.377405e-03	ci left: 1.446471e-01	ci right 1.452819e-01	k: 685681	n:4730000
KS ci ratio: 2.013488e-01	ci left: 7.206153e-05	ci right 8.839171e-05	k: 378	n:4730000
MAPK1   4730000 perm   10509 sec   (450 perm/sec)   p_kst 7.991543e-05   p_cons 1.449643e-01   p_joint 7.991543e-05

Joint ci ratio: 2.008196e-01	ci left: 7.231020e-05	ci right 8.864839e-05	k: 380	n:4740000
Cons ci ratio: 4.372832e-03	ci left: 1.446448e-01	ci right 1.452789e-01	k: 687118	n:4740000
KS ci ratio: 2.008196e-01	ci left: 7.231020e-05	ci right 8.864839e-05	k: 380	n:4740000
MAPK1   4740000 perm   10552 sec   (449 perm/sec)   p_kst 8.016878e-05   p_cons 1.449616e-01   p_joint 8.016878e-05

Joint ci ratio: 2.005566e-01	ci left: 7.235792e-05	ci right 8.868285e-05	k: 381	n:4750000
Cons ci ratio: 4.368092e-03	ci left: 1.446528e-01	ci right 1.452862e-01	k: 688604	n:4750000
KS ci ratio: 2.005566e-01	ci left: 7.235792e-05	ci right 8.868285e-05	k: 381	n:4750000
MAPK1   4750000 perm   10595 sec   (448 perm/sec)   p_kst 8.021053e-05   p_cons 1.449693e-01   p_joint 8.021053e-05

Joint ci ratio: 2.002946e-01	ci left: 7.240545e-05	ci right 8.871715e-05	k: 382	n:4760000
Cons ci ratio: 4.363707e-03	ci left: 1.446414e-01	ci right 1.452742e-01	k: 689998	n:4760000
KS ci ratio: 2.002946e-01	ci left: 7.240545e-05	ci right 8.871715e-05	k: 382	n:4760000
MAPK1   4760000 perm   10638 sec   (447 perm/sec)   p_kst 8.025210e-05   p_cons 1.449576e-01   p_joint 8.025210e-05

Joint ci ratio: 2.000336e-01	ci left: 7.245279e-05	ci right 8.875130e-05	k: 383	n:4770000
Cons ci ratio: 4.359122e-03	ci left: 1.446422e-01	ci right 1.452743e-01	k: 691450	n:4770000
KS ci ratio: 2.000336e-01	ci left: 7.245279e-05	ci right 8.875130e-05	k: 383	n:4770000
MAPK1   4770000 perm   10681 sec   (447 perm/sec)   p_kst 8.029350e-05   p_cons 1.449581e-01   p_joint 8.029350e-05

Joint ci ratio: 2.000336e-01	ci left: 7.230122e-05	ci right 8.856563e-05	k: 383	n:4780000
Cons ci ratio: 4.354426e-03	ci left: 1.446502e-01	ci right 1.452816e-01	k: 692936	n:4780000
KS ci ratio: 2.000336e-01	ci left: 7.230122e-05	ci right 8.856563e-05	k: 383	n:4780000
MAPK1   4780000 perm   10725 sec   (446 perm/sec)   p_kst 8.012552e-05   p_cons 1.449657e-01   p_joint 8.012552e-05

Joint ci ratio: 2.000336e-01	ci left: 7.215028e-05	ci right 8.838073e-05	k: 383	n:4790000
Cons ci ratio: 4.349624e-03	ci left: 1.446650e-01	ci right 1.452958e-01	k: 694455	n:4790000
KS ci ratio: 2.000336e-01	ci left: 7.215028e-05	ci right 8.838073e-05	k: 383	n:4790000
MAPK1   4790000 perm   10769 sec   (445 perm/sec)   p_kst 7.995825e-05   p_cons 1.449802e-01   p_joint 7.995825e-05

Joint ci ratio: 2.000336e-01	ci left: 7.199996e-05	ci right 8.819661e-05	k: 383	n:4800000
Cons ci ratio: 4.344823e-03	ci left: 1.446805e-01	ci right 1.453107e-01	k: 695978	n:4800000
KS ci ratio: 2.000336e-01	ci left: 7.199996e-05	ci right 8.819661e-05	k: 383	n:4800000
MAPK1   4800000 perm   10812 sec   (444 perm/sec)   p_kst 7.979167e-05   p_cons 1.449954e-01   p_joint 7.979167e-05

Joint ci ratio: 1.997737e-01	ci left: 7.204777e-05	ci right 8.823154e-05	k: 384	n:4810000
Cons ci ratio: 4.340315e-03	ci left: 1.446803e-01	ci right 1.453098e-01	k: 697425	n:4810000
KS ci ratio: 1.997737e-01	ci left: 7.204777e-05	ci right 8.823154e-05	k: 384	n:4810000
MAPK1   4810000 perm   10856 sec   (443 perm/sec)   p_kst 7.983368e-05   p_cons 1.449948e-01   p_joint 7.983368e-05

Joint ci ratio: 1.997737e-01	ci left: 7.189829e-05	ci right 8.804849e-05	k: 384	n:4820000
Cons ci ratio: 4.335854e-03	ci left: 1.446781e-01	ci right 1.453070e-01	k: 698863	n:4820000
KS ci ratio: 1.997737e-01	ci left: 7.189829e-05	ci right 8.804849e-05	k: 384	n:4820000
MAPK1   4820000 perm   10900 sec   (442 perm/sec)   p_kst 7.966805e-05   p_cons 1.449923e-01   p_joint 7.966805e-05

Joint ci ratio: 1.995148e-01	ci left: 7.194612e-05	ci right 8.808357e-05	k: 385	n:4830000
Cons ci ratio: 4.331171e-03	ci left: 1.446894e-01	ci right 1.453176e-01	k: 700366	n:4830000
KS ci ratio: 1.995148e-01	ci left: 7.194612e-05	ci right 8.808357e-05	k: 385	n:4830000
MAPK1   4830000 perm   10943 sec   (441 perm/sec)   p_kst 7.971014e-05   p_cons 1.450033e-01   p_joint 7.971014e-05

Joint ci ratio: 1.995148e-01	ci left: 7.179747e-05	ci right 8.790158e-05	k: 385	n:4840000
Cons ci ratio: 4.326904e-03	ci left: 1.446778e-01	ci right 1.453053e-01	k: 701758	n:4840000
KS ci ratio: 1.995148e-01	ci left: 7.179747e-05	ci right 8.790158e-05	k: 385	n:4840000
MAPK1   4840000 perm   10987 sec   (441 perm/sec)   p_kst 7.954545e-05   p_cons 1.449913e-01   p_joint 7.954545e-05

Joint ci ratio: 1.995148e-01	ci left: 7.164944e-05	ci right 8.772034e-05	k: 385	n:4850000
Cons ci ratio: 4.322408e-03	ci left: 1.446800e-01	ci right 1.453069e-01	k: 703217	n:4850000
KS ci ratio: 1.995148e-01	ci left: 7.164944e-05	ci right 8.772034e-05	k: 385	n:4850000
MAPK1   4850000 perm   11030 sec   (440 perm/sec)   p_kst 7.938144e-05   p_cons 1.449932e-01   p_joint 7.938144e-05

Joint ci ratio: 1.995148e-01	ci left: 7.150201e-05	ci right 8.753984e-05	k: 385	n:4860000
Cons ci ratio: 4.317977e-03	ci left: 1.446793e-01	ci right 1.453055e-01	k: 704662	n:4860000
KS ci ratio: 1.995148e-01	ci left: 7.150201e-05	ci right 8.753984e-05	k: 385	n:4860000
MAPK1   4860000 perm   11074 sec   (439 perm/sec)   p_kst 7.921811e-05   p_cons 1.449922e-01   p_joint 7.921811e-05

Joint ci ratio: 1.989999e-01	ci left: 7.174538e-05	ci right 8.779123e-05	k: 387	n:4870000
Cons ci ratio: 4.313234e-03	ci left: 1.446972e-01	ci right 1.453229e-01	k: 706198	n:4870000
KS ci ratio: 1.989999e-01	ci left: 7.174538e-05	ci right 8.779123e-05	k: 387	n:4870000
MAPK1   4870000 perm   11117 sec   (438 perm/sec)   p_kst 7.946612e-05   p_cons 1.450099e-01   p_joint 7.946612e-05

Joint ci ratio: 1.987439e-01	ci left: 7.179307e-05	ci right 8.782644e-05	k: 388	n:4880000
Cons ci ratio: 4.308513e-03	ci left: 1.447147e-01	ci right 1.453398e-01	k: 707732	n:4880000
KS ci ratio: 1.987439e-01	ci left: 7.179307e-05	ci right 8.782644e-05	k: 388	n:4880000
MAPK1   4880000 perm   11160 sec   (437 perm/sec)   p_kst 7.950820e-05   p_cons 1.450270e-01   p_joint 7.950820e-05

Joint ci ratio: 1.979819e-01	ci left: 7.222929e-05	ci right 8.829076e-05	k: 391	n:4890000
Cons ci ratio: 4.304124e-03	ci left: 1.447140e-01	ci right 1.453384e-01	k: 709177	n:4890000
KS ci ratio: 1.979819e-01	ci left: 7.222929e-05	ci right 8.829076e-05	k: 391	n:4890000
MAPK1   4890000 perm   11204 sec   (436 perm/sec)   p_kst 7.995910e-05   p_cons 1.450260e-01   p_joint 7.995910e-05

Joint ci ratio: 1.979820e-01	ci left: 7.208188e-05	ci right 8.811057e-05	k: 391	n:4900000
Cons ci ratio: 4.299498e-03	ci left: 1.447277e-01	ci right 1.453515e-01	k: 710693	n:4900000
KS ci ratio: 1.979820e-01	ci left: 7.208188e-05	ci right 8.811057e-05	k: 391	n:4900000
MAPK1   4900000 perm   11249 sec   (436 perm/sec)   p_kst 7.979592e-05   p_cons 1.450394e-01   p_joint 7.979592e-05

Joint ci ratio: 1.977299e-01	ci left: 7.212865e-05	ci right 8.814486e-05	k: 392	n:4910000
Cons ci ratio: 4.295171e-03	ci left: 1.447249e-01	ci right 1.453480e-01	k: 712128	n:4910000
KS ci ratio: 1.977299e-01	ci left: 7.212865e-05	ci right 8.814486e-05	k: 392	n:4910000
MAPK1   4910000 perm   11293 sec   (435 perm/sec)   p_kst 7.983707e-05   p_cons 1.450363e-01   p_joint 7.983707e-05

Joint ci ratio: 1.977299e-01	ci left: 7.198205e-05	ci right 8.796571e-05	k: 392	n:4920000
Cons ci ratio: 4.290798e-03	ci left: 1.447255e-01	ci right 1.453481e-01	k: 713580	n:4920000
KS ci ratio: 1.977299e-01	ci left: 7.198205e-05	ci right 8.796571e-05	k: 392	n:4920000
MAPK1   4920000 perm   11338 sec   (434 perm/sec)   p_kst 7.967480e-05   p_cons 1.450366e-01   p_joint 7.967480e-05

Joint ci ratio: 1.974788e-01	ci left: 7.202885e-05	ci right 8.800014e-05	k: 393	n:4930000
Cons ci ratio: 4.286232e-03	ci left: 1.447381e-01	ci right 1.453600e-01	k: 715091	n:4930000
KS ci ratio: 1.974788e-01	ci left: 7.202885e-05	ci right 8.800014e-05	k: 393	n:4930000
MAPK1   4930000 perm   11382 sec   (433 perm/sec)   p_kst 7.971602e-05   p_cons 1.450489e-01   p_joint 7.971602e-05

Joint ci ratio: 1.974789e-01	ci left: 7.188304e-05	ci right 8.782200e-05	k: 393	n:4940000
Cons ci ratio: 4.281792e-03	ci left: 1.447442e-01	ci right 1.453655e-01	k: 716570	n:4940000
KS ci ratio: 1.974789e-01	ci left: 7.188304e-05	ci right 8.782200e-05	k: 393	n:4940000
MAPK1   4940000 perm   11427 sec   (432 perm/sec)   p_kst 7.955466e-05   p_cons 1.450547e-01   p_joint 7.955466e-05

Joint ci ratio: 1.972287e-01	ci left: 7.192986e-05	ci right 8.785658e-05	k: 394	n:4950000
Cons ci ratio: 4.277592e-03	ci left: 1.447372e-01	ci right 1.453578e-01	k: 717984	n:4950000
KS ci ratio: 1.972287e-01	ci left: 7.192986e-05	ci right 8.785658e-05	k: 394	n:4950000
MAPK1   4950000 perm   11471 sec   (432 perm/sec)   p_kst 7.959596e-05   p_cons 1.450473e-01   p_joint 7.959596e-05

Joint ci ratio: 1.967313e-01	ci left: 7.216818e-05	ci right 8.810253e-05	k: 396	n:4960000
Cons ci ratio: 4.273092e-03	ci left: 1.447483e-01	ci right 1.453683e-01	k: 719488	n:4960000
KS ci ratio: 1.967313e-01	ci left: 7.216818e-05	ci right 8.810253e-05	k: 396	n:4960000
MAPK1   4960000 perm   11516 sec   (431 perm/sec)   p_kst 7.983871e-05   p_cons 1.450581e-01   p_joint 7.983871e-05

Joint ci ratio: 1.964840e-01	ci left: 7.221427e-05	ci right 8.813636e-05	k: 397	n:4970000
Cons ci ratio: 4.268813e-03	ci left: 1.447472e-01	ci right 1.453667e-01	k: 720932	n:4970000
KS ci ratio: 1.964840e-01	ci left: 7.221427e-05	ci right 8.813636e-05	k: 397	n:4970000
MAPK1   4970000 perm   11561 sec   (430 perm/sec)   p_kst 7.987928e-05   p_cons 1.450567e-01   p_joint 7.987928e-05

Joint ci ratio: 1.962376e-01	ci left: 7.226020e-05	ci right 8.817004e-05	k: 398	n:4980000
Cons ci ratio: 4.264652e-03	ci left: 1.447402e-01	ci right 1.453590e-01	k: 722346	n:4980000
KS ci ratio: 1.962376e-01	ci left: 7.226020e-05	ci right 8.817004e-05	k: 398	n:4980000
MAPK1   4980000 perm   11607 sec   (429 perm/sec)   p_kst 7.991968e-05   p_cons 1.450494e-01   p_joint 7.991968e-05

Joint ci ratio: 1.959921e-01	ci left: 7.230595e-05	ci right 8.820358e-05	k: 399	n:4990000
Cons ci ratio: 4.260526e-03	ci left: 1.447318e-01	ci right 1.453500e-01	k: 723753	n:4990000
KS ci ratio: 1.959921e-01	ci left: 7.230595e-05	ci right 8.820358e-05	k: 399	n:4990000
MAPK1   4990000 perm   11651 sec   (428 perm/sec)   p_kst 7.995992e-05   p_cons 1.450407e-01   p_joint 7.995992e-05

Joint ci ratio: 1.959921e-01	ci left: 7.216134e-05	ci right 8.802717e-05	k: 399	n:5000000
Cons ci ratio: 4.256357e-03	ci left: 1.447267e-01	ci right 1.453442e-01	k: 725176	n:5000000
KS ci ratio: 1.959921e-01	ci left: 7.216134e-05	ci right 8.802717e-05	k: 399	n:5000000
MAPK1   5000000 perm   11697 sec   (427 perm/sec)   p_kst 7.980000e-05   p_cons 1.450352e-01   p_joint 7.980000e-05

Outputting figure to mutsig2_images.part000000000102/MAPK1.3_1115_5000000_7.98e-05_0.14504_7.98e-05.png
                gene_name: MAPK1
               theta_stop: 0.20 
                    nperm: 5000000 
                     p_ks: 7.98e-05 
        ci_ks_bounds_left: 7.22e-05 
       ci_ks_bounds_right: 8.80e-05 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 7.98e-05 
     ci_joint_bounds_left: 7.22e-05 
    ci_joint_bounds_right: 8.80e-05 

Current progress: 10 percent done.
MARCH6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.836740e-03	ci left: 9.753575e-01	ci right 9.811593e-01	k: 9784	n:10000
Cons ci ratio: 7.951784e-02	ci left: 1.876681e-01	ci right 2.033097e-01	k: 1954	n:10000
KS ci ratio: 2.074603e-02	ci left: 7.729656e-01	ci right 7.892703e-01	k: 7812	n:10000
MARCH6   10000 perm   2 sec   (5297 perm/sec)   p_kst 7.812000e-01   p_cons 1.954000e-01   p_joint 9.784000e-01

Outputting figure to mutsig2_images.part000000000102/MARCH6.3_2837_10000_0.7812_0.1954_0.9784.png
                gene_name: MARCH6
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 20 percent done.
MAST4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.729533e-02	ci left: 1.604251e-01	ci right 1.751689e-01	k: 1677	n:10000
Cons ci ratio: 4.002490e-01	ci left: 7.602648e-03	ci right 1.149110e-02	k: 94	n:10000
KS ci ratio: 1.056506e-01	ci left: 1.145714e-01	ci right 1.274503e-01	k: 1209	n:10000
MAST4   10000 perm   3 sec   (3482 perm/sec)   p_kst 1.209000e-01   p_cons 9.400000e-03   p_joint 1.677000e-01

Joint ci ratio: 1.092276e-01	ci left: 5.718621e-02	ci right 6.384227e-02	k: 1209	n:20000
Cons ci ratio: 3.048355e-01	ci left: 6.950867e-03	ci right 9.495224e-03	k: 163	n:20000
KS ci ratio: 7.434114e-02	ci left: 1.174943e-01	ci right 1.266159e-01	k: 2440	n:20000
MAST4   20000 perm   6 sec   (3154 perm/sec)   p_kst 1.220000e-01   p_cons 8.150000e-03   p_joint 6.045000e-02

Joint ci ratio: 6.145235e-02	ci left: 1.157510e-01	ci right 1.231228e-01	k: 3582	n:30000
Cons ci ratio: 2.483906e-01	ci left: 7.210699e-03	ci right 9.286228e-03	k: 246	n:30000
KS ci ratio: 6.078004e-02	ci left: 1.180534e-01	ci right 1.254867e-01	k: 3652	n:30000
MAST4   30000 perm   10 sec   (3043 perm/sec)   p_kst 1.217333e-01   p_cons 8.200000e-03   p_joint 1.194000e-01

Joint ci ratio: 4.816353e-02	ci left: 1.386424e-01	ci right 1.455096e-01	k: 5682	n:40000
Cons ci ratio: 2.145667e-01	ci left: 7.386910e-03	ci right 9.185572e-03	k: 330	n:40000
KS ci ratio: 5.284538e-02	ci left: 1.177203e-01	ci right 1.241349e-01	k: 4836	n:40000
MAST4   40000 perm   13 sec   (2963 perm/sec)   p_kst 1.209000e-01   p_cons 8.250000e-03   p_joint 1.420500e-01

Joint ci ratio: 4.527089e-02	ci left: 1.274401e-01	ci right 1.333629e-01	k: 6519	n:50000
Cons ci ratio: 1.888885e-01	ci left: 7.733026e-03	ci right 9.364803e-03	k: 426	n:50000
KS ci ratio: 4.779055e-02	ci left: 1.157585e-01	ci right 1.214459e-01	k: 5929	n:50000
MAST4   50000 perm   17 sec   (2900 perm/sec)   p_kst 1.185800e-01   p_cons 8.520000e-03   p_joint 1.303800e-01

Joint ci ratio: 3.621768e-02	ci left: 1.603834e-01	ci right 1.663159e-01	k: 9800	n:60000
Cons ci ratio: 1.723293e-01	ci left: 7.812861e-03	ci right 9.301928e-03	k: 512	n:60000
KS ci ratio: 4.355724e-02	ci left: 1.163368e-01	ci right 1.215335e-01	k: 7135	n:60000
MAST4   60000 perm   21 sec   (2860 perm/sec)   p_kst 1.189167e-01   p_cons 8.533333e-03   p_joint 1.633333e-01

Joint ci ratio: 3.353721e-02	ci left: 1.605544e-01	ci right 1.660450e-01	k: 11430	n:70000
Cons ci ratio: 1.596134e-01	ci left: 7.860658e-03	ci right 9.237688e-03	k: 597	n:70000
KS ci ratio: 4.032437e-02	ci left: 1.165393e-01	ci right 1.213495e-01	k: 8325	n:70000
MAST4   70000 perm   25 sec   (2824 perm/sec)   p_kst 1.189286e-01   p_cons 8.528571e-03   p_joint 1.632857e-01

Joint ci ratio: 3.102558e-02	ci left: 1.637629e-01	ci right 1.689363e-01	k: 13307	n:80000
Cons ci ratio: 1.502421e-01	ci left: 7.803267e-03	ci right 9.082765e-03	k: 674	n:80000
KS ci ratio: 3.769626e-02	ci left: 1.168259e-01	ci right 1.213268e-01	k: 9525	n:80000
MAST4   80000 perm   29 sec   (2789 perm/sec)   p_kst 1.190625e-01   p_cons 8.425000e-03   p_joint 1.663375e-01

Joint ci ratio: 2.962044e-02	ci left: 1.604817e-01	ci right 1.653178e-01	k: 14660	n:90000
Cons ci ratio: 1.423485e-01	ci left: 7.760478e-03	ci right 8.960423e-03	k: 751	n:90000
KS ci ratio: 3.549294e-02	ci left: 1.172332e-01	ci right 1.214803e-01	k: 10741	n:90000
MAST4   90000 perm   33 sec   (2754 perm/sec)   p_kst 1.193444e-01   p_cons 8.344444e-03   p_joint 1.628889e-01

Joint ci ratio: 3.071451e-02	ci left: 1.379145e-01	ci right 1.422264e-01	k: 14006	n:100000
Cons ci ratio: 1.347638e-01	ci left: 7.824303e-03	ci right 8.964487e-03	k: 838	n:100000
KS ci ratio: 3.365806e-02	ci left: 1.174261e-01	ci right 1.214560e-01	k: 11943	n:100000
MAST4   100000 perm   37 sec   (2721 perm/sec)   p_kst 1.194300e-01   p_cons 8.380000e-03   p_joint 1.400600e-01

Joint ci ratio: 2.920880e-02	ci left: 1.386411e-01	ci right 1.427597e-01	k: 15476	n:110000
Cons ci ratio: 1.289795e-01	ci left: 7.789906e-03	ci right 8.872621e-03	k: 915	n:110000
KS ci ratio: 3.197491e-02	ci left: 1.182837e-01	ci right 1.221363e-01	k: 13222	n:110000
MAST4   110000 perm   41 sec   (2684 perm/sec)   p_kst 1.202000e-01   p_cons 8.318182e-03   p_joint 1.406909e-01

Joint ci ratio: 2.949169e-02	ci left: 1.264375e-01	ci right 1.302305e-01	k: 15399	n:120000
Cons ci ratio: 1.227641e-01	ci left: 7.907524e-03	ci right 8.949775e-03	k: 1010	n:120000
KS ci ratio: 3.065000e-02	ci left: 1.181168e-01	ci right 1.218016e-01	k: 14394	n:120000
MAST4   120000 perm   45 sec   (2650 perm/sec)   p_kst 1.199500e-01   p_cons 8.416667e-03   p_joint 1.283250e-01

Joint ci ratio: 2.796789e-02	ci left: 1.294379e-01	ci right 1.331170e-01	k: 17065	n:130000
Cons ci ratio: 1.180704e-01	ci left: 7.911026e-03	ci right 8.911087e-03	k: 1092	n:130000
KS ci ratio: 2.944070e-02	ci left: 1.182382e-01	ci right 1.217788e-01	k: 15600	n:130000
MAST4   130000 perm   50 sec   (2619 perm/sec)   p_kst 1.200000e-01   p_cons 8.400000e-03   p_joint 1.312692e-01

Joint ci ratio: 2.694528e-02	ci left: 1.295492e-01	ci right 1.330947e-01	k: 18384	n:140000
Cons ci ratio: 1.138768e-01	ci left: 7.914679e-03	ci right 8.877277e-03	k: 1174	n:140000
KS ci ratio: 2.836121e-02	ci left: 1.183660e-01	ci right 1.217783e-01	k: 16809	n:140000
MAST4   140000 perm   54 sec   (2588 perm/sec)   p_kst 1.200643e-01   p_cons 8.385714e-03   p_joint 1.313143e-01

Joint ci ratio: 2.268983e-02	ci left: 1.640737e-01	ci right 1.678459e-01	k: 24893	n:150000
Cons ci ratio: 1.099683e-01	ci left: 7.937844e-03	ci right 8.867975e-03	k: 1259	n:150000
KS ci ratio: 2.740189e-02	ci left: 1.184059e-01	ci right 1.217021e-01	k: 18007	n:150000
MAST4   150000 perm   59 sec   (2558 perm/sec)   p_kst 1.200467e-01   p_cons 8.393333e-03   p_joint 1.659533e-01

Joint ci ratio: 2.071276e-02	ci left: 1.810146e-01	ci right 1.848094e-01	k: 29265	n:160000
Cons ci ratio: 1.056862e-01	ci left: 8.074231e-03	ci right 8.981213e-03	k: 1363	n:160000
KS ci ratio: 2.654239e-02	ci left: 1.183742e-01	ci right 1.215646e-01	k: 19194	n:160000
MAST4   160000 perm   63 sec   (2531 perm/sec)   p_kst 1.199625e-01   p_cons 8.518750e-03   p_joint 1.829062e-01

Joint ci ratio: 2.073368e-02	ci left: 1.719310e-01	ci right 1.755389e-01	k: 29534	n:170000
Cons ci ratio: 1.030791e-01	ci left: 8.000275e-03	ci right 8.875436e-03	k: 1433	n:170000
KS ci ratio: 2.578489e-02	ci left: 1.181371e-01	ci right 1.212288e-01	k: 20345	n:170000
MAST4   170000 perm   68 sec   (2504 perm/sec)   p_kst 1.196765e-01   p_cons 8.429412e-03   p_joint 1.737294e-01

Joint ci ratio: 2.198534e-02	ci left: 1.484529e-01	ci right 1.517584e-01	k: 27018	n:180000
Cons ci ratio: 1.004204e-01	ci left: 7.972702e-03	ci right 8.821024e-03	k: 1510	n:180000
KS ci ratio: 2.504245e-02	ci left: 1.183143e-01	ci right 1.213202e-01	k: 21566	n:180000
MAST4   180000 perm   73 sec   (2477 perm/sec)   p_kst 1.198111e-01   p_cons 8.388889e-03   p_joint 1.501000e-01

Joint ci ratio: 1.959117e-02	ci left: 1.723344e-01	ci right 1.757492e-01	k: 33067	n:190000
Cons ci ratio: 9.789524e-02	ci left: 7.958561e-03	ci right 8.782860e-03	k: 1589	n:190000
KS ci ratio: 2.437281e-02	ci left: 1.183692e-01	ci right 1.212950e-01	k: 22767	n:190000
MAST4   190000 perm   78 sec   (2448 perm/sec)   p_kst 1.198263e-01   p_cons 8.363158e-03   p_joint 1.740368e-01

Outputting figure to mutsig2_images.part000000000102/MAST4.3_8118_190000_0.11983_0.0083632_0.17404.png
                gene_name: MAST4
               theta_stop: 0.098 
                    nperm: 190000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.0084 
      ci_cons_bounds_left: 0.0080 
     ci_cons_bounds_right: 0.0088 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 30 percent done.
MAP3K15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.191375e-02	ci left: 4.566832e-01	ci right 4.763364e-01	k: 4665	n:10000
Cons ci ratio: 1.230204e-02	ci left: 9.046320e-01	ci right 9.159277e-01	k: 9104	n:10000
KS ci ratio: 6.033790e-02	ci left: 2.877571e-01	ci right 3.057615e-01	k: 2967	n:10000
MAP3K15   10000 perm   2 sec   (4949 perm/sec)   p_kst 2.967000e-01   p_cons 9.104000e-01   p_joint 4.665000e-01

Outputting figure to mutsig2_images.part000000000102/MAP3K15.2_4058_10000_0.2967_0.9104_0.4665.png
                gene_name: MAP3K15
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 40 percent done.
MAP3K4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.033322e-01	ci left: 1.192622e-01	ci right 1.323567e-01	k: 1257	n:10000
Cons ci ratio: 2.008231e-01	ci left: 3.300513e-02	ci right 4.046787e-02	k: 366	n:10000
KS ci ratio: 2.219129e-02	ci left: 7.487731e-01	ci right 7.656768e-01	k: 7573	n:10000
MAP3K4   10000 perm   2 sec   (4555 perm/sec)   p_kst 7.573000e-01   p_cons 3.660000e-02   p_joint 1.257000e-01

Joint ci ratio: 1.081846e-01	ci left: 5.825809e-02	ci right 6.497006e-02	k: 1231	n:20000
Cons ci ratio: 1.416066e-01	ci left: 3.428157e-02	ci right 3.955417e-02	k: 737	n:20000
KS ci ratio: 1.597120e-02	ci left: 7.446937e-01	ci right 7.567333e-01	k: 15015	n:20000
MAP3K4   20000 perm   5 sec   (4092 perm/sec)   p_kst 7.507500e-01   p_cons 3.685000e-02   p_joint 6.155000e-02

Joint ci ratio: 1.140274e-01	ci left: 3.573495e-02	ci right 4.008846e-02	k: 1136	n:30000
Cons ci ratio: 1.168330e-01	ci left: 3.404990e-02	ci right 3.830720e-02	k: 1084	n:30000
KS ci ratio: 1.301898e-02	ci left: 7.464349e-01	ci right 7.562498e-01	k: 22541	n:30000
MAP3K4   30000 perm   8 sec   (3947 perm/sec)   p_kst 7.513667e-01   p_cons 3.613333e-02   p_joint 3.786667e-02

Joint ci ratio: 5.476959e-02	ci left: 1.104071e-01	ci right 1.166491e-01	k: 4540	n:40000
Cons ci ratio: 1.016066e-01	ci left: 3.404932e-02	ci right 3.771846e-02	k: 1434	n:40000
KS ci ratio: 1.126623e-02	ci left: 7.473853e-01	ci right 7.558782e-01	k: 30066	n:40000
MAP3K4   40000 perm   10 sec   (3839 perm/sec)   p_kst 7.516500e-01   p_cons 3.585000e-02   p_joint 1.135000e-01

Joint ci ratio: 9.613937e-02	ci left: 3.063081e-02	ci right 3.374382e-02	k: 1608	n:50000
Cons ci ratio: 9.042984e-02	ci left: 3.457974e-02	ci right 3.787439e-02	k: 1810	n:50000
KS ci ratio: 1.009060e-02	ci left: 7.473258e-01	ci right 7.549250e-01	k: 37557	n:50000
MAP3K4   50000 perm   13 sec   (3744 perm/sec)   p_kst 7.511400e-01   p_cons 3.620000e-02   p_joint 3.216000e-02

Outputting figure to mutsig2_images.part000000000102/MAP3K4.2_4935_50000_0.75114_0.0362_0.03216.png
                gene_name: MAP3K4
               theta_stop: 0.096 
                    nperm: 50000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.036 
      ci_cons_bounds_left: 0.035 
     ci_cons_bounds_right: 0.038 
                  p_joint: 0.032 
     ci_joint_bounds_left: 0.031 
    ci_joint_bounds_right: 0.034 

Current progress: 50 percent done.
MAP4K3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.156770e-01	ci left: 9.701134e-02	ci right 1.090210e-01	k: 1029	n:10000
Cons ci ratio: 1.435388e-01	ci left: 6.439839e-02	ci right 7.445420e-02	k: 693	n:10000
KS ci ratio: 2.857317e-02	ci left: 6.435768e-01	ci right 6.623341e-01	k: 6530	n:10000
MAP4K3   10000 perm   2 sec   (5642 perm/sec)   p_kst 6.530000e-01   p_cons 6.930000e-02   p_joint 1.029000e-01

Joint ci ratio: 8.364291e-02	ci left: 9.479621e-02	ci right 1.031208e-01	k: 1978	n:20000
Cons ci ratio: 1.012254e-01	ci left: 6.620866e-02	ci right 7.331704e-02	k: 1394	n:20000
KS ci ratio: 2.004265e-02	ci left: 6.500219e-01	ci right 6.632325e-01	k: 13133	n:20000
MAP4K3   20000 perm   4 sec   (4923 perm/sec)   p_kst 6.566500e-01   p_cons 6.970000e-02   p_joint 9.890000e-02

Joint ci ratio: 5.785045e-02	ci left: 1.288801e-01	ci right 1.365912e-01	k: 3981	n:30000
Cons ci ratio: 8.182361e-02	ci left: 6.815148e-02	ci right 7.399858e-02	k: 2131	n:30000
KS ci ratio: 1.656928e-02	ci left: 6.456086e-01	ci right 6.564288e-01	k: 19531	n:30000
MAP4K3   30000 perm   6 sec   (4697 perm/sec)   p_kst 6.510333e-01   p_cons 7.103333e-02   p_joint 1.327000e-01

Outputting figure to mutsig2_images.part000000000102/MAP4K3.2_2821_30000_0.65103_0.071033_0.1327.png
                gene_name: MAP4K3
               theta_stop: 0.082 
                    nperm: 30000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.071 
      ci_cons_bounds_left: 0.068 
     ci_cons_bounds_right: 0.074 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 60 percent done.
MAP7D2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.087517e-02	ci left: 9.233773e-01	ci right 9.335714e-01	k: 9286	n:10000
Cons ci ratio: 4.943000e-02	ci left: 3.764427e-01	ci right 3.956238e-01	k: 3860	n:10000
KS ci ratio: 2.525240e-02	ci left: 6.976675e-01	ci right 7.156120e-01	k: 7067	n:10000
MAP7D2   10000 perm   2 sec   (5664 perm/sec)   p_kst 7.067000e-01   p_cons 3.860000e-01   p_joint 9.286000e-01

Outputting figure to mutsig2_images.part000000000102/MAP7D2.2_2386_10000_0.7067_0.386_0.9286.png
                gene_name: MAP7D2
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 70 percent done.
MAP7D3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.793285e-01	ci left: 4.149837e-02	ci right 4.976893e-02	k: 455	n:10000
Cons ci ratio: 1.715849e-01	ci left: 4.533038e-02	ci right 5.393440e-02	k: 495	n:10000
KS ci ratio: 6.273467e-02	ci left: 2.719080e-01	ci right 2.896199e-01	k: 2807	n:10000
MAP7D3   10000 perm   2 sec   (5530 perm/sec)   p_kst 2.807000e-01   p_cons 4.950000e-02   p_joint 4.550000e-02

Joint ci ratio: 1.231716e-01	ci left: 4.522388e-02	ci right 5.120834e-02	k: 963	n:20000
Cons ci ratio: 1.237799e-01	ci left: 4.478715e-02	ci right 5.074522e-02	k: 954	n:20000
KS ci ratio: 4.452567e-02	ci left: 2.730399e-01	ci right 2.855244e-01	k: 5585	n:20000
MAP7D3   20000 perm   4 sec   (4893 perm/sec)   p_kst 2.792500e-01   p_cons 4.770000e-02   p_joint 4.815000e-02

Joint ci ratio: 1.057021e-01	ci left: 4.151182e-02	ci right 4.617704e-02	k: 1314	n:30000
Cons ci ratio: 1.017208e-01	ci left: 4.476252e-02	ci right 4.959233e-02	k: 1414	n:30000
KS ci ratio: 3.658525e-02	ci left: 2.716760e-01	ci right 2.818340e-01	k: 8302	n:30000
MAP7D3   30000 perm   6 sec   (4660 perm/sec)   p_kst 2.767333e-01   p_cons 4.713333e-02   p_joint 4.380000e-02

Joint ci ratio: 9.693766e-02	ci left: 3.736799e-02	ci right 4.119926e-02	k: 1570	n:40000
Cons ci ratio: 8.815854e-02	ci left: 4.501985e-02	ci right 4.919622e-02	k: 1883	n:40000
KS ci ratio: 3.155110e-02	ci left: 2.740362e-01	ci right 2.828460e-01	k: 11137	n:40000
MAP7D3   40000 perm   9 sec   (4495 perm/sec)   p_kst 2.784250e-01   p_cons 4.707500e-02   p_joint 3.925000e-02

Outputting figure to mutsig2_images.part000000000102/MAP7D3.2_2723_40000_0.27842_0.047075_0.03925.png
                gene_name: MAP7D3
               theta_stop: 0.097 
                    nperm: 40000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.047 
      ci_cons_bounds_left: 0.045 
     ci_cons_bounds_right: 0.049 
                  p_joint: 0.039 
     ci_joint_bounds_left: 0.037 
    ci_joint_bounds_right: 0.041 

Current progress: 80 percent done.
MARK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.471454e-02	ci left: 5.506055e-01	ci right 5.701593e-01	k: 5604	n:10000
KS ci ratio: 1.704638e-02	ci left: 8.336838e-01	ci right 8.481171e-01	k: 8410	n:10000
MARK1   10000 perm   2 sec   (5595 perm/sec)   p_kst 8.410000e-01   p_cons 5.604000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000102/MARK1.2_2460_10000_0.841_0.5604_1.png
                gene_name: MARK1
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 90 percent done.
MAST1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.067200e-02	ci left: 2.854779e-01	ci right 3.034419e-01	k: 2944	n:10000
Cons ci ratio: 3.321714e-02	ci left: 5.722601e-01	ci right 5.916921e-01	k: 5820	n:10000
KS ci ratio: 2.595468e-01	ci left: 1.940213e-02	ci right 2.528070e-02	k: 222	n:10000
MAST1   10000 perm   2 sec   (4528 perm/sec)   p_kst 2.220000e-02   p_cons 5.820000e-01   p_joint 2.944000e-01

Joint ci ratio: 6.182768e-02	ci left: 1.621508e-01	ci right 1.725461e-01	k: 3346	n:20000
Cons ci ratio: 2.344842e-02	ci left: 5.759796e-01	ci right 5.896963e-01	k: 11657	n:20000
KS ci ratio: 1.920746e-01	ci left: 1.843815e-02	ci right 2.240301e-02	k: 407	n:20000
MAST1   20000 perm   5 sec   (4067 perm/sec)   p_kst 2.035000e-02   p_cons 5.828500e-01   p_joint 1.673000e-01

Joint ci ratio: 5.422957e-02	ci left: 1.442959e-01	ci right 1.523723e-01	k: 4449	n:30000
Cons ci ratio: 1.917284e-02	ci left: 5.765613e-01	ci right 5.877562e-01	k: 17465	n:30000
KS ci ratio: 1.599248e-01	ci left: 1.806137e-02	ci right 2.123262e-02	k: 588	n:30000
MAST1   30000 perm   8 sec   (3862 perm/sec)   p_kst 1.960000e-02   p_cons 5.821667e-01   p_joint 1.483000e-01

Joint ci ratio: 1.917274e-02	ci left: 5.060881e-01	ci right 5.159103e-01	k: 20440	n:40000
Cons ci ratio: 1.731930e-02	ci left: 5.566455e-01	ci right 5.663956e-01	k: 22461	n:40000
KS ci ratio: 1.373737e-01	ci left: 1.857798e-02	ci right 2.134233e-02	k: 797	n:40000
MAST1   40000 perm   11 sec   (3766 perm/sec)   p_kst 1.992500e-02   p_cons 5.615250e-01   p_joint 5.110000e-01

Joint ci ratio: 1.713708e-02	ci left: 5.069480e-01	ci right 5.157307e-01	k: 25567	n:50000
Cons ci ratio: 1.544837e-02	ci left: 5.585186e-01	ci right 5.672341e-01	k: 28144	n:50000
KS ci ratio: 1.227142e-01	ci left: 1.877140e-02	ci right 2.124477e-02	k: 999	n:50000
MAST1   50000 perm   14 sec   (3680 perm/sec)   p_kst 1.998000e-02   p_cons 5.628800e-01   p_joint 5.113400e-01

Joint ci ratio: 3.788019e-02	ci left: 1.485736e-01	ci right 1.543268e-01	k: 9086	n:60000
Cons ci ratio: 1.412766e-02	ci left: 5.580189e-01	ci right 5.659751e-01	k: 33720	n:60000
KS ci ratio: 1.128894e-01	ci left: 1.858679e-02	ci right 2.082667e-02	k: 1181	n:60000
MAST1   60000 perm   17 sec   (3615 perm/sec)   p_kst 1.968333e-02   p_cons 5.620000e-01   p_joint 1.514333e-01

Joint ci ratio: 1.772737e-02	ci left: 4.075943e-01	ci right 4.148988e-01	k: 28787	n:70000
Cons ci ratio: 1.309680e-02	ci left: 5.576715e-01	ci right 5.650377e-01	k: 39295	n:70000
KS ci ratio: 1.037127e-01	ci left: 1.896175e-02	ci right 2.104973e-02	k: 1399	n:70000
MAST1   70000 perm   20 sec   (3537 perm/sec)   p_kst 1.998571e-02   p_cons 5.613571e-01   p_joint 4.112429e-01

Joint ci ratio: 1.356081e-02	ci left: 5.074045e-01	ci right 5.143447e-01	k: 40870	n:80000
Cons ci ratio: 1.226452e-02	ci left: 5.573651e-01	ci right 5.642555e-01	k: 44865	n:80000
KS ci ratio: 9.689096e-02	ci left: 1.907766e-02	ci right 2.103236e-02	k: 1603	n:80000
MAST1   80000 perm   23 sec   (3486 perm/sec)   p_kst 2.003750e-02   p_cons 5.608125e-01   p_joint 5.108750e-01

Outputting figure to mutsig2_images.part000000000102/MAST1.2_4817_80000_0.020037_0.56081_0.51087.png
                gene_name: MAST1
               theta_stop: 0.097 
                    nperm: 80000 
                     p_ks: 0.020 
        ci_ks_bounds_left: 0.019 
       ci_ks_bounds_right: 0.021 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.51 
     ci_joint_bounds_left: 0.51 
    ci_joint_bounds_right: 0.51 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000102
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 102 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4398123: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000103> was used as the working directory.
Started at Wed Oct 24 16:14:07 2012
Results reported at Wed Oct 24 16:16:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000103.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000103.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 103  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000103.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    166.59 sec.
    Max Memory :      1431 MB
    Max Swap   :      4022 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
103
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 103
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 103: processing genes 9151 - 9240
Calculating significance of each gene.
Using projection method.
9151	MATN4	1
9152	MATR3	1
9153	MAVS	1
9154	MAX	2.998178e-02
9155	MAZ	1
9156	MB	1
9157	MBD1	1
9158	MBD2	1
9159	MBD3	1
9160	MBD3L1	1.548199e-02
9161	MBD4	1
9162	MBD5	1
9163	MBD6	7.243124e-02
9164	MBIP	1
9165	MBL2	1
9166	MBLAC1	1
9167	MBLAC2	1
9168	MBNL1	1
9169	MBNL2	1
9170	MBNL3	1
9171	MBOAT1	1
9172	MBOAT2	1
9173	MBOAT7	1
9174	MBP	1
9175	MBTD1	1.967698e-01
9176	MBTPS1	2.892864e-01
9177	MBTPS2	1
9178	MC1R	1
9179	MC2R	1
9180	MC3R	1
9181	MC4R	1
9182	MC5R	1.641874e-01
9183	MCAM	1
9184	MCART1	1
9185	MCART2	1
9186	MCART6	1
9187	MCAT	1
9188	MCC	1
9189	MCCC1	1
9190	MCCC2	1
9191	MCCD1	1
9192	MCEE	1
9193	MCF2	1.639163e-02
9194	MCF2L	4.533850e-01
9195	MCF2L2	1
9196	MCFD2	1
9197	MCHR1	1
9198	MCHR2	7.824230e-02
9199	MCL1	1
9200	MCM10	1
9201	MCM2	1.704407e-01
9202	MCM3	1
9203	MCM3AP	5.956334e-01
9204	MCM4	1
9205	MCM5	1
9206	MCM6	1
In gene MCM7 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 2220    n = 1	mu =   4.43e-07
9207	MCM7	5.382966e-03
9208	MCM8	3.692665e-01
9209	MCM9	1
9210	MCOLN1	7.368259e-02
9211	MCOLN2	1
9212	MCOLN3	1
9213	MCPH1	1
9214	MCRS1	1.626442e-01
9215	MCTP1	1
9216	MCTP2	3.915662e-01
9217	MCTS1	1
9218	MDC1	1
9219	MDFI	1
9220	MDFIC	1
9221	MDGA1	1
9222	MDGA2	1.091109e-01
9223	MDH1	1
9224	MDH1B	1
9225	MDH2	1
9226	MDK	1.124429e-02
9227	MDM1	1.858758e-01
9228	MDM2	1
9229	MDM4	1
9230	MDN1	1.658121e-01
9231	MDP1	1
9232	ME1	1
9233	ME2	1
9234	ME3	1
9235	MEA1	1
9236	MEAF6	1
9237	MECOM	1
9238	MECP2	2.461494e-01
9239	MECR	1
9240	MED1	9.407291e-03
Done

Running MutSig 2:
Scatter job 103: processing genes 9151 - 9240
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MDN1
Processing conservation and coverage...
58% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.499685e-02	ci left: 7.019041e-01	ci right 7.197729e-01	k: 7109	n:10000
Cons ci ratio: 2.528286e-02	ci left: 6.971632e-01	ci right 7.151166e-01	k: 7062	n:10000
KS ci ratio: 3.749872e-02	ci left: 5.122545e-01	ci right 5.319326e-01	k: 5221	n:10000
MDN1   10000 perm   4 sec   (2645 perm/sec)   p_kst 5.221000e-01   p_cons 7.062000e-01   p_joint 7.109000e-01

Outputting figure to mutsig2_images.part000000000103/MDN1.4_17199_10000_0.5221_0.7062_0.7109.png
                gene_name: MDN1
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 14 percent done.
MED1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.978118e-02	ci left: 6.244707e-01	ci right 6.434512e-01	k: 6340	n:10000
Cons ci ratio: 6.421114e-02	ci left: 2.627020e-01	ci right 2.802313e-01	k: 2714	n:10000
KS ci ratio: 4.334736e-02	ci left: 4.400155e-01	ci right 4.596137e-01	k: 4498	n:10000
MED1   10000 perm   2 sec   (4432 perm/sec)   p_kst 4.498000e-01   p_cons 2.714000e-01   p_joint 6.340000e-01

Outputting figure to mutsig2_images.part000000000103/MED1.4_4814_10000_0.4498_0.2714_0.634.png
                gene_name: MED1
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 29 percent done.
MBD6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.067232e-02	ci left: 3.648027e-01	ci right 3.838706e-01	k: 3743	n:10000
Cons ci ratio: 1.094953e-01	ci left: 1.073461e-01	ci right 1.198799e-01	k: 1135	n:10000
KS ci ratio: 1.108764e-01	ci left: 1.049071e-01	ci right 1.173205e-01	k: 1110	n:10000
MBD6   10000 perm   2 sec   (5635 perm/sec)   p_kst 1.110000e-01   p_cons 1.135000e-01   p_joint 3.743000e-01

Joint ci ratio: 7.493679e-02	ci left: 1.158219e-01	ci right 1.248888e-01	k: 2406	n:20000
Cons ci ratio: 7.818539e-02	ci left: 1.072678e-01	ci right 1.160454e-01	k: 2232	n:20000
KS ci ratio: 7.882259e-02	ci left: 1.056956e-01	ci right 1.144182e-01	k: 2200	n:20000
MBD6   20000 perm   4 sec   (5064 perm/sec)   p_kst 1.100000e-01   p_cons 1.116000e-01   p_joint 1.203000e-01

Outputting figure to mutsig2_images.part000000000103/MBD6.2_3056_20000_0.11_0.1116_0.1203.png
                gene_name: MBD6
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.12 

Current progress: 43 percent done.
MCF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.302283e-02	ci left: 2.154651e-01	ci right 2.318962e-01	k: 2236	n:10000
Cons ci ratio: 3.040660e-02	ci left: 6.147227e-01	ci right 6.338048e-01	k: 6243	n:10000
KS ci ratio: 1.020373e-01	ci left: 1.219999e-01	ci right 1.352172e-01	k: 1285	n:10000
MCF2   10000 perm   3 sec   (3539 perm/sec)   p_kst 1.285000e-01   p_cons 6.243000e-01   p_joint 2.236000e-01

Joint ci ratio: 4.423439e-02	ci left: 2.756715e-01	ci right 2.881919e-01	k: 5638	n:20000
Cons ci ratio: 2.145595e-02	ci left: 6.185488e-01	ci right 6.320148e-01	k: 12506	n:20000
KS ci ratio: 7.191211e-02	ci left: 1.246790e-01	ci right 1.340291e-01	k: 2586	n:20000
MCF2   20000 perm   5 sec   (3854 perm/sec)   p_kst 1.293000e-01   p_cons 6.253000e-01   p_joint 2.819000e-01

Outputting figure to mutsig2_images.part000000000103/MCF2.2_3201_20000_0.1293_0.6253_0.2819.png
                gene_name: MCF2
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 57 percent done.
MCM7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.742813e-02	ci left: 6.619944e-01	ci right 6.805058e-01	k: 6713	n:10000
Cons ci ratio: 8.867088e-03	ci left: 9.470021e-01	ci right 9.555325e-01	k: 9514	n:10000
KS ci ratio: 3.145934e-02	ci left: 5.985520e-01	ci right 6.177849e-01	k: 6082	n:10000
MCM7   10000 perm   2 sec   (5995 perm/sec)   p_kst 6.082000e-01   p_cons 9.514000e-01   p_joint 6.713000e-01

Outputting figure to mutsig2_images.part000000000103/MCM7.2_2220_10000_0.6082_0.9514_0.6713.png
                gene_name: MCM7
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    ci_joint_bounds_right: 0.68 

Current progress: 71 percent done.
MCRS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.202967e-02	ci left: 3.525721e-01	ci right 3.715083e-01	k: 3620	n:10000
Cons ci ratio: 8.876129e-02	ci left: 1.559077e-01	ci right 1.704891e-01	k: 1631	n:10000
KS ci ratio: 9.683164e-02	ci left: 1.339403e-01	ci right 1.476696e-01	k: 1407	n:10000
MCRS1   10000 perm   2 sec   (6513 perm/sec)   p_kst 1.407000e-01   p_cons 1.631000e-01   p_joint 3.620000e-01

Outputting figure to mutsig2_images.part000000000103/MCRS1.2_1498_10000_0.1407_0.1631_0.362.png
                gene_name: MCRS1
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 86 percent done.
MDGA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.703470e-02	ci left: 4.001384e-01	ci right 4.195142e-01	k: 4098	n:10000
Cons ci ratio: 2.821473e-02	ci left: 6.493117e-01	ci right 6.679958e-01	k: 6587	n:10000
KS ci ratio: 5.008264e-02	ci left: 3.702737e-01	ci right 3.893963e-01	k: 3798	n:10000
MDGA2   10000 perm   3 sec   (3621 perm/sec)   p_kst 3.798000e-01   p_cons 6.587000e-01   p_joint 4.098000e-01

Outputting figure to mutsig2_images.part000000000103/MDGA2.2_2939_10000_0.3798_0.6587_0.4098.png
                gene_name: MDGA2
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.67 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000103
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 103 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4398125: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000104> was used as the working directory.
Started at Wed Oct 24 16:14:07 2012
Results reported at Wed Oct 24 16:16:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000104.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000104.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 104  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000104.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    214.48 sec.
    Max Memory :       924 MB
    Max Swap   :      3835 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
104
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 104
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 104: processing genes 9241 - 9330
Calculating significance of each gene.
Using projection method.
9241	MED10	1
9242	MED11	1
9243	MED12	2.783766e-01
9244	MED12L	1.768380e-01
9245	MED13	4.527388e-01
9246	MED13L	1.764397e-01
9247	MED14	1
9248	MED15	1
9249	MED16	1
9250	MED17	6.929751e-02
9251	MED18	8.952764e-02
9252	MED19	1
9253	MED20	1
9254	MED21	1
9255	MED22	1
9256	MED23	1
9257	MED24	1
9258	MED25	1
9259	MED26	1
9260	MED27	1
9261	MED28	1
9262	MED29	1
9263	MED30	1
9264	MED31	4.118367e-03
9265	MED4	1
9266	MED6	1
9267	MED7	3.084959e-02
9268	MED8	1
9269	MED9	3.840755e-02
9270	MEF2A	1
9271	MEF2B	1
9272	MEF2C	8.085723e-02
9273	MEF2D	1
9274	MEFV	1
9275	MEGF10	3.197844e-01
9276	MEGF11	1
9277	MEGF6	1
9278	MEGF8	3.491149e-01
9279	MEGF9	1
9280	MEI1	1
9281	MEIG1	1
9282	MEIS1	1
9283	MEIS2	1
9284	MEIS3	1
9285	MELK	1
9286	MEMO1	1
9287	MEN1	1
9288	MEOX1	1
9289	MEOX2	1
9290	MEP1A	1
9291	MEP1B	1
9292	MEPCE	1
9293	MEPE	1.786479e-01
9294	MERTK	2.978597e-01
9295	MESDC1	1
9296	MESDC2	6.689708e-02
9297	MESP2	1
9298	MEST	1
9299	MET	1
9300	METAP1	1
9301	METAP2	1
9302	METRNL	1
9303	METT10D	1
9304	METT11D1	1
9305	METT5D1	1
9306	METTL1	1
9307	METTL10	1
9308	METTL11A	1
9309	METTL12	1
9310	METTL13	1.304555e-01
9311	METTL14	1
9312	METTL2A	1
9313	METTL2B	1.172875e-01
9314	METTL3	2.375894e-01
9315	METTL4	1
9316	METTL5	1
9317	METTL6	1
9318	METTL7A	1
9319	METTL7B	1
9320	METTL8	1
9321	METTL9	1
9322	MEX3A	1
9323	MEX3B	1
9324	MEX3C	1.688795e-01
9325	MEX3D	1
9326	MFAP1	1
9327	MFAP2	1
9328	MFAP3	1
9329	MFAP3L	1.045249e-01
9330	MFAP4	3.285746e-02
Done

Running MutSig 2:
Scatter job 104: processing genes 9241 - 9330
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MED12L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.281241e-02	ci left: 2.714129e-01	ci right 2.891153e-01	k: 2802	n:10000
KS ci ratio: 8.566287e-03	ci left: 9.502311e-01	ci right 9.585016e-01	k: 9545	n:10000
MED12L   10000 perm   3 sec   (3917 perm/sec)   p_kst 9.545000e-01   p_cons 2.802000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000104/MED12L.2_6610_10000_0.9545_0.2802_1.png
                gene_name: MED12L
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
MED13L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.483567e-02	ci left: 3.288264e-01	ci right 3.474680e-01	k: 3381	n:10000
Cons ci ratio: 5.136070e-02	ci left: 3.585374e-01	ci right 3.775395e-01	k: 3680	n:10000
KS ci ratio: 6.102425e-02	ci left: 2.831000e-01	ci right 3.010213e-01	k: 2920	n:10000
MED13L   10000 perm   3 sec   (3945 perm/sec)   p_kst 2.920000e-01   p_cons 3.680000e-01   p_joint 3.381000e-01

Outputting figure to mutsig2_images.part000000000104/MED13L.2_6757_10000_0.292_0.368_0.3381.png
                gene_name: MED13L
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.35 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000104
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 104 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 4398128: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000105> was used as the working directory.
Started at Wed Oct 24 16:14:07 2012
Results reported at Wed Oct 24 16:16:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000105.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000105.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 105  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000105.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    196.64 sec.
    Max Memory :      1447 MB
    Max Swap   :      4004 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
105
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 105
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 105: processing genes 9331 - 9420
Calculating significance of each gene.
Using projection method.
9331	MFAP5	1
9332	MFF	6.241143e-02
9333	MFGE8	1
9334	MFHAS1	1
9335	MFI2	1
9336	MFN1	1
9337	MFN2	1
9338	MFNG	1
9339	MFRP	1
9340	MFSD1	1
9341	MFSD10	1
9342	MFSD11	1
9343	MFSD2A	1
9344	MFSD2B	1
9345	MFSD3	1
9346	MFSD4	1
9347	MFSD5	1
9348	MFSD6	1.804600e-01
9349	MFSD6L	1
9350	MFSD7	1
9351	MFSD8	1
9352	MFSD9	1
9353	MGA	3.078304e-01
9354	MGAM	3.112554e-02
9355	MGAT1	1
9356	MGAT2	2.210036e-01
9357	MGAT3	1
9358	MGAT4A	1
9359	MGAT4B	1
In gene MGAT4C the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 1449    n = 1	mu =   4.43e-07
9360	MGAT4C	2.001314e-03
9361	MGAT5	1
9362	MGAT5B	2.824435e-01
9363	MGC26647	1
9364	MGC29506	1
9365	MGC42105	1
9366	MGEA5	5.958535e-02
9367	MGLL	1
9368	MGMT	1
9369	MGP	1
9370	MGRN1	1
9371	MGST1	1
9372	MGST2	1
9373	MGST3	1
9374	MIA	1
9375	MIA2	3.086957e-01
9376	MIA3	5.199305e-01
9377	MIB1	1
9378	MIB2	1
9379	MICAL1	1.877903e-01
9380	MICAL2	1
9381	MICAL3	1
9382	MICALCL	1
9383	MICALL1	3.093424e-01
9384	MICALL2	1
9385	MICB	1
9386	MID1	1
9387	MID1IP1	1
9388	MID2	1
9389	MIDN	1
9390	MIER1	2.813204e-01
9391	MIER2	1
9392	MIER3	1
9393	MIF	1
9394	MIF4GD	1
9395	MIIP	1
9396	MINA	1
9397	MINK1	1
9398	MINPP1	1
9399	MIOS	1
9400	MIOX	6.500136e-02
9401	MIP	1
9402	MIPEP	1
9403	MIPOL1	1
9404	MIS12	1
9405	MITD1	1
9406	MITF	1
9407	MIXL1	1
9408	MKI67	4.867194e-02
9409	MKI67IP	1
9410	MKKS	1
9411	MKL1	1
9412	MKL2	1
9413	MKLN1	1.426991e-01
9414	MKNK1	2.055901e-01
9415	MKNK2	1
9416	MKRN1	1
9417	MKRN2	1
9418	MKRN3	1.581301e-01
9419	MKS1	1
9420	MKX	1
Done

Running MutSig 2:
Scatter job 105: processing genes 9331 - 9420
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MGAT4C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.080236e-02	ci left: 3.636092e-01	ci right 3.826648e-01	k: 3731	n:10000
Cons ci ratio: 4.435067e-02	ci left: 4.287437e-01	ci right 4.482921e-01	k: 4385	n:10000
KS ci ratio: 7.921578e-02	ci left: 1.888498e-01	ci right 2.045273e-01	k: 1966	n:10000
MGAT4C   10000 perm   2 sec   (5340 perm/sec)   p_kst 1.966000e-01   p_cons 4.385000e-01   p_joint 3.731000e-01

Outputting figure to mutsig2_images.part000000000105/MGAT4C.3_1449_10000_0.1966_0.4385_0.3731.png
                gene_name: MGAT4C
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.38 

Current progress: 25 percent done.
MKI67
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.973629e-02	ci left: 6.251744e-01	ci right 6.441471e-01	k: 6347	n:10000
Cons ci ratio: 5.006139e-02	ci left: 3.704727e-01	ci right 3.895972e-01	k: 3800	n:10000
KS ci ratio: 1.691241e-02	ci left: 8.358217e-01	ci right 8.501778e-01	k: 8431	n:10000
MKI67   10000 perm   3 sec   (2934 perm/sec)   p_kst 8.431000e-01   p_cons 3.800000e-01   p_joint 6.347000e-01

Outputting figure to mutsig2_images.part000000000105/MKI67.3_9827_10000_0.8431_0.38_0.6347.png
                gene_name: MKI67
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.64 

Current progress: 50 percent done.
MGA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.951867e-02	ci left: 6.285922e-01	ci right 6.475273e-01	k: 6381	n:10000
Cons ci ratio: 6.145499e-03	ci left: 9.729141e-01	ci right 9.790043e-01	k: 9761	n:10000
KS ci ratio: 1.115553e-01	ci left: 1.037366e-01	ci right 1.160916e-01	k: 1098	n:10000
MGA   10000 perm   3 sec   (3128 perm/sec)   p_kst 1.098000e-01   p_cons 9.761000e-01   p_joint 6.381000e-01

Joint ci ratio: 2.080380e-02	ci left: 6.329513e-01	ci right 6.463081e-01	k: 12793	n:20000
Cons ci ratio: 4.308820e-03	ci left: 9.742528e-01	ci right 9.785071e-01	k: 19529	n:20000
KS ci ratio: 7.832365e-02	ci left: 1.069239e-01	ci right 1.156895e-01	k: 2225	n:20000
MGA   20000 perm   7 sec   (2944 perm/sec)   p_kst 1.112500e-01   p_cons 9.764500e-01   p_joint 6.396500e-01

Outputting figure to mutsig2_images.part000000000105/MGA.2_9290_20000_0.11125_0.97645_0.63965.png
                gene_name: MGA
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 75 percent done.
MGAM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.851016e-02	ci left: 6.445828e-01	ci right 6.633275e-01	k: 6540	n:10000
KS ci ratio: 6.158604e-03	ci left: 9.728080e-01	ci right 9.789104e-01	k: 9760	n:10000
MGAM   10000 perm   2 sec   (4245 perm/sec)   p_kst 9.760000e-01   p_cons 6.540000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000105/MGAM.2_5762_10000_0.976_0.654_1.png
                gene_name: MGAM
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.98 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000105
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 105 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1705>
Subject: Job 4398130: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000106> was used as the working directory.
Started at Wed Oct 24 16:14:10 2012
Results reported at Wed Oct 24 16:16:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000106.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000106.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 106  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000106.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    157.98 sec.
    Max Memory :      1460 MB
    Max Swap   :      3982 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
106
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 106
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 106: processing genes 9421 - 9509
Calculating significance of each gene.
Using projection method.
9421	MLANA	1
9422	MLC1	6.569181e-02
9423	MLEC	1
9424	MLF1	1
9425	MLF1IP	1
9426	MLF2	1
9427	MLH1	3.685905e-02
9428	MLH3	1
9429	MLKL	1
9430	MLL	6.348817e-01
In gene MLL2 the following bins exceed PROBCAP:
    CESC-C5-A1ML-TP	categ 7	N = 13615   n = 1	mu =   3.53e-08
9431	MLL2	2.762193e-02
9432	MLL3	8.894566e-04
9433	MLL4	2.181137e-01
9434	MLL5	3.272791e-01
9435	MLLT1	1
9436	MLLT10	4.166422e-01
9437	MLLT11	1
9438	MLLT3	1.805578e-01
9439	MLLT4	6.315108e-01
9440	MLLT6	1.546292e-01
9441	MLN	1
9442	MLNR	3.117233e-02
9443	MLPH	1
9444	MLST8	1
9445	MLX	1
9446	MLXIP	1
9447	MLXIPL	2.413244e-01
9448	MLYCD	1
9449	MMAA	1
9450	MMAB	1.129127e-01
9451	MMACHC	1
9452	MMADHC	1
9453	MMD	1
9454	MMD2	1
9455	MME	1
9456	MMEL1	5.878379e-04
9457	MMGT1	3.665539e-02
9458	MMP1	1
9459	MMP10	1
9460	MMP11	1
9461	MMP12	2.712173e-02
9462	MMP13	1
9463	MMP14	1
9464	MMP15	1
9465	MMP16	2.121530e-01
9466	MMP17	1
9467	MMP19	1
9468	MMP2	1
9469	MMP20	1
9470	MMP21	1
9471	MMP24	1
9472	MMP25	1
9473	MMP26	1.309130e-01
9474	MMP27	1.531842e-01
9475	MMP28	1
9476	MMP3	1
9477	MMP7	1
9478	MMP8	1.224865e-01
9479	MMP9	1
9480	MMRN1	2.317905e-01
9481	MMRN2	1
9482	MMS19	1
9483	MN1	1
9484	MNAT1	1
9485	MND1	1
9486	MNDA	5.679076e-02
9487	MNS1	1.300565e-01
9488	MNT	1
9489	MNX1	1
9490	MOAP1	1
9491	MOB2	1
9492	MOBKL1A	1
9493	MOBKL1B	1
9494	MOBKL2A	1
9495	MOBKL2B	1
9496	MOBKL2C	1
9497	MOBKL3	1
9498	MOBP	1
9499	MOCOS	1
9500	MOCS1	1
9501	MOCS2	1
9502	MOCS3	1
9503	MOG	1
9504	MOGAT1	4.983731e-02
9505	MOGAT2	1
9506	MOGAT3	1
9507	MOGS	1.466182e-01
9508	MON1A	1
9509	MON1B	1
Done

Running MutSig 2:
Scatter job 106: processing genes 9421 - 9509
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MLL3
Processing conservation and coverage...
66% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.084238e-02	ci left: 9.237903e-01	ci right 9.339582e-01	k: 9290	n:10000
Cons ci ratio: 1.399478e-02	ci left: 8.806319e-01	ci right 8.931418e-01	k: 8870	n:10000
KS ci ratio: 2.284895e-02	ci left: 7.377518e-01	ci right 7.549045e-01	k: 7464	n:10000
MLL3   10000 perm   4 sec   (2663 perm/sec)   p_kst 7.464000e-01   p_cons 8.870000e-01   p_joint 9.290000e-01

Outputting figure to mutsig2_images.part000000000106/MLL3.9_14972_10000_0.7464_0.887_0.929.png
                gene_name: MLL3
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 25 percent done.
MLL2
Processing conservation and coverage...
59% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.716131e-02	ci left: 3.988435e-01	ci right 4.182098e-01	k: 4085	n:10000
Cons ci ratio: 6.015053e-02	ci left: 2.890454e-01	ci right 3.070724e-01	k: 2980	n:10000
KS ci ratio: 6.800406e-02	ci left: 2.408450e-01	ci right 2.579012e-01	k: 2493	n:10000
MLL2   10000 perm   4 sec   (2759 perm/sec)   p_kst 2.493000e-01   p_cons 2.980000e-01   p_joint 4.085000e-01

Outputting figure to mutsig2_images.part000000000106/MLL2.6_16830_10000_0.2493_0.298_0.4085.png
                gene_name: MLL2
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.30 
      ci_cons_bounds_left: 0.29 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 50 percent done.
MMEL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.607094e-02	ci left: 6.841568e-01	ci right 7.023305e-01	k: 6933	n:10000
Cons ci ratio: 3.797060e-03	ci left: 9.887288e-01	ci right 9.925772e-01	k: 9908	n:10000
KS ci ratio: 3.732628e-02	ci left: 5.145559e-01	ci right 5.342298e-01	k: 5244	n:10000
MMEL1   10000 perm   2 sec   (5834 perm/sec)   p_kst 5.244000e-01   p_cons 9.908000e-01   p_joint 6.933000e-01

Outputting figure to mutsig2_images.part000000000106/MMEL1.4_2432_10000_0.5244_0.9908_0.6933.png
                gene_name: MMEL1
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.69 
     ci_joint_bounds_left: 0.68 
    ci_joint_bounds_right: 0.70 

Current progress: 75 percent done.
MLH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.776290e-02	ci left: 1.316879e-01	ci right 1.453234e-01	k: 1384	n:10000
Cons ci ratio: 6.714328e-02	ci left: 2.455898e-01	ci right 2.627536e-01	k: 2541	n:10000
KS ci ratio: 2.458026e-01	ci left: 2.174701e-02	ci right 2.793403e-02	k: 247	n:10000
MLH1   10000 perm   2 sec   (6213 perm/sec)   p_kst 2.470000e-02   p_cons 2.541000e-01   p_joint 1.384000e-01

Joint ci ratio: 8.741912e-02	ci left: 8.734272e-02	ci right 9.537654e-02	k: 1826	n:20000
Cons ci ratio: 4.778660e-02	ci left: 2.456968e-01	ci right 2.577755e-01	k: 5034	n:20000
KS ci ratio: 1.798538e-01	ci left: 2.111042e-02	ci right 2.532976e-02	k: 463	n:20000
MLH1   20000 perm   4 sec   (5540 perm/sec)   p_kst 2.315000e-02   p_cons 2.517000e-01   p_joint 9.130000e-02

Joint ci ratio: 5.902684e-02	ci left: 1.243706e-01	ci right 1.319682e-01	k: 3844	n:30000
Cons ci ratio: 3.890583e-02	ci left: 2.478894e-01	ci right 2.577585e-01	k: 7584	n:30000
KS ci ratio: 1.496256e-01	ci left: 2.069096e-02	ci right 2.406909e-02	k: 670	n:30000
MLH1   30000 perm   6 sec   (5272 perm/sec)   p_kst 2.233333e-02   p_cons 2.528000e-01   p_joint 1.281333e-01

Joint ci ratio: 5.293880e-02	ci left: 1.173496e-01	ci right 1.237556e-01	k: 4821	n:40000
Cons ci ratio: 3.331066e-02	ci left: 2.528721e-01	ci right 2.614632e-01	k: 10286	n:40000
KS ci ratio: 1.293339e-01	ci left: 2.099627e-02	ci right 2.392362e-02	k: 897	n:40000
MLH1   40000 perm   8 sec   (5102 perm/sec)   p_kst 2.242500e-02   p_cons 2.571500e-01   p_joint 1.205250e-01

Joint ci ratio: 6.312603e-02	ci left: 6.933532e-02	ci right 7.387457e-02	k: 3579	n:50000
Cons ci ratio: 2.967863e-02	ci left: 2.548059e-01	ci right 2.625021e-01	k: 12932	n:50000
KS ci ratio: 1.158120e-01	ci left: 2.110127e-02	ci right 2.371459e-02	k: 1119	n:50000
MLH1   50000 perm   10 sec   (4969 perm/sec)   p_kst 2.238000e-02   p_cons 2.586400e-01   p_joint 7.158000e-02

Joint ci ratio: 3.985701e-02	ci left: 1.360593e-01	ci right 1.416090e-01	k: 8329	n:60000
Cons ci ratio: 2.716786e-02	ci left: 2.540877e-01	ci right 2.611024e-01	k: 15455	n:60000
KS ci ratio: 1.059638e-01	ci left: 2.111710e-02	ci right 2.349609e-02	k: 1337	n:60000
MLH1   60000 perm   12 sec   (4854 perm/sec)   p_kst 2.228333e-02   p_cons 2.575833e-01   p_joint 1.388167e-01

Joint ci ratio: 3.676948e-02	ci left: 1.371113e-01	ci right 1.422614e-01	k: 9777	n:70000
Cons ci ratio: 2.515162e-02	ci left: 2.543634e-01	ci right 2.608567e-01	k: 18032	n:70000
KS ci ratio: 9.775179e-02	ci left: 2.135828e-02	ci right 2.356726e-02	k: 1571	n:70000
MLH1   70000 perm   15 sec   (4750 perm/sec)   p_kst 2.244286e-02   p_cons 2.576000e-01   p_joint 1.396714e-01

Outputting figure to mutsig2_images.part000000000106/MLH1.2_2347_70000_0.022443_0.2576_0.13967.png
                gene_name: MLH1
               theta_stop: 0.098 
                    nperm: 70000 
                     p_ks: 0.022 
        ci_ks_bounds_left: 0.021 
       ci_ks_bounds_right: 0.024 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.14 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000106
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 106 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4398132: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000107> was used as the working directory.
Started at Wed Oct 24 16:14:10 2012
Results reported at Wed Oct 24 16:15:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000107.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000107.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 107  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000107.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    131.50 sec.
    Max Memory :      1073 MB
    Max Swap   :      3880 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
107
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 107
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 107: processing genes 9510 - 9599
Calculating significance of each gene.
Using projection method.
9510	MON2	2.420170e-02
9511	MORC1	1
9512	MORC2	1
9513	MORC3	1
9514	MORC4	1.782984e-01
9515	MORF4	1
9516	MORF4L1	1
9517	MORF4L2	1
9518	MORN1	1
9519	MORN3	1
9520	MORN4	1
9521	MORN5	1
9522	MOS	1
9523	MOSC1	1
9524	MOSC2	1
9525	MOSPD1	1
9526	MOSPD2	1
9527	MOSPD3	1
9528	MOV10	2.912582e-01
9529	MOV10L1	1
9530	MOXD1	1
9531	MPDU1	1
9532	MPDZ	1
9533	MPEG1	1.896633e-01
9534	MPG	1
9535	MPHOSPH10	1
9536	MPHOSPH6	1
9537	MPHOSPH8	1
9538	MPHOSPH9	1
9539	MPI	1
9540	MPL	1
9541	MPND	1
9542	MPO	1
9543	MPP1	1
9544	MPP2	1
9545	MPP3	1
9546	MPP4	1
9547	MPP5	1
9548	MPP6	1
9549	MPP7	1
9550	MPPE1	1
9551	MPPED1	1
9552	MPPED2	1
9553	MPRIP	1
9554	MPST	1
9555	MPV17	1
9556	MPV17L	1
9557	MPV17L2	1
9558	MPZ	1
9559	MPZL1	5.336682e-02
9560	MPZL2	1
9561	MPZL3	1
9562	MR1	1
9563	MRAP	1
9564	MRAP2	1
9565	MRAS	1
9566	MRC2	1
9567	MRE11A	1
9568	MREG	1
9569	MRFAP1	1
9570	MRFAP1L1	1
9571	MRGPRD	1
9572	MRGPRE	1
9573	MRGPRF	1
9574	MRGPRX1	1
9575	MRGPRX2	1
9576	MRGPRX3	1
9577	MRGPRX4	1
9578	MRI1	1
9579	MRM1	1
9580	MRO	1
9581	MRP63	1
9582	MRPL1	1
9583	MRPL10	1
9584	MRPL11	1
9585	MRPL12	1
9586	MRPL13	1
9587	MRPL14	1
9588	MRPL15	1
9589	MRPL16	1
9590	MRPL17	1
9591	MRPL18	9.424733e-02
9592	MRPL19	1
9593	MRPL2	1
9594	MRPL20	1
9595	MRPL21	4.853298e-02
9596	MRPL22	1
9597	MRPL23	1
9598	MRPL24	1
9599	MRPL27	1
Done

Running MutSig 2:
Scatter job 107: processing genes 9510 - 9599
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MON2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.021741e-01	ci left: 1.217066e-01	ci right 1.349108e-01	k: 1282	n:10000
KS ci ratio: 1.135109e-02	ci left: 9.172915e-01	ci right 9.278607e-01	k: 9227	n:10000
MON2   10000 perm   2 sec   (4745 perm/sec)   p_kst 9.227000e-01   p_cons 1.282000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 7.336872e-02	ci left: 1.202987e-01	ci right 1.295107e-01	k: 2497	n:20000
KS ci ratio: 8.052736e-03	ci left: 9.184011e-01	ci right 9.258757e-01	k: 18444	n:20000
MON2   20000 perm   6 sec   (3089 perm/sec)   p_kst 9.222000e-01   p_cons 1.248500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000107/MON2.3_5294_20000_0.9222_0.12485_1.png
                gene_name: MON2
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000107
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 107 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4398134: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000108> was used as the working directory.
Started at Wed Oct 24 16:14:10 2012
Results reported at Wed Oct 24 16:15:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000108.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000108.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 108  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000108.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    124.42 sec.
    Max Memory :      1054 MB
    Max Swap   :      3872 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
108
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 108
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 108: processing genes 9600 - 9689
Calculating significance of each gene.
Using projection method.
9600	MRPL28	1
9601	MRPL3	1.681668e-02
9602	MRPL30	1
9603	MRPL32	1
9604	MRPL33	1
9605	MRPL34	1
9606	MRPL35	1.058731e-01
9607	MRPL36	1
9608	MRPL37	1
9609	MRPL38	1
9610	MRPL39	1
9611	MRPL4	1
9612	MRPL40	1
9613	MRPL41	1
9614	MRPL42	1
9615	MRPL43	1
9616	MRPL44	1
9617	MRPL45	1
9618	MRPL46	1
9619	MRPL47	1
9620	MRPL48	1
9621	MRPL49	1
9622	MRPL50	1
9623	MRPL51	1
9624	MRPL52	1
9625	MRPL53	1
9626	MRPL54	1
9627	MRPL55	1
9628	MRPL9	1
9629	MRPS10	1
9630	MRPS11	1
9631	MRPS12	1
9632	MRPS14	1
9633	MRPS15	1
9634	MRPS16	1
9635	MRPS17	1
9636	MRPS18A	1
9637	MRPS18B	1
9638	MRPS18C	1
9639	MRPS2	1
9640	MRPS21	1.138587e-02
9641	MRPS22	1.435437e-01
9642	MRPS23	1
9643	MRPS24	1
9644	MRPS25	1
9645	MRPS26	1
9646	MRPS27	1
9647	MRPS28	1
9648	MRPS30	8.852445e-02
9649	MRPS31	1
9650	MRPS33	1
9651	MRPS34	1
9652	MRPS35	1
9653	MRPS36	1
9654	MRPS5	1
9655	MRPS6	1
9656	MRPS7	1
9657	MRPS9	1
9658	MRRF	1
9659	MRS2	1
9660	MRTO4	1
9661	MRVI1	2.044514e-02
9662	MS4A1	1
9663	MS4A10	1
9664	MS4A12	1
9665	MS4A13	1.602065e-02
9666	MS4A14	5.188031e-02
9667	MS4A15	1
9668	MS4A2	1
9669	MS4A3	8.041113e-02
9670	MS4A4A	1
9671	MS4A5	1
9672	MS4A6A	1
9673	MS4A6E	1
9674	MS4A7	1
9675	MS4A8B	1
9676	MSC	1
9677	MSGN1	1
9678	MSH2	2.654439e-01
9679	MSH3	1
9680	MSH4	1
9681	MSH5	1
9682	MSH6	1
9683	MSI1	1
9684	MSI2	1
9685	MSL1	1
9686	MSL2	1
9687	MSL3	1
9688	MSLN	1
9689	MSLNL	1
Done

Running MutSig 2:
Scatter job 108: processing genes 9600 - 9689
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MRVI1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.870226e-02	ci left: 8.068419e-01	ci right 8.221744e-01	k: 8146	n:10000
Cons ci ratio: 2.754004e-02	ci left: 6.601821e-01	ci right 6.787191e-01	k: 6695	n:10000
KS ci ratio: 1.345173e-02	ci left: 8.885187e-01	ci right 9.006503e-01	k: 8947	n:10000
MRVI1   10000 perm   2 sec   (5603 perm/sec)   p_kst 8.947000e-01   p_cons 6.695000e-01   p_joint 8.146000e-01

Outputting figure to mutsig2_images.part000000000108/MRVI1.3_2792_10000_0.8947_0.6695_0.8146.png
                gene_name: MRVI1
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.82 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000108
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 108 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4398138: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000109> was used as the working directory.
Started at Wed Oct 24 16:14:20 2012
Results reported at Wed Oct 24 16:16:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000109.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000109.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 109  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000109.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     92.33 sec.
    Max Memory :      1706 MB
    Max Swap   :      4084 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
109
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 109
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 109: processing genes 9690 - 9778
Calculating significance of each gene.
Using projection method.
9690	MSMB	1
9691	MSMP	1
9692	MSN	1
9693	MSR1	1
9694	MSRA	1.012428e-01
9695	MSRB2	1
9696	MSRB3	5.765113e-03
9697	MST1	8.904245e-02
9698	MST1R	6.713859e-03
9699	MST4	1
9700	MSTN	8.224212e-02
9701	MSTO1	1
9702	MSX1	1
9703	MSX2	1
9704	MT1A	1
9705	MT1B	1
9706	MT1E	1
9707	MT1F	1
9708	MT1G	1
9709	MT1H	1
9710	MT1M	1
9711	MT1X	1
9712	MT2A	1
9713	MT3	1
9714	MT4	1
9715	MTA1	1
In gene MTA2 the following bins exceed PROBCAP:
    CESC-C5-A0TN-TP	categ 6	N = 2077    n = 1	mu =   6.94e-08
9716	MTA2	6.689938e-03
9717	MTA3	1
9718	MTAP	1
9719	MTBP	1
9720	MTCH1	1
9721	MTCH2	1
9722	MTCP1	1
9723	MTCP1NB	1
9724	MTDH	9.817299e-02
9725	MTERF	1
9726	MTERFD1	1
9727	MTERFD2	1
9728	MTERFD3	1
9729	MTF1	1
9730	MTF2	1
9731	MTFMT	1
9732	MTFR1	1.725410e-01
9733	MTG1	1
9734	MTHFD1	1
9735	MTHFD1L	1
9736	MTHFD2	1
9737	MTHFD2L	1
9738	MTHFR	3.022579e-02
9739	MTHFS	1
9740	MTHFSD	1
9741	MTIF2	2.661975e-01
9742	MTIF3	1
9743	MTL5	1.374724e-01
9744	MTM1	1
9745	MTMR1	2.629121e-02
9746	MTMR10	1
9747	MTMR11	1.500284e-01
9748	MTMR12	1
9749	MTMR14	1
9750	MTMR15	1.463370e-01
9751	MTMR2	1
9752	MTMR3	1
9753	MTMR4	1
9754	MTMR6	1
9755	MTMR7	1
9756	MTMR8	1.469453e-01
9757	MTMR9	1.023522e-01
9758	MTNR1A	1
9759	MTNR1B	1
9760	MTO1	1
9761	MTOR	2.212162e-01
9762	MTP18	1
9763	MTPAP	1
9764	MTPN	1
9765	MTR	1
9766	MTRF1	1.630145e-01
9767	MTRF1L	1
9768	MTRR	2.531753e-01
9769	MTSS1	3.418638e-01
9770	MTSS1L	1
9771	MTTP	1
9772	MTUS1	1
9773	MTUS2	1
9774	MTX1	1
9775	MTX2	1
9776	MTX3	1
9777	MUC1	1
9778	MUC13	2.238828e-01
Done

Running MutSig 2:
Scatter job 109: processing genes 9690 - 9778
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MST1R
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.467933e-02	ci left: 5.511066e-01	ci right 5.706579e-01	k: 5609	n:10000
Cons ci ratio: 1.011880e-02	ci left: 9.326804e-01	ci right 9.422628e-01	k: 9376	n:10000
KS ci ratio: 7.027581e-02	ci left: 2.288905e-01	ci right 2.456629e-01	k: 2372	n:10000
MST1R   10000 perm   2 sec   (4184 perm/sec)   p_kst 2.372000e-01   p_cons 9.376000e-01   p_joint 5.609000e-01

Outputting figure to mutsig2_images.part000000000109/MST1R.3_4283_10000_0.2372_0.9376_0.5609.png
                gene_name: MST1R
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.57 

Current progress: 14 percent done.
MTA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.641285e-03	ci left: 9.768488e-01	ci right 9.824669e-01	k: 9798	n:10000
Cons ci ratio: 4.885111e-02	ci left: 3.820160e-01	ci right 4.012472e-01	k: 3916	n:10000
KS ci ratio: 7.067756e-03	ci left: 9.649925e-01	ci right 9.719311e-01	k: 9686	n:10000
MTA2   10000 perm   2 sec   (6507 perm/sec)   p_kst 9.686000e-01   p_cons 3.916000e-01   p_joint 9.798000e-01

Outputting figure to mutsig2_images.part000000000109/MTA2.2_2079_10000_0.9686_0.3916_0.9798.png
                gene_name: MTA2
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 29 percent done.
MTDH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.350447e-02	ci left: 2.670569e-01	ci right 2.846738e-01	k: 2758	n:10000
KS ci ratio: 8.096203e-02	ci left: 1.821553e-01	ci right 1.976258e-01	k: 1898	n:10000
MTDH   10000 perm   1 sec   (7451 perm/sec)   p_kst 1.898000e-01   p_cons 2.758000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000109/MTDH.2_1797_10000_0.1898_0.2758_1.png
                gene_name: MTDH
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.28 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 43 percent done.
MTHFR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.436877e-02	ci left: 8.751064e-01	ci right 8.878705e-01	k: 8816	n:10000
Cons ci ratio: 7.901581e-02	ci left: 1.896376e-01	ci right 2.053390e-01	k: 1974	n:10000
KS ci ratio: 2.517934e-02	ci left: 6.988779e-01	ci right 7.168009e-01	k: 7079	n:10000
MTHFR   10000 perm   1 sec   (6995 perm/sec)   p_kst 7.079000e-01   p_cons 1.974000e-01   p_joint 8.816000e-01

Outputting figure to mutsig2_images.part000000000109/MTHFR.2_2015_10000_0.7079_0.1974_0.8816.png
                gene_name: MTHFR
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 57 percent done.
MTMR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.632250e-02	ci left: 6.800247e-01	ci right 6.982650e-01	k: 6892	n:10000
Cons ci ratio: 4.559696e-02	ci left: 4.151844e-01	ci right 4.346594e-01	k: 4249	n:10000
KS ci ratio: 3.154520e-02	ci left: 5.972468e-01	ci right 6.164909e-01	k: 6069	n:10000
MTMR1   10000 perm   1 sec   (7130 perm/sec)   p_kst 6.069000e-01   p_cons 4.249000e-01   p_joint 6.892000e-01

Outputting figure to mutsig2_images.part000000000109/MTMR1.2_2058_10000_0.6069_0.4249_0.6892.png
                gene_name: MTMR1
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.69 
     ci_joint_bounds_left: 0.68 
    ci_joint_bounds_right: 0.70 

Current progress: 71 percent done.
MTMR15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.451967e-02	ci left: 8.728564e-01	ci right 8.857217e-01	k: 8794	n:10000
Cons ci ratio: 1.604104e-02	ci left: 8.495769e-01	ci right 8.634147e-01	k: 8566	n:10000
KS ci ratio: 2.458394e-02	ci left: 7.087653e-01	ci right 7.265077e-01	k: 7177	n:10000
MTMR15   10000 perm   1 sec   (6688 perm/sec)   p_kst 7.177000e-01   p_cons 8.566000e-01   p_joint 8.794000e-01

Outputting figure to mutsig2_images.part000000000109/MTMR15.2_3131_10000_0.7177_0.8566_0.8794.png
                gene_name: MTMR15
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.87 
    ci_joint_bounds_right: 0.89 

Current progress: 86 percent done.
MTOR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.948217e-02	ci left: 3.759451e-01	ci right 3.951216e-01	k: 3855	n:10000
KS ci ratio: 9.234243e-03	ci left: 9.429466e-01	ci right 9.517905e-01	k: 9475	n:10000
MTOR   10000 perm   2 sec   (4976 perm/sec)   p_kst 9.475000e-01   p_cons 3.855000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000109/MTOR.2_7878_10000_0.9475_0.3855_1.png
                gene_name: MTOR
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.94 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000109
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 109 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 4398140: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000110> was used as the working directory.
Started at Wed Oct 24 16:14:23 2012
Results reported at Wed Oct 24 16:18:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000110.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000110.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 110  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000110.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    277.89 sec.
    Max Memory :      1533 MB
    Max Swap   :      3997 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
110
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 110
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 110: processing genes 9779 - 9868
Calculating significance of each gene.
Using projection method.
9779	MUC15	1
9780	MUC16	9.903376e-01
In gene MUC17 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 13534   n = 1	mu =   4.43e-07
9781	MUC17	1.998109e-01
9782	MUC2	1
9783	MUC20	1
9784	MUC21	1
9785	MUC4	6.256320e-02
9786	MUC5B	6.688641e-01
9787	MUC6	5.089593e-01
9788	MUC7	1
9789	MUCL1	1
9790	MUDENG	1
9791	MUL1	1
9792	MUM1	1.644557e-01
9793	MUM1L1	1
9794	MURC	1
9795	MUS81	1
9796	MUSK	1.176958e-01
9797	MUSTN1	1
9798	MUT	1
9799	MUTED	1
9800	MUTYH	1.131815e-01
9801	MVD	1
9802	MVK	1
9803	MVP	9.868041e-02
9804	MX1	2.021782e-01
9805	MX2	1
9806	MXD1	1
9807	MXD3	1
9808	MXD4	1
9809	MXI1	1
9810	MXRA5	4.208797e-02
9811	MXRA7	1
9812	MXRA8	1
9813	MYADM	3.304731e-02
9814	MYB	1
9815	MYBBP1A	1
9816	MYBL1	1
9817	MYBL2	1
9818	MYBPC1	1
9819	MYBPC2	3.795931e-01
9820	MYBPC3	1
9821	MYBPH	1
9822	MYBPHL	1
9823	MYC	1
9824	MYCBP	2.293151e-02
9825	MYCBP2	2.569782e-01
9826	MYCBPAP	1
9827	MYCL1	1
9828	MYCN	1
9829	MYCT1	1
9830	MYD88	1
9831	MYEF2	1
9832	MYEOV	9.379706e-02
9833	MYEOV2	1
9834	MYF5	1
9835	MYF6	4.459571e-02
9836	MYH1	2.378746e-01
9837	MYH10	1.953645e-01
9838	MYH11	3.870988e-01
9839	MYH13	6.754041e-01
9840	MYH14	6.258233e-02
9841	MYH15	1.596057e-01
9842	MYH2	3.022508e-01
9843	MYH3	7.009870e-01
9844	MYH4	1
9845	MYH6	4.702888e-01
9846	MYH7	4.716299e-02
9847	MYH7B	4.553833e-01
9848	MYH8	9.753056e-03
In gene MYH9 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 6043    n = 1	mu =   4.43e-07
9849	MYH9	5.041367e-03
9850	MYL1	1
9851	MYL10	1
9852	MYL12A	1
9853	MYL12B	1
9854	MYL2	1
9855	MYL3	1
9856	MYL4	1
9857	MYL5	1
9858	MYL6	1
9859	MYL6B	1
9860	MYL7	1
9861	MYL9	1
9862	MYLIP	1
9863	MYLK	1
9864	MYLK2	1
9865	MYLK3	2.471154e-01
9866	MYLK4	2.137043e-01
9867	MYLPF	1
9868	MYNN	1
Done

Running MutSig 2:
Scatter job 110: processing genes 9779 - 9868
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MUC16
Processing conservation and coverage...
22% 45% 68% 91% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.180519e-02	ci left: 3.545604e-01	ci right 3.735189e-01	k: 3640	n:10000
Cons ci ratio: 8.092922e-03	ci left: 9.551367e-01	ci right 9.629931e-01	k: 9592	n:10000
KS ci ratio: 1.067067e-01	ci left: 1.125202e-01	ci right 1.253028e-01	k: 1188	n:10000
MUC16   10000 perm   7 sec   (1478 perm/sec)   p_kst 1.188000e-01   p_cons 9.592000e-01   p_joint 3.640000e-01

Joint ci ratio: 5.147250e-02	ci left: 2.189803e-01	ci right 2.305998e-01	k: 4495	n:20000
Cons ci ratio: 5.705026e-03	ci left: 9.565722e-01	ci right 9.620933e-01	k: 19188	n:20000
KS ci ratio: 7.850234e-02	ci left: 1.064817e-01	ci right 1.152318e-01	k: 2216	n:20000
MUC16   20000 perm   16 sec   (1232 perm/sec)   p_kst 1.108000e-01   p_cons 9.594000e-01   p_joint 2.247500e-01

Outputting figure to mutsig2_images.part000000000110/MUC16.10_43860_20000_0.1108_0.9594_0.22475.png
                gene_name: MUC16
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 7 percent done.
MUC17
Processing conservation and coverage...
73% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.074603e-02	ci left: 7.729656e-01	ci right 7.892703e-01	k: 7812	n:10000
KS ci ratio: 2.245076e-02	ci left: 7.444244e-01	ci right 7.614280e-01	k: 7530	n:10000
MUC17   10000 perm   3 sec   (3044 perm/sec)   p_kst 7.530000e-01   p_cons 7.812000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000110/MUC17.7_13534_10000_0.753_0.7812_1.png
                gene_name: MUC17
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 13 percent done.
MYH9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.537082e-02	ci left: 2.048126e-01	ci right 2.209550e-01	k: 2128	n:10000
Cons ci ratio: 7.122053e-02	ci left: 2.241507e-01	ci right 2.408054e-01	k: 2324	n:10000
KS ci ratio: 6.273467e-02	ci left: 2.719080e-01	ci right 2.896199e-01	k: 2807	n:10000
MYH9   10000 perm   2 sec   (4185 perm/sec)   p_kst 2.807000e-01   p_cons 2.324000e-01   p_joint 2.128000e-01

Outputting figure to mutsig2_images.part000000000110/MYH9.6_6043_10000_0.2807_0.2324_0.2128.png
                gene_name: MYH9
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 20 percent done.
MXRA5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.257984e-01	ci left: 8.290659e-02	ci right 9.413446e-02	k: 884	n:10000
Cons ci ratio: 8.380712e-02	ci left: 1.719241e-01	ci right 1.870631e-01	k: 1794	n:10000
KS ci ratio: 1.785097e-01	ci left: 4.188120e-02	ci right 5.018585e-02	k: 459	n:10000
MXRA5   10000 perm   3 sec   (3972 perm/sec)   p_kst 4.590000e-02   p_cons 1.794000e-01   p_joint 8.840000e-02

Joint ci ratio: 1.229707e-01	ci left: 4.536948e-02	ci right 5.136270e-02	k: 966	n:20000
Cons ci ratio: 5.858627e-02	ci left: 1.775143e-01	ci right 1.882781e-01	k: 3657	n:20000
KS ci ratio: 1.281378e-01	ci left: 4.182901e-02	ci right 4.760429e-02	k: 893	n:20000
MXRA5   20000 perm   5 sec   (3637 perm/sec)   p_kst 4.465000e-02   p_cons 1.828500e-01   p_joint 4.830000e-02

Joint ci ratio: 1.189535e-01	ci left: 3.285172e-02	ci right 3.703897e-02	k: 1047	n:30000
Cons ci ratio: 4.641768e-02	ci left: 1.875893e-01	ci right 1.965370e-01	k: 5761	n:30000
KS ci ratio: 1.038971e-01	ci left: 4.294170e-02	ci right 4.768020e-02	k: 1358	n:30000
MXRA5   30000 perm   9 sec   (3504 perm/sec)   p_kst 4.526667e-02   p_cons 1.920333e-01   p_joint 3.490000e-02

Joint ci ratio: 1.023486e-01	ci left: 3.356163e-02	ci right 3.720622e-02	k: 1414	n:40000
Cons ci ratio: 4.030832e-02	ci left: 1.873563e-01	ci right 1.950886e-01	k: 7648	n:40000
KS ci ratio: 9.029144e-02	ci left: 4.296459e-02	ci right 4.705179e-02	k: 1799	n:40000
MXRA5   40000 perm   12 sec   (3429 perm/sec)   p_kst 4.497500e-02   p_cons 1.912000e-01   p_joint 3.535000e-02

Joint ci ratio: 1.008679e-01	ci left: 2.783916e-02	ci right 3.081582e-02	k: 1465	n:50000
Cons ci ratio: 3.611656e-02	ci left: 1.872249e-01	ci right 1.941311e-01	k: 9533	n:50000
KS ci ratio: 8.154030e-02	ci left: 4.237569e-02	ci right 4.599747e-02	k: 2208	n:50000
MXRA5   50000 perm   15 sec   (3362 perm/sec)   p_kst 4.416000e-02   p_cons 1.906600e-01   p_joint 2.930000e-02

Joint ci ratio: 8.797033e-02	ci left: 3.062238e-02	ci right 3.345645e-02	k: 1921	n:60000
Cons ci ratio: 3.318824e-02	ci left: 1.855098e-01	ci right 1.917870e-01	k: 11318	n:60000
KS ci ratio: 7.455071e-02	ci left: 4.240542e-02	ci right 4.570553e-02	k: 2642	n:60000
MXRA5   60000 perm   18 sec   (3300 perm/sec)   p_kst 4.403333e-02   p_cons 1.886333e-01   p_joint 3.201667e-02

Outputting figure to mutsig2_images.part000000000110/MXRA5.4_8511_60000_0.044033_0.18863_0.032017.png
                gene_name: MXRA5
               theta_stop: 0.088 
                    nperm: 60000 
                     p_ks: 0.044 
        ci_ks_bounds_left: 0.042 
       ci_ks_bounds_right: 0.046 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.032 
     ci_joint_bounds_left: 0.031 
    ci_joint_bounds_right: 0.033 

Current progress: 27 percent done.
MYCBP2
Processing conservation and coverage...
69% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.440474e-02	ci left: 4.281453e-01	ci right 4.476909e-01	k: 4379	n:10000
KS ci ratio: 1.026480e-02	ci left: 9.309212e-01	ci right 9.406231e-01	k: 9359	n:10000
MYCBP2   10000 perm   3 sec   (3234 perm/sec)   p_kst 9.359000e-01   p_cons 4.379000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000110/MYCBP2.4_14369_10000_0.9359_0.4379_1.png
                gene_name: MYCBP2
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
MYH7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.287501e-02	ci left: 1.441328e-01	ci right 1.582710e-01	k: 1511	n:10000
Cons ci ratio: 8.633875e-02	ci left: 1.634706e-01	ci right 1.783216e-01	k: 1708	n:10000
KS ci ratio: 7.815390e-02	ci left: 1.930849e-01	ci right 2.088897e-01	k: 2009	n:10000
MYH7   10000 perm   2 sec   (4666 perm/sec)   p_kst 2.009000e-01   p_cons 1.708000e-01   p_joint 1.511000e-01

Outputting figure to mutsig2_images.part000000000110/MYH7.4_5960_10000_0.2009_0.1708_0.1511.png
                gene_name: MYH7
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.16 

Current progress: 40 percent done.
MYH8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.950888e-02	ci left: 4.861529e-01	ci right 5.058495e-01	k: 4960	n:10000
Cons ci ratio: 1.504163e-02	ci left: 8.649871e-01	ci right 8.781956e-01	k: 8717	n:10000
KS ci ratio: 4.834243e-02	ci left: 3.869933e-01	ci right 4.062670e-01	k: 3966	n:10000
MYH8   10000 perm   2 sec   (4554 perm/sec)   p_kst 3.966000e-01   p_cons 8.717000e-01   p_joint 4.960000e-01

Outputting figure to mutsig2_images.part000000000110/MYH8.4_5966_10000_0.3966_0.8717_0.496.png
                gene_name: MYH8
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.88 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 47 percent done.
MYH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.575590e-02	ci left: 4.134900e-01	ci right 4.329547e-01	k: 4232	n:10000
Cons ci ratio: 1.639828e-02	ci left: 8.439706e-01	ci right 8.580243e-01	k: 8511	n:10000
KS ci ratio: 4.575590e-02	ci left: 4.134900e-01	ci right 4.329547e-01	k: 4232	n:10000
MYH1   10000 perm   2 sec   (4846 perm/sec)   p_kst 4.232000e-01   p_cons 8.511000e-01   p_joint 4.232000e-01

Outputting figure to mutsig2_images.part000000000110/MYH1.3_5972_10000_0.4232_0.8511_0.4232.png
                gene_name: MYH1
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 53 percent done.
MYH15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.675415e-02	ci left: 5.222622e-01	ci right 5.419191e-01	k: 5321	n:10000
Cons ci ratio: 1.308071e-01	ci left: 7.698582e-02	ci right 8.785890e-02	k: 823	n:10000
KS ci ratio: 1.438252e-02	ci left: 8.749018e-01	ci right 8.876752e-01	k: 8814	n:10000
MYH15   10000 perm   2 sec   (4633 perm/sec)   p_kst 8.814000e-01   p_cons 8.230000e-02   p_joint 5.321000e-01

Joint ci ratio: 3.675857e-02	ci left: 3.557832e-01	ci right 3.691568e-01	k: 7249	n:20000
Cons ci ratio: 9.240486e-02	ci left: 7.872292e-02	ci right 8.639896e-02	k: 1650	n:20000
KS ci ratio: 9.993046e-03	ci left: 8.804976e-01	ci right 8.893901e-01	k: 17700	n:20000
MYH15   20000 perm   5 sec   (4206 perm/sec)   p_kst 8.850000e-01   p_cons 8.250000e-02   p_joint 3.624500e-01

Outputting figure to mutsig2_images.part000000000110/MYH15.3_6009_20000_0.885_0.0825_0.36245.png
                gene_name: MYH15
               theta_stop: 0.092 
                    nperm: 20000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.083 
      ci_cons_bounds_left: 0.079 
     ci_cons_bounds_right: 0.086 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 60 percent done.
MYH6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.892855e-02	ci left: 4.935506e-01	ci right 5.132474e-01	k: 5034	n:10000
Cons ci ratio: 1.125939e-01	ci left: 1.019814e-01	ci right 1.142479e-01	k: 1080	n:10000
KS ci ratio: 3.409876e-02	ci left: 5.594255e-01	ci right 5.789342e-01	k: 5692	n:10000
MYH6   10000 perm   2 sec   (4654 perm/sec)   p_kst 5.692000e-01   p_cons 1.080000e-01   p_joint 5.034000e-01

Joint ci ratio: 2.770819e-02	ci left: 4.931959e-01	ci right 5.071041e-01	k: 10003	n:20000
Cons ci ratio: 7.935020e-02	ci left: 1.044183e-01	ci right 1.130958e-01	k: 2174	n:20000
KS ci ratio: 2.444149e-02	ci left: 5.556412e-01	ci right 5.694406e-01	k: 11251	n:20000
MYH6   20000 perm   5 sec   (4246 perm/sec)   p_kst 5.625500e-01   p_cons 1.087000e-01   p_joint 5.001500e-01

Outputting figure to mutsig2_images.part000000000110/MYH6.3_5968_20000_0.56255_0.1087_0.50015.png
                gene_name: MYH6
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 67 percent done.
MUC4
Processing conservation and coverage...
Processing mutations... 
Skipping 1 mutations outside exons of this gene.
Fewer than 2 mutations to analyze: skipping this gene...
Current progress: 73 percent done.
MUC5B
Processing conservation and coverage...
57% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.973370e-02	ci left: 3.735570e-01	ci right 3.927111e-01	k: 3831	n:10000
Cons ci ratio: 4.536454e-02	ci left: 4.176764e-01	ci right 4.371659e-01	k: 4274	n:10000
KS ci ratio: 1.108203e-01	ci left: 1.050046e-01	ci right 1.174229e-01	k: 1111	n:10000
MUC5B   10000 perm   3 sec   (2873 perm/sec)   p_kst 1.111000e-01   p_cons 4.274000e-01   p_joint 3.831000e-01

Joint ci ratio: 2.361516e-02	ci left: 5.725223e-01	ci right 5.862546e-01	k: 11588	n:20000
Cons ci ratio: 3.076864e-02	ci left: 4.410411e-01	ci right 4.548740e-01	k: 8959	n:20000
KS ci ratio: 7.824457e-02	ci left: 1.071204e-01	ci right 1.158929e-01	k: 2229	n:20000
MUC5B   20000 perm   8 sec   (2645 perm/sec)   p_kst 1.114500e-01   p_cons 4.479500e-01   p_joint 5.794000e-01

Outputting figure to mutsig2_images.part000000000110/MUC5B.2_17494_20000_0.11145_0.44795_0.5794.png
                gene_name: MUC5B
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 80 percent done.
MUM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.924448e-02	ci left: 6.329156e-01	ci right 6.518014e-01	k: 6424	n:10000
KS ci ratio: 5.498298e-02	ci left: 3.276348e-01	ci right 3.462602e-01	k: 3369	n:10000
MUM1   10000 perm   2 sec   (6207 perm/sec)   p_kst 3.369000e-01   p_cons 6.424000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000110/MUM1.2_2188_10000_0.3369_0.6424_1.png
                gene_name: MUM1
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 87 percent done.
MYH10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.053201e-02	ci left: 3.660957e-01	ci right 3.851768e-01	k: 3756	n:10000
Cons ci ratio: 9.131878e-03	ci left: 9.440897e-01	ci right 9.528467e-01	k: 9486	n:10000
KS ci ratio: 6.340926e-02	ci left: 2.676508e-01	ci right 2.852796e-01	k: 2764	n:10000
MYH10   10000 perm   2 sec   (4757 perm/sec)   p_kst 2.764000e-01   p_cons 9.486000e-01   p_joint 3.756000e-01

Outputting figure to mutsig2_images.part000000000110/MYH10.2_6091_10000_0.2764_0.9486_0.3756.png
                gene_name: MYH10
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 93 percent done.
MYH14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.481309e-02	ci left: 2.072778e-01	ci right 2.234884e-01	k: 2153	n:10000
Cons ci ratio: 1.315017e-02	ci left: 8.928248e-01	ci right 9.047417e-01	k: 8989	n:10000
KS ci ratio: 8.162590e-02	ci left: 1.796951e-01	ci right 1.950875e-01	k: 1873	n:10000
MYH14   10000 perm   2 sec   (4585 perm/sec)   p_kst 1.873000e-01   p_cons 8.989000e-01   p_joint 2.153000e-01

Outputting figure to mutsig2_images.part000000000110/MYH14.2_6279_10000_0.1873_0.8989_0.2153.png
                gene_name: MYH14
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000110
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 110 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1553>
Subject: Job 4398145: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1553>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000111> was used as the working directory.
Started at Wed Oct 24 16:14:29 2012
Results reported at Wed Oct 24 16:17:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000111.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000111.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 111  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000111.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    259.21 sec.
    Max Memory :      1622 MB
    Max Swap   :      4104 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
111
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 111
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 111: processing genes 9869 - 9958
Calculating significance of each gene.
Using projection method.
9869	MYO10	6.544332e-01
9870	MYO15A	7.569712e-02
9871	MYO16	1
9872	MYO18A	3.764513e-01
9873	MYO18B	1
9874	MYO19	1
9875	MYO1A	4.564592e-01
9876	MYO1B	1
9877	MYO1C	1
9878	MYO1D	1
9879	MYO1E	1
9880	MYO1F	3.952564e-01
9881	MYO1G	1
9882	MYO1H	2.865951e-01
9883	MYO3A	1
9884	MYO3B	1
9885	MYO5A	1.489495e-01
9886	MYO5B	1
9887	MYO5C	1.107117e-01
9888	MYO6	1
9889	MYO7A	1
9890	MYO7B	1
9891	MYO9A	4.995384e-01
9892	MYO9B	4.576941e-01
9893	MYOC	1
9894	MYOCD	1
9895	MYOD1	1
9896	MYOF	2.457425e-02
9897	MYOG	1
9898	MYOM1	1
9899	MYOM2	2.646822e-01
9900	MYOM3	6.621554e-02
9901	MYOT	1.341474e-01
9902	MYOZ1	1
9903	MYOZ2	1
9904	MYOZ3	1
9905	MYPN	1
9906	MYPOP	1
9907	MYRIP	2.923605e-01
9908	MYSM1	2.382505e-01
9909	MYST1	1.300168e-01
9910	MYST2	1
9911	MYST3	2.350240e-01
9912	MYST4	1
9913	MYT1	1.841519e-01
9914	MYT1L	2.467436e-02
9915	MZF1	1
9916	N4BP1	1
9917	N4BP2	1
9918	N4BP2L1	1
9919	N4BP2L2	1
9920	N4BP3	1.063691e-01
9921	N6AMT1	1
9922	N6AMT2	1
9923	NAA10	1
9924	NAA11	1
9925	NAA15	1.029863e-02
9926	NAA16	1.674909e-01
9927	NAA20	1
9928	NAA25	1
9929	NAA30	1
9930	NAA35	1
9931	NAA38	1
9932	NAA40	1
9933	NAA50	1
9934	NAAA	1
9935	NAALAD2	1
9936	NAALADL1	1
9937	NAALADL2	2.552685e-01
9938	NAB1	1
9939	NAB2	1
9940	NACA	1
9941	NACA2	1
9942	NACC1	7.753234e-02
9943	NACC2	1
9944	NADK	1
9945	NADSYN1	1
9946	NAE1	1
9947	NAF1	1
9948	NAGA	1.671323e-01
9949	NAGK	1
9950	NAGLU	1
9951	NAGPA	1
9952	NAGS	1
9953	NAIF1	1
9954	NALCN	1
9955	NAMPT	1
9956	NANOG	1
9957	NANOS2	1
9958	NANOS3	1
Done

Running MutSig 2:
Scatter job 111: processing genes 9869 - 9958
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MYO15A
Processing conservation and coverage...
92% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.205735e-03	ci left: 9.539874e-01	ci right 9.619430e-01	k: 9581	n:10000
KS ci ratio: 1.161133e-02	ci left: 9.138916e-01	ci right 9.246627e-01	k: 9194	n:10000
MYO15A   10000 perm   3 sec   (2890 perm/sec)   p_kst 9.194000e-01   p_cons 9.581000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000111/MYO15A.3_10849_10000_0.9194_0.9581_1.png
                gene_name: MYO15A
               theta_stop: 0.012 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 12 percent done.
MYOF
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.855334e-02	ci left: 2.378802e-01	ci right 2.548678e-01	k: 2463	n:10000
Cons ci ratio: 4.282482e-03	ci left: 9.859942e-01	ci right 9.903144e-01	k: 9883	n:10000
KS ci ratio: 8.811689e-02	ci left: 1.578715e-01	ci right 1.725241e-01	k: 1651	n:10000
MYOF   10000 perm   3 sec   (3490 perm/sec)   p_kst 1.651000e-01   p_cons 9.883000e-01   p_joint 2.463000e-01

Outputting figure to mutsig2_images.part000000000111/MYOF.3_6402_10000_0.1651_0.9883_0.2463.png
                gene_name: MYOF
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

Current progress: 25 percent done.
MYO5A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.794086e-02	ci left: 3.909759e-01	ci right 4.102820e-01	k: 4006	n:10000
Cons ci ratio: 2.561827e-02	ci left: 6.916168e-01	ci right 7.096662e-01	k: 7007	n:10000
KS ci ratio: 7.591471e-02	ci left: 2.024465e-01	ci right 2.185225e-01	k: 2104	n:10000
MYO5A   10000 perm   2 sec   (4520 perm/sec)   p_kst 2.104000e-01   p_cons 7.007000e-01   p_joint 4.006000e-01

Outputting figure to mutsig2_images.part000000000111/MYO5A.2_5732_10000_0.2104_0.7007_0.4006.png
                gene_name: MYO5A
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.40 
     ci_joint_bounds_left: 0.39 
    ci_joint_bounds_right: 0.41 

Current progress: 38 percent done.
MYO5C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.921899e-02	ci left: 1.545332e-01	ci right 1.690644e-01	k: 1617	n:10000
KS ci ratio: 3.227051e-02	ci left: 5.863057e-01	ci right 6.056384e-01	k: 5960	n:10000
MYO5C   10000 perm   2 sec   (4472 perm/sec)   p_kst 5.960000e-01   p_cons 1.617000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000111/MYO5C.2_5393_10000_0.596_0.1617_1.png
                gene_name: MYO5C
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.17 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
MYO9A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.405090e-02	ci left: 7.176482e-01	ci right 7.352197e-01	k: 7265	n:10000
Cons ci ratio: 5.921521e-02	ci left: 2.955875e-01	ci right 3.137265e-01	k: 3046	n:10000
KS ci ratio: 1.713548e-02	ci left: 8.322587e-01	ci right 8.467429e-01	k: 8396	n:10000
MYO9A   10000 perm   3 sec   (3799 perm/sec)   p_kst 8.396000e-01   p_cons 3.046000e-01   p_joint 7.265000e-01

Outputting figure to mutsig2_images.part000000000111/MYO9A.2_7811_10000_0.8396_0.3046_0.7265.png
                gene_name: MYO9A
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.30 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.73 
     ci_joint_bounds_left: 0.72 
    ci_joint_bounds_right: 0.74 

Current progress: 62 percent done.
MYOM3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.628172e-02	ci left: 8.458050e-01	ci right 8.597888e-01	k: 8529	n:10000
KS ci ratio: 5.598589e-03	ci left: 9.771688e-01	ci right 9.827467e-01	k: 9801	n:10000
MYOM3   10000 perm   2 sec   (4897 perm/sec)   p_kst 9.801000e-01   p_cons 8.529000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000111/MYOM3.2_4458_10000_0.9801_0.8529_1.png
                gene_name: MYOM3
               theta_stop: 0.016 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.98 
       ci_ks_bounds_right: 0.98 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
MYT1L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.127937e-02	ci left: 4.642721e-01	ci right 4.839430e-01	k: 4741	n:10000
Cons ci ratio: 5.254030e-02	ci left: 3.480992e-01	ci right 3.669838e-01	k: 3575	n:10000
KS ci ratio: 2.105514e-02	ci left: 7.678000e-01	ci right 7.842389e-01	k: 7761	n:10000
MYT1L   10000 perm   2 sec   (5214 perm/sec)   p_kst 7.761000e-01   p_cons 3.575000e-01   p_joint 4.741000e-01

Outputting figure to mutsig2_images.part000000000111/MYT1L.2_3635_10000_0.7761_0.3575_0.4741.png
                gene_name: MYT1L
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 88 percent done.
NAA15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.361591e-02	ci left: 2.663640e-01	ci right 2.839672e-01	k: 2751	n:10000
Cons ci ratio: 6.875699e-02	ci left: 2.367933e-01	ci right 2.537553e-01	k: 2452	n:10000
KS ci ratio: 3.056233e-02	ci left: 6.123115e-01	ci right 6.314175e-01	k: 6219	n:10000
NAA15   10000 perm   2 sec   (5378 perm/sec)   p_kst 6.219000e-01   p_cons 2.452000e-01   p_joint 2.751000e-01

Outputting figure to mutsig2_images.part000000000111/NAA15.2_2681_10000_0.6219_0.2452_0.2751.png
                gene_name: NAA15
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.28 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000111
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 111 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4398149: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000112> was used as the working directory.
Started at Wed Oct 24 16:14:32 2012
Results reported at Wed Oct 24 16:17:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000112.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000112.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 112  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000112.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    215.70 sec.
    Max Memory :      1645 MB
    Max Swap   :      4006 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
112
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 112
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 112: processing genes 9959 - 10048
Calculating significance of each gene.
Using projection method.
9959	NANP	1
9960	NANS	1
9961	NAP1L1	1
9962	NAP1L2	1
9963	NAP1L3	1
9964	NAP1L4	1
9965	NAP1L5	1
9966	NAPA	1
9967	NAPB	1
9968	NAPEPLD	1.079128e-01
9969	NAPG	1
9970	NAPRT1	1
9971	NAPSA	1
9972	NARF	1
9973	NARFL	4.188878e-02
9974	NARG2	1
9975	NARS	1
9976	NARS2	1
9977	NASP	3.772305e-01
9978	NAT1	1
9979	NAT10	1
9980	NAT15	1
9981	NAT2	1
9982	NAT6	1
9983	NAT8	1
9984	NAT8B	8.882086e-02
9985	NAT8L	1
9986	NAT9	1
9987	NAV1	4.957328e-01
9988	NAV2	1
9989	NAV3	1.115234e-01
9990	NBAS	6.274065e-01
9991	NBEA	1
9992	NBEAL1	1.372787e-01
9993	NBEAL2	1.972998e-01
9994	NBL1	1
9995	NBN	1
9996	NBPF1	2.705924e-02
9997	NBPF14	1
9998	NBPF15	1.790822e-02
9999	NBPF16	1
10000/17942 10000	NBPF3	6.980624e-02
10001	NBPF7	1
10002	NBR1	3.554803e-01
10003	NCALD	1
10004	NCAM1	1
10005	NCAM2	1
10006	NCAN	5.217099e-02
10007	NCAPD2	5.553224e-01
10008	NCAPD3	1
10009	NCAPG	1.982007e-01
10010	NCAPG2	1
10011	NCAPH	1
10012	NCAPH2	5.237727e-02
10013	NCBP1	1
10014	NCBP2	1
10015	NCCRP1	1
10016	NCDN	1
10017	NCEH1	1
10018	NCF1	1
10019	NCF2	1
10020	NCF4	1
10021	NCK1	5.922050e-02
10022	NCK2	1
10023	NCKAP1	6.951055e-04
10024	NCKAP1L	4.805254e-01
10025	NCKAP5	1
10026	NCKAP5L	1
10027	NCKIPSD	1
10028	NCL	1
10029	NCLN	1
10030	NCOA1	5.530366e-01
10031	NCOA2	1
10032	NCOA3	3.867719e-01
10033	NCOA4	1
10034	NCOA5	1
In gene NCOA6 the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 6244    n = 1	mu =   4.43e-07
10035	NCOA6	3.025312e-01
10036	NCOA7	1
10037	NCOR1	3.248391e-01
10038	NCOR2	1
10039	NCR1	1
10040	NCR2	1
10041	NCR3	8.237888e-03
10042	NCS1	1
10043	NCSTN	5.613680e-02
10044	NDC80	3.894923e-02
10045	NDE1	1
10046	NDEL1	1
10047	NDFIP1	1
10048	NDFIP2	1
Done

Running MutSig 2:
Scatter job 112: processing genes 9959 - 10048
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NCKAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.981304e-02	ci left: 2.312609e-01	ci right 2.480910e-01	k: 2396	n:10000
Cons ci ratio: 2.519761e-02	ci left: 6.985753e-01	ci right 7.165037e-01	k: 7076	n:10000
KS ci ratio: 6.981304e-02	ci left: 2.312609e-01	ci right 2.480910e-01	k: 2396	n:10000
NCKAP1   10000 perm   2 sec   (4991 perm/sec)   p_kst 2.396000e-01   p_cons 7.076000e-01   p_joint 2.396000e-01

Outputting figure to mutsig2_images.part000000000112/NCKAP1.4_3533_10000_0.2396_0.7076_0.2396.png
                gene_name: NCKAP1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.25 

Current progress: 10 percent done.
NAV3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.377898e-02	ci left: 4.351271e-01	ci right 4.547050e-01	k: 4449	n:10000
Cons ci ratio: 4.826174e-02	ci left: 3.877898e-01	ci right 4.070700e-01	k: 3974	n:10000
KS ci ratio: 4.446792e-02	ci left: 4.274473e-01	ci right 4.469893e-01	k: 4372	n:10000
NAV3   10000 perm   2 sec   (4293 perm/sec)   p_kst 4.372000e-01   p_cons 3.974000e-01   p_joint 4.449000e-01

Outputting figure to mutsig2_images.part000000000112/NAV3.3_7248_10000_0.4372_0.3974_0.4449.png
                gene_name: NAV3
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.44 
    ci_joint_bounds_right: 0.45 

Current progress: 20 percent done.
NDC80
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.755860e-02	ci left: 1.321775e-01	ci right 1.458335e-01	k: 1389	n:10000
Cons ci ratio: 3.220289e-01	ci left: 1.224928e-02	ci right 1.703957e-02	k: 145	n:10000
KS ci ratio: 9.344901e-03	ci left: 9.417001e-01	ci right 9.506377e-01	k: 9463	n:10000
NDC80   10000 perm   2 sec   (4884 perm/sec)   p_kst 9.463000e-01   p_cons 1.450000e-02   p_joint 1.389000e-01

Joint ci ratio: 8.552611e-02	ci left: 9.097040e-02	ci right 9.914776e-02	k: 1900	n:20000
Cons ci ratio: 2.238557e-01	ci left: 1.340842e-02	ci right 1.683467e-02	k: 301	n:20000
KS ci ratio: 6.589192e-03	ci left: 9.433422e-01	ci right 9.496272e-01	k: 18931	n:20000
NDC80   20000 perm   4 sec   (4639 perm/sec)   p_kst 9.465500e-01   p_cons 1.505000e-02   p_joint 9.500000e-02

Joint ci ratio: 8.084807e-02	ci left: 6.972131e-02	ci right 7.562844e-02	k: 2179	n:30000
Cons ci ratio: 1.913204e-01	ci left: 1.247871e-02	ci right 1.515000e-02	k: 413	n:30000
KS ci ratio: 5.351889e-03	ci left: 9.444728e-01	ci right 9.495736e-01	k: 28412	n:30000
NDC80   30000 perm   6 sec   (4704 perm/sec)   p_kst 9.470667e-01   p_cons 1.376667e-02   p_joint 7.263333e-02

Joint ci ratio: 7.795902e-02	ci left: 5.712769e-02	ci right 6.178652e-02	k: 2377	n:40000
Cons ci ratio: 1.666096e-01	ci left: 1.251184e-02	ci right 1.480957e-02	k: 545	n:40000
KS ci ratio: 4.621480e-03	ci left: 9.451162e-01	ci right 9.495186e-01	k: 37894	n:40000
NDC80   40000 perm   9 sec   (4680 perm/sec)   p_kst 9.473500e-01   p_cons 1.362500e-02   p_joint 5.942500e-02

Joint ci ratio: 4.016780e-02	ci left: 1.567766e-01	ci right 1.632229e-01	k: 7999	n:50000
Cons ci ratio: 1.434243e-01	ci left: 1.366336e-02	ci right 1.579353e-02	k: 735	n:50000
KS ci ratio: 4.108095e-03	ci left: 9.459770e-01	ci right 9.498908e-01	k: 47398	n:50000
NDC80   50000 perm   11 sec   (4629 perm/sec)   p_kst 9.479600e-01   p_cons 1.470000e-02   p_joint 1.599800e-01

Joint ci ratio: 4.148214e-02	ci left: 1.268561e-01	ci right 1.322464e-01	k: 7772	n:60000
Cons ci ratio: 1.352851e-01	ci left: 1.286567e-02	ci right 1.474845e-02	k: 827	n:60000
KS ci ratio: 3.756774e-03	ci left: 9.459732e-01	ci right 9.495500e-01	k: 56867	n:60000
NDC80   60000 perm   13 sec   (4564 perm/sec)   p_kst 9.477833e-01   p_cons 1.378333e-02   p_joint 1.295333e-01

Joint ci ratio: 3.962272e-02	ci left: 1.202355e-01	ci right 1.251101e-01	k: 8586	n:70000
Cons ci ratio: 1.263822e-01	ci left: 1.269969e-02	ci right 1.442670e-02	k: 948	n:70000
KS ci ratio: 3.473934e-03	ci left: 9.462279e-01	ci right 9.495348e-01	k: 66353	n:70000
NDC80   70000 perm   16 sec   (4502 perm/sec)   p_kst 9.479000e-01   p_cons 1.354286e-02   p_joint 1.226571e-01

Joint ci ratio: 5.392428e-02	ci left: 6.028919e-02	ci right 6.364266e-02	k: 4956	n:80000
Cons ci ratio: 1.184732e-01	ci left: 1.269961e-02	ci right 1.431095e-02	k: 1079	n:80000
KS ci ratio: 3.255276e-03	ci left: 9.461601e-01	ci right 9.492574e-01	k: 75818	n:80000
NDC80   80000 perm   18 sec   (4396 perm/sec)   p_kst 9.477250e-01   p_cons 1.348750e-02   p_joint 6.195000e-02

Joint ci ratio: 4.522895e-02	ci left: 7.528839e-02	ci right 7.878337e-02	k: 6932	n:90000
Cons ci ratio: 1.115581e-01	ci left: 1.277782e-02	ci right 1.429822e-02	k: 1217	n:90000
KS ci ratio: 3.065027e-03	ci left: 9.463830e-01	ci right 9.492991e-01	k: 85307	n:90000
NDC80   90000 perm   21 sec   (4269 perm/sec)   p_kst 9.478556e-01   p_cons 1.352222e-02   p_joint 7.702222e-02

Joint ci ratio: 4.063188e-02	ci left: 8.341726e-02	ci right 8.688684e-02	k: 8514	n:100000
Cons ci ratio: 1.055701e-01	ci left: 1.288153e-02	ci right 1.432689e-02	k: 1359	n:100000
KS ci ratio: 2.896981e-03	ci left: 9.468286e-01	ci right 9.495853e-01	k: 94822	n:100000
NDC80   100000 perm   24 sec   (4107 perm/sec)   p_kst 9.482200e-01   p_cons 1.359000e-02   p_joint 8.514000e-02

Joint ci ratio: 4.029024e-02	ci left: 7.763772e-02	ci right 8.083906e-02	k: 8715	n:110000
Cons ci ratio: 1.005211e-01	ci left: 1.295044e-02	ci right 1.432993e-02	k: 1499	n:110000
KS ci ratio: 2.765006e-03	ci left: 9.467911e-01	ci right 9.494216e-01	k: 104293	n:110000
NDC80   110000 perm   28 sec   (3908 perm/sec)   p_kst 9.481182e-01   p_cons 1.362727e-02   p_joint 7.922727e-02

Joint ci ratio: 3.857579e-02	ci left: 7.770287e-02	ci right 8.076750e-02	k: 9507	n:120000
Cons ci ratio: 9.604436e-02	ci left: 1.303364e-02	ci right 1.435668e-02	k: 1642	n:120000
KS ci ratio: 2.645299e-03	ci left: 9.469226e-01	ci right 9.494390e-01	k: 113783	n:120000
NDC80   120000 perm   31 sec   (3885 perm/sec)   p_kst 9.481917e-01   p_cons 1.368333e-02   p_joint 7.922500e-02

Outputting figure to mutsig2_images.part000000000112/NDC80.3_1993_120000_0.94819_0.013683_0.079225.png
                gene_name: NDC80
               theta_stop: 0.096 
                    nperm: 120000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.014 
      ci_cons_bounds_left: 0.013 
     ci_cons_bounds_right: 0.014 
                  p_joint: 0.079 
     ci_joint_bounds_left: 0.078 
    ci_joint_bounds_right: 0.081 

Current progress: 30 percent done.
NBEAL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.015541e-02	ci left: 1.852067e-01	ci right 2.007725e-01	k: 1929	n:10000
Cons ci ratio: 9.427224e-03	ci left: 9.407656e-01	ci right 9.497727e-01	k: 9454	n:10000
KS ci ratio: 1.757246e-01	ci left: 4.322176e-02	ci right 5.164440e-02	k: 473	n:10000
NBEAL1   10000 perm   2 sec   (4259 perm/sec)   p_kst 4.730000e-02   p_cons 9.454000e-01   p_joint 1.929000e-01

Joint ci ratio: 6.454585e-02	ci left: 1.506511e-01	ci right 1.607492e-01	k: 3113	n:20000
Cons ci ratio: 6.608688e-03	ci left: 9.430340e-01	ci right 9.493355e-01	k: 18925	n:20000
KS ci ratio: 1.223735e-01	ci left: 4.580631e-02	ci right 5.182574e-02	k: 975	n:20000
NBEAL1   20000 perm   5 sec   (3838 perm/sec)   p_kst 4.875000e-02   p_cons 9.462500e-01   p_joint 1.556500e-01

Joint ci ratio: 7.414297e-02	ci left: 8.206446e-02	ci right 8.841614e-02	k: 2556	n:30000
Cons ci ratio: 5.406793e-03	ci left: 9.434163e-01	ci right 9.485635e-01	k: 28381	n:30000
KS ci ratio: 1.005700e-01	ci left: 4.577092e-02	ci right 5.065039e-02	k: 1445	n:30000
NBEAL1   30000 perm   8 sec   (3697 perm/sec)   p_kst 4.816667e-02   p_cons 9.460333e-01   p_joint 8.520000e-02

Joint ci ratio: 6.416192e-02	ci left: 8.260495e-02	ci right 8.810542e-02	k: 3413	n:40000
Cons ci ratio: 4.683665e-03	ci left: 9.437400e-01	ci right 9.481950e-01	k: 37840	n:40000
KS ci ratio: 8.664882e-02	ci left: 4.656204e-02	ci right 5.080379e-02	k: 1946	n:40000
NBEAL1   40000 perm   11 sec   (3617 perm/sec)   p_kst 4.865000e-02   p_cons 9.460000e-01   p_joint 8.532500e-02

Outputting figure to mutsig2_images.part000000000112/NBEAL1.2_8301_40000_0.04865_0.946_0.085325.png
                gene_name: NBEAL1
               theta_stop: 0.087 
                    nperm: 40000 
                     p_ks: 0.049 
        ci_ks_bounds_left: 0.047 
       ci_ks_bounds_right: 0.051 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.085 
     ci_joint_bounds_left: 0.083 
    ci_joint_bounds_right: 0.088 

Current progress: 40 percent done.
NBEAL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.253245e-02	ci left: 5.823922e-01	ci right 6.017541e-01	k: 5921	n:10000
Cons ci ratio: 4.021046e-02	ci left: 4.773583e-01	ci right 4.970491e-01	k: 4872	n:10000
KS ci ratio: 1.079994e-01	ci left: 1.100791e-01	ci right 1.227454e-01	k: 1163	n:10000
NBEAL2   10000 perm   2 sec   (4199 perm/sec)   p_kst 1.163000e-01   p_cons 4.872000e-01   p_joint 5.921000e-01

Joint ci ratio: 4.043889e-02	ci left: 3.131388e-01	ci right 3.261136e-01	k: 6392	n:20000
Cons ci ratio: 2.879907e-02	ci left: 4.739038e-01	ci right 4.878018e-01	k: 9617	n:20000
KS ci ratio: 7.836327e-02	ci left: 1.068256e-01	ci right 1.155878e-01	k: 2223	n:20000
NBEAL2   20000 perm   5 sec   (3802 perm/sec)   p_kst 1.111500e-01   p_cons 4.808500e-01   p_joint 3.196000e-01

Outputting figure to mutsig2_images.part000000000112/NBEAL2.2_8481_20000_0.11115_0.48085_0.3196.png
                gene_name: NBEAL2
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 50 percent done.
NBPF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.002348e-02	ci left: 9.338193e-01	ci right 9.433233e-01	k: 9387	n:10000
Cons ci ratio: 4.008195e-02	ci left: 4.789571e-01	ci right 4.986494e-01	k: 4888	n:10000
KS ci ratio: 1.077657e-02	ci left: 9.246163e-01	ci right 9.347317e-01	k: 9298	n:10000
NBPF1   10000 perm   2 sec   (5536 perm/sec)   p_kst 9.298000e-01   p_cons 4.888000e-01   p_joint 9.387000e-01

Outputting figure to mutsig2_images.part000000000112/NBPF1.2_3517_10000_0.9298_0.4888_0.9387.png
                gene_name: NBPF1
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 60 percent done.
NCAM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.650160e-02	ci left: 8.423403e-01	ci right 8.564555e-01	k: 8495	n:10000
Cons ci ratio: 1.329427e-02	ci left: 8.907739e-01	ci right 9.027938e-01	k: 8969	n:10000
KS ci ratio: 1.161173e-01	ci left: 9.632952e-02	ci right 1.083033e-01	k: 1022	n:10000
NCAM2   10000 perm   2 sec   (6245 perm/sec)   p_kst 1.022000e-01   p_cons 8.969000e-01   p_joint 8.495000e-01

Joint ci ratio: 5.777784e-03	ci left: 9.555403e-01	ci right 9.611255e-01	k: 19168	n:20000
Cons ci ratio: 9.961120e-03	ci left: 8.811584e-01	ci right 8.900292e-01	k: 17713	n:20000
KS ci ratio: 8.244601e-02	ci left: 9.734785e-02	ci right 1.057684e-01	k: 2030	n:20000
NCAM2   20000 perm   4 sec   (5547 perm/sec)   p_kst 1.015000e-01   p_cons 8.856500e-01   p_joint 9.584000e-01

Outputting figure to mutsig2_images.part000000000112/NCAM2.2_2586_20000_0.1015_0.88565_0.9584.png
                gene_name: NCAM2
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.097 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.96 

Current progress: 70 percent done.
NCAN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.865273e-02	ci left: 8.076544e-01	ci right 8.229615e-01	k: 8154	n:10000
Cons ci ratio: 3.336753e-02	ci left: 5.700537e-01	ci right 5.894998e-01	k: 5798	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
NCAN   10000 perm   2 sec   (5679 perm/sec)   p_kst 1   p_cons 5.798000e-01   p_joint 8.154000e-01

Outputting figure to mutsig2_images.part000000000112/NCAN.2_4022_10000_1_0.5798_0.8154.png
                gene_name: NCAN
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.82 

Current progress: 80 percent done.
NCAPH2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.218871e-02	ci left: 9.061740e-01	ci right 9.173848e-01	k: 9119	n:10000
KS ci ratio: 6.363186e-02	ci left: 2.662650e-01	ci right 2.838662e-01	k: 2750	n:10000
NCAPH2   10000 perm   2 sec   (6467 perm/sec)   p_kst 2.750000e-01   p_cons 9.119000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000112/NCAPH2.2_1940_10000_0.275_0.9119_1.png
                gene_name: NCAPH2
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 90 percent done.
NCSTN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.732659e-02	ci left: 1.603269e-01	ci right 1.750672e-01	k: 1676	n:10000
Cons ci ratio: 2.205248e-02	ci left: 7.510997e-01	ci right 7.679489e-01	k: 7596	n:10000
KS ci ratio: 2.111979e-01	ci left: 2.977507e-02	ci right 3.690017e-02	k: 332	n:10000
NCSTN   10000 perm   2 sec   (6283 perm/sec)   p_kst 3.320000e-02   p_cons 7.596000e-01   p_joint 1.676000e-01

Joint ci ratio: 5.680686e-02	ci left: 1.868086e-01	ci right 1.977810e-01	k: 3845	n:20000
Cons ci ratio: 1.609494e-02	ci left: 7.417710e-01	ci right 7.538569e-01	k: 14957	n:20000
KS ci ratio: 1.445823e-01	ci left: 3.288174e-02	ci right 3.805446e-02	k: 708	n:20000
NCSTN   20000 perm   4 sec   (5271 perm/sec)   p_kst 3.540000e-02   p_cons 7.478500e-01   p_joint 1.922500e-01

Joint ci ratio: 8.228152e-02	ci left: 6.743212e-02	ci right 7.325142e-02	k: 2109	n:30000
Cons ci ratio: 1.322338e-02	ci left: 7.405308e-01	ci right 7.504217e-01	k: 22365	n:30000
KS ci ratio: 1.193672e-01	ci left: 3.262511e-02	ci right 3.679896e-02	k: 1040	n:30000
NCSTN   30000 perm   6 sec   (5166 perm/sec)   p_kst 3.466667e-02   p_cons 7.455000e-01   p_joint 7.030000e-02

Joint ci ratio: 2.624290e-02	ci left: 3.533496e-01	ci right 3.627710e-01	k: 14322	n:40000
Cons ci ratio: 1.145633e-02	ci left: 7.410504e-01	ci right 7.496140e-01	k: 29814	n:40000
KS ci ratio: 1.035301e-01	ci left: 3.280592e-02	ci right 3.641205e-02	k: 1383	n:40000
NCSTN   40000 perm   8 sec   (5069 perm/sec)   p_kst 3.457500e-02   p_cons 7.453500e-01   p_joint 3.580500e-01

Joint ci ratio: 2.349254e-02	ci left: 3.534571e-01	ci right 3.618794e-01	k: 17883	n:50000
Cons ci ratio: 1.020071e-02	ci left: 7.432255e-01	ci right 7.508658e-01	k: 37353	n:50000
KS ci ratio: 9.369993e-02	ci left: 3.223311e-02	ci right 3.542131e-02	k: 1690	n:50000
NCSTN   50000 perm   10 sec   (4983 perm/sec)   p_kst 3.380000e-02   p_cons 7.470600e-01   p_joint 3.576600e-01

Outputting figure to mutsig2_images.part000000000112/NCSTN.2_2198_50000_0.0338_0.74706_0.35766.png
                gene_name: NCSTN
               theta_stop: 0.094 
                    nperm: 50000 
                     p_ks: 0.034 
        ci_ks_bounds_left: 0.032 
       ci_ks_bounds_right: 0.035 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.36 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000112
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 112 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 4398152: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000113> was used as the working directory.
Started at Wed Oct 24 16:14:32 2012
Results reported at Wed Oct 24 16:17:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000113.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000113.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 113  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000113.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    154.62 sec.
    Max Memory :      1312 MB
    Max Swap   :      3939 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
113
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 113
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 113: processing genes 10049 - 10137
Calculating significance of each gene.
Using projection method.
10049	NDN	1
10050	NDNL2	1
10051	NDOR1	1
10052	NDP	1
10053	NDRG1	1
10054	NDRG2	1
10055	NDRG3	1
10056	NDRG4	1
10057	NDST1	1
10058	NDST2	2.485745e-01
10059	NDST3	3.821271e-01
10060	NDST4	2.153785e-01
10061	NDUFA1	1
10062	NDUFA10	1
10063	NDUFA11	1
10064	NDUFA12	1
10065	NDUFA13	1
10066	NDUFA2	1
10067	NDUFA3	1
10068	NDUFA4	1
10069	NDUFA4L2	1
10070	NDUFA5	1
10071	NDUFA6	1
10072	NDUFA7	1
10073	NDUFA8	1
10074	NDUFA9	1
10075	NDUFAB1	1
10076	NDUFAF1	1
10077	NDUFAF2	1
10078	NDUFAF3	1
10079	NDUFAF4	1
10080	NDUFB1	1
10081	NDUFB10	1
10082	NDUFB11	1
10083	NDUFB2	1
10084	NDUFB3	1
10085	NDUFB4	1
10086	NDUFB5	1
10087	NDUFB6	1
10088	NDUFB7	1
10089	NDUFB8	1
10090	NDUFB9	1
10091	NDUFC1	1
10092	NDUFC2	1
10093	NDUFS1	1
10094	NDUFS2	1
10095	NDUFS3	1
10096	NDUFS4	1.742846e-02
10097	NDUFS5	1
10098	NDUFS6	1
10099	NDUFS7	1
10100	NDUFS8	1
10101	NDUFV1	1
10102	NDUFV2	1
10103	NDUFV3	1
10104	NEB	1
10105	NEBL	1
10106	NECAB1	1
10107	NECAB2	1
10108	NECAB3	1
10109	NECAP1	1
10110	NECAP2	1
10111	NEDD1	1
10112	NEDD4	7.429601e-02
10113	NEDD4L	1
10114	NEDD8	1
10115	NEDD9	1.226341e-01
10116	NEFH	5.203044e-02
10117	NEFL	1
10118	NEFM	1
10119	NEGR1	1
10120	NEIL1	1
10121	NEIL2	1
10122	NEIL3	1
10123	NEK1	1
10124	NEK10	1
10125	NEK11	1
10126	NEK2	1
10127	NEK3	1
10128	NEK4	3.618672e-01
10129	NEK5	2.205600e-01
10130	NEK6	1.827649e-02
10131	NEK7	1
10132	NEK8	2.229364e-01
10133	NEK9	1
10134	NELF	1
10135	NELL1	1
10136	NELL2	1
10137	NENF	1
Done

Running MutSig 2:
Scatter job 113: processing genes 10049 - 10137
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NEB
Processing conservation and coverage...
37% 75% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.276929e-02	ci left: 1.755630e-01	ci right 1.908220e-01	k: 1831	n:10000
Cons ci ratio: 5.263190e-02	ci left: 3.473041e-01	ci right 3.661794e-01	k: 3567	n:10000
KS ci ratio: 1.061000e-01	ci left: 1.136922e-01	ci right 1.265300e-01	k: 1200	n:10000
NEB   10000 perm   10 sec   (973 perm/sec)   p_kst 1.200000e-01   p_cons 3.567000e-01   p_joint 1.831000e-01

Joint ci ratio: 6.694336e-02	ci left: 1.414288e-01	ci right 1.512743e-01	k: 2926	n:20000
Cons ci ratio: 3.726903e-02	ci left: 3.494600e-01	ci right 3.627819e-01	k: 7122	n:20000
KS ci ratio: 7.696846e-02	ci left: 1.103641e-01	ci right 1.192483e-01	k: 2295	n:20000
NEB   20000 perm   20 sec   (976 perm/sec)   p_kst 1.147500e-01   p_cons 3.561000e-01   p_joint 1.463000e-01

Outputting figure to mutsig2_images.part000000000113/NEB.3_26407_20000_0.11475_0.3561_0.1463.png
                gene_name: NEB
               theta_stop: 0.077 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.15 

Current progress: 25 percent done.
NEDD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.909115e-02	ci left: 8.004455e-01	ci right 8.159745e-01	k: 8083	n:10000
Cons ci ratio: 3.196988e-02	ci left: 5.908220e-01	ci right 6.101194e-01	k: 6005	n:10000
KS ci ratio: 8.789393e-02	ci left: 1.585590e-01	ci right 1.732362e-01	k: 1658	n:10000
NEDD4   10000 perm   2 sec   (5004 perm/sec)   p_kst 1.658000e-01   p_cons 6.005000e-01   p_joint 8.083000e-01

Outputting figure to mutsig2_images.part000000000113/NEDD4.2_4371_10000_0.1658_0.6005_0.8083.png
                gene_name: NEDD4
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.82 

Current progress: 50 percent done.
NEFH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.056434e-02	ci left: 3.657973e-01	ci right 3.848754e-01	k: 3753	n:10000
Cons ci ratio: 3.500427e-02	ci left: 5.464973e-01	ci right 5.660699e-01	k: 5563	n:10000
KS ci ratio: 9.659224e-02	ci left: 1.345280e-01	ci right 1.482816e-01	k: 1413	n:10000
NEFH   10000 perm   2 sec   (5533 perm/sec)   p_kst 1.413000e-01   p_cons 5.563000e-01   p_joint 3.753000e-01

Outputting figure to mutsig2_images.part000000000113/NEFH.2_3079_10000_0.1413_0.5563_0.3753.png
                gene_name: NEFH
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.38 

Current progress: 75 percent done.
NEK5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.131539e-02	ci left: 7.634461e-01	ci right 7.799953e-01	k: 7718	n:10000
Cons ci ratio: 1.100567e-02	ci left: 9.217260e-01	ci right 9.320237e-01	k: 9270	n:10000
KS ci ratio: 5.715629e-02	ci left: 3.106623e-01	ci right 3.290427e-01	k: 3198	n:10000
NEK5   10000 perm   2 sec   (5372 perm/sec)   p_kst 3.198000e-01   p_cons 9.270000e-01   p_joint 7.718000e-01

Outputting figure to mutsig2_images.part000000000113/NEK5.2_2207_10000_0.3198_0.927_0.7718.png
                gene_name: NEK5
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.78 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000113
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 113 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1712>
Subject: Job 4398155: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1712>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000114> was used as the working directory.
Started at Wed Oct 24 16:14:34 2012
Results reported at Wed Oct 24 16:25:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000114.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000114.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 114  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000114.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    691.78 sec.
    Max Memory :      1623 MB
    Max Swap   :      4100 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
114
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 114
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 114: processing genes 10138 - 10227
Calculating significance of each gene.
Using projection method.
10138	NEO1	3.694134e-01
10139	NES	1
10140	NET1	1
10141	NETO1	2.613634e-01
10142	NETO2	2.415429e-01
10143	NEU1	1
10144	NEU2	4.475081e-02
10145	NEU3	1
10146	NEU4	1
10147	NEURL	1
10148	NEURL2	1
10149	NEURL4	2.340237e-01
10150	NEUROD1	1
10151	NEUROD2	1
10152	NEUROD4	1.485263e-01
10153	NEUROD6	1
10154	NEUROG1	1
10155	NEUROG2	1
10156	NEUROG3	1
10157	NEXN	1
10158	NF1	3.820640e-01
10159	NF2	2.281702e-02
10160	NFAM1	1
10161	NFASC	1
10162	NFAT5	1
10163	NFATC1	1
10164	NFATC2	1
10165	NFATC2IP	1
10166	NFATC3	4.717414e-01
10167	NFATC4	1
10168	NFE2	1
10169	NFE2L1	1
10170	NFE2L2	1.626641e-05
10171	NFE2L3	1.441004e-01
10172	NFIA	1
10173	NFIB	1
10174	NFIC	1
10175	NFIL3	1
10176	NFIX	1
10177	NFKB1	1
10178	NFKB2	2.765856e-01
10179	NFKBIA	1
10180	NFKBIB	1
10181	NFKBID	1.596622e-02
10182	NFKBIE	1
10183	NFKBIL1	1
10184	NFKBIL2	2.974274e-02
10185	NFKBIZ	1
10186	NFRKB	1
10187	NFS1	1
10188	NFU1	1
10189	NFX1	1
10190	NFXL1	1
10191	NFYA	1.721628e-01
10192	NFYB	5.034861e-04
10193	NFYC	1
10194	NGB	1
10195	NGDN	1
10196	NGEF	1
10197	NGF	1
10198	NGFR	1
10199	NGFRAP1	1
10200	NGLY1	1
10201	NGRN	1
10202	NHEDC1	1
10203	NHEDC2	1.757906e-01
10204	NHEJ1	1
10205	NHLH1	1
10206	NHLH2	1
10207	NHLRC1	1
10208	NHLRC2	1
10209	NHLRC3	1
10210	NHLRC4	1
10211	NHP2	1
10212	NHP2L1	3.468798e-02
10213	NHS	1
10214	NHSL2	1
10215	NICN1	1
10216	NID1	1
10217	NID2	1
10218	NIF3L1	1
10219	NIN	3.065549e-01
10220	NINJ1	1
10221	NINJ2	1
10222	NINL	5.575769e-01
10223	NIP7	1
10224	NIPA1	1
10225	NIPA2	1
10226	NIPAL1	1
10227	NIPAL2	1
Done

Running MutSig 2:
Scatter job 114: processing genes 10138 - 10227
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NFE2L2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.246035e-02	ci left: 3.487950e-01	ci right 3.676877e-01	k: 3582	n:10000
Cons ci ratio: 1.708612e-01	ci left: 4.571402e-02	ci right 5.435051e-02	k: 499	n:10000
KS ci ratio: 2.095216e-02	ci left: 7.695217e-01	ci right 7.859162e-01	k: 7778	n:10000
NFE2L2   10000 perm   2 sec   (5340 perm/sec)   p_kst 7.778000e-01   p_cons 4.990000e-02   p_joint 3.582000e-01

Joint ci ratio: 4.739036e-02	ci left: 2.488215e-01	ci right 2.609498e-01	k: 5097	n:20000
Cons ci ratio: 1.185293e-01	ci left: 4.876885e-02	ci right 5.496225e-02	k: 1036	n:20000
KS ci ratio: 1.472745e-02	ci left: 7.740421e-01	ci right 7.855765e-01	k: 15597	n:20000
NFE2L2   20000 perm   6 sec   (3261 perm/sec)   p_kst 7.798500e-01   p_cons 5.180000e-02   p_joint 2.548500e-01

Joint ci ratio: 3.754057e-02	ci left: 2.615362e-01	ci right 2.715757e-01	k: 7996	n:30000
Cons ci ratio: 9.705946e-02	ci left: 4.905845e-02	ci right 5.409551e-02	k: 1546	n:30000
KS ci ratio: 1.211997e-02	ci left: 7.723806e-01	ci right 7.818323e-01	k: 23314	n:30000
NFE2L2   30000 perm   8 sec   (3582 perm/sec)   p_kst 7.771333e-01   p_cons 5.153333e-02   p_joint 2.665333e-01

Outputting figure to mutsig2_images.part000000000114/NFE2L2.6_1838_30000_0.77713_0.051533_0.26653.png
                gene_name: NFE2L2
               theta_stop: 0.097 
                    nperm: 30000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.052 
      ci_cons_bounds_left: 0.049 
     ci_cons_bounds_right: 0.054 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.27 

Current progress: 17 percent done.
NF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.133596e-01	ci left: 1.007141e-01	ci right 1.129160e-01	k: 1067	n:10000
Cons ci ratio: 6.026393e-03	ci left: 9.738693e-01	ci right 9.798485e-01	k: 9770	n:10000
KS ci ratio: 1.509149e-01	ci left: 5.841227e-02	ci right 6.804410e-02	k: 631	n:10000
NF1   10000 perm   3 sec   (3819 perm/sec)   p_kst 6.310000e-02   p_cons 9.770000e-01   p_joint 1.067000e-01

Joint ci ratio: 8.109712e-02	ci left: 1.003422e-01	ci right 1.088731e-01	k: 2091	n:20000
Cons ci ratio: 4.322824e-03	ci left: 9.740963e-01	ci right 9.783637e-01	k: 19526	n:20000
KS ci ratio: 1.043132e-01	ci left: 6.249976e-02	ci right 6.942708e-02	k: 1318	n:20000
NF1   20000 perm   6 sec   (3507 perm/sec)   p_kst 6.590000e-02   p_cons 9.763000e-01   p_joint 1.045500e-01

Joint ci ratio: 6.898663e-02	ci left: 9.380472e-02	ci right 1.005402e-01	k: 2914	n:30000
Cons ci ratio: 3.543649e-03	ci left: 9.743082e-01	ci right 9.777988e-01	k: 29283	n:30000
KS ci ratio: 8.518353e-02	ci left: 6.311792e-02	ci right 6.876649e-02	k: 1977	n:30000
NF1   30000 perm   9 sec   (3385 perm/sec)   p_kst 6.590000e-02   p_cons 9.761000e-01   p_joint 9.713333e-02

Outputting figure to mutsig2_images.part000000000114/NF1.4_8813_30000_0.0659_0.9761_0.097133.png
                gene_name: NF1
               theta_stop: 0.085 
                    nperm: 30000 
                     p_ks: 0.066 
        ci_ks_bounds_left: 0.063 
       ci_ks_bounds_right: 0.069 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.097 
     ci_joint_bounds_left: 0.094 
    ci_joint_bounds_right: 0.10 

Current progress: 33 percent done.
NF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.079590e-03	ci left: 9.734446e-01	ci right 9.794734e-01	k: 9766	n:10000
KS ci ratio: 5.230335e-03	ci left: 9.798420e-01	ci right 9.850715e-01	k: 9826	n:10000
NF2   10000 perm   2 sec   (6182 perm/sec)   p_kst 9.826000e-01   p_cons 9.766000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000114/NF2.2_1892_10000_0.9826_0.9766_1.png
                gene_name: NF2
               theta_stop: 0.0061 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.98 
       ci_ks_bounds_right: 0.99 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
NFKBIL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.655618e-02	ci left: 6.761958e-01	ci right 6.944962e-01	k: 6854	n:10000
Cons ci ratio: 2.496038e-02	ci left: 7.025094e-01	ci right 7.203673e-01	k: 7115	n:10000
KS ci ratio: 8.773547e-02	ci left: 1.590500e-01	ci right 1.737448e-01	k: 1663	n:10000
NFKBIL2   10000 perm   2 sec   (5315 perm/sec)   p_kst 1.663000e-01   p_cons 7.115000e-01   p_joint 6.854000e-01

Outputting figure to mutsig2_images.part000000000114/NFKBIL2.2_4241_10000_0.1663_0.7115_0.6854.png
                gene_name: NFKBIL2
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.69 
     ci_joint_bounds_left: 0.68 
    ci_joint_bounds_right: 0.69 

Current progress: 67 percent done.
NFYB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.529567e-01	ci left: 3.627180e-03	ci right 6.472945e-03	k: 49	n:10000
Cons ci ratio: 8.984102e-01	ci left: 1.067132e-03	ci right 2.843290e-03	k: 18	n:10000
KS ci ratio: 2.169949e-01	ci left: 2.816365e-02	ci right 3.511272e-02	k: 315	n:10000
NFYB   10000 perm   1 sec   (7077 perm/sec)   p_kst 3.150000e-02   p_cons 1.800000e-03   p_joint 4.900000e-03

Joint ci ratio: 3.833774e-01	ci left: 4.205484e-03	ci right 6.242447e-03	k: 103	n:20000
Cons ci ratio: 6.716860e-01	ci left: 1.136048e-03	ci right 2.316440e-03	k: 33	n:20000
KS ci ratio: 1.538196e-01	ci left: 2.902635e-02	ci right 3.391111e-02	k: 628	n:20000
NFYB   20000 perm   3 sec   (6251 perm/sec)   p_kst 3.140000e-02   p_cons 1.650000e-03   p_joint 5.150000e-03

Joint ci ratio: 3.110310e-01	ci left: 4.448416e-03	ci right 6.116268e-03	k: 157	n:30000
Cons ci ratio: 5.431258e-01	ci left: 1.266016e-03	ci right 2.234588e-03	k: 51	n:30000
KS ci ratio: 1.256973e-01	ci left: 2.942306e-02	ci right 3.340170e-02	k: 941	n:30000
NFYB   30000 perm   5 sec   (5902 perm/sec)   p_kst 3.136667e-02   p_cons 1.700000e-03   p_joint 5.233333e-03

Joint ci ratio: 2.691479e-01	ci left: 4.565414e-03	ci right 6.007842e-03	k: 210	n:40000
Cons ci ratio: 4.522124e-01	ci left: 1.452919e-03	ci right 2.321957e-03	k: 74	n:40000
KS ci ratio: 1.088128e-01	ci left: 2.971253e-02	ci right 3.315593e-02	k: 1256	n:40000
NFYB   40000 perm   7 sec   (5667 perm/sec)   p_kst 3.140000e-02   p_cons 1.850000e-03   p_joint 5.250000e-03

Joint ci ratio: 2.458216e-01	ci left: 4.438180e-03	ci right 5.700334e-03	k: 252	n:50000
Cons ci ratio: 4.128281e-01	ci left: 1.429723e-03	ci right 2.189994e-03	k: 89	n:50000
KS ci ratio: 9.685697e-02	ci left: 3.018157e-02	ci right 3.327311e-02	k: 1585	n:50000
NFYB   50000 perm   9 sec   (5490 perm/sec)   p_kst 3.170000e-02   p_cons 1.780000e-03   p_joint 5.040000e-03

Joint ci ratio: 2.206370e-01	ci left: 4.655960e-03	ci right 5.826015e-03	k: 313	n:60000
Cons ci ratio: 3.684121e-01	ci left: 1.537248e-03	ci right 2.245659e-03	k: 112	n:60000
KS ci ratio: 8.816005e-02	ci left: 3.049190e-02	ci right 3.332029e-02	k: 1913	n:60000
NFYB   60000 perm   11 sec   (5344 perm/sec)   p_kst 3.188333e-02   p_cons 1.866667e-03   p_joint 5.216667e-03

Joint ci ratio: 2.096096e-01	ci left: 4.450330e-03	ci right 5.505632e-03	k: 347	n:70000
Cons ci ratio: 3.475256e-01	ci left: 1.499663e-03	ci right 2.142762e-03	k: 126	n:70000
KS ci ratio: 8.190503e-02	ci left: 3.038642e-02	ci right 3.299545e-02	k: 2217	n:70000
NFYB   70000 perm   13 sec   (5218 perm/sec)   p_kst 3.167143e-02   p_cons 1.800000e-03   p_joint 4.957143e-03

Joint ci ratio: 1.980113e-01	ci left: 4.392248e-03	ci right 5.369190e-03	k: 389	n:80000
Cons ci ratio: 3.321990e-01	ci left: 1.449402e-03	ci right 2.037678e-03	k: 138	n:80000
KS ci ratio: 7.680090e-02	ci left: 3.032496e-02	ci right 3.275917e-02	k: 2522	n:80000
NFYB   80000 perm   16 sec   (5100 perm/sec)   p_kst 3.152500e-02   p_cons 1.725000e-03   p_joint 4.862500e-03

Joint ci ratio: 1.841215e-01	ci left: 4.549647e-03	ci right 5.482696e-03	k: 450	n:90000
Cons ci ratio: 3.125753e-01	ci left: 1.472190e-03	ci right 2.027382e-03	k: 156	n:90000
KS ci ratio: 7.233465e-02	ci left: 3.045577e-02	ci right 3.275233e-02	k: 2843	n:90000
NFYB   90000 perm   18 sec   (4994 perm/sec)   p_kst 3.158889e-02   p_cons 1.733333e-03   p_joint 5.000000e-03

Joint ci ratio: 1.746926e-01	ci left: 4.572244e-03	ci right 5.456841e-03	k: 500	n:100000
Cons ci ratio: 2.952195e-01	ci left: 1.500499e-03	ci right 2.029073e-03	k: 175	n:100000
KS ci ratio: 6.856672e-02	ci left: 3.056371e-02	ci right 3.274356e-02	k: 3164	n:100000
NFYB   100000 perm   20 sec   (4896 perm/sec)   p_kst 3.164000e-02   p_cons 1.750000e-03   p_joint 5.000000e-03

Joint ci ratio: 1.693814e-01	ci left: 4.434943e-03	ci right 5.264223e-03	k: 532	n:110000
Cons ci ratio: 2.833936e-01	ci left: 1.490561e-03	ci right 1.990843e-03	k: 190	n:110000
KS ci ratio: 6.535160e-02	ci left: 3.063668e-02	ci right 3.271538e-02	k: 3483	n:110000
NFYB   110000 perm   23 sec   (4800 perm/sec)   p_kst 3.166364e-02   p_cons 1.727273e-03   p_joint 4.836364e-03

Joint ci ratio: 1.619543e-01	ci left: 4.464766e-03	ci right 5.259453e-03	k: 582	n:120000
Cons ci ratio: 2.715663e-01	ci left: 1.498162e-03	ci right 1.976434e-03	k: 207	n:120000
KS ci ratio: 6.283219e-02	ci left: 3.042866e-02	ci right 3.241074e-02	k: 3769	n:120000
NFYB   120000 perm   25 sec   (4708 perm/sec)   p_kst 3.140833e-02   p_cons 1.725000e-03   p_joint 4.850000e-03

Joint ci ratio: 1.543270e-01	ci left: 4.557233e-03	ci right 5.326644e-03	k: 641	n:130000
Cons ci ratio: 2.616893e-01	ci left: 1.497772e-03	ci right 1.955683e-03	k: 223	n:130000
KS ci ratio: 6.035325e-02	ci left: 3.048135e-02	ci right 3.238578e-02	k: 4085	n:130000
NFYB   130000 perm   28 sec   (4601 perm/sec)   p_kst 3.142308e-02   p_cons 1.715385e-03   p_joint 4.930769e-03

Joint ci ratio: 1.496278e-01	ci left: 4.513430e-03	ci right 5.250164e-03	k: 682	n:140000
Cons ci ratio: 2.565930e-01	ci left: 1.450894e-03	ci right 1.884451e-03	k: 232	n:140000
KS ci ratio: 5.835882e-02	ci left: 3.030953e-02	ci right 3.213853e-02	k: 4370	n:140000
NFYB   140000 perm   31 sec   (4516 perm/sec)   p_kst 3.121429e-02   p_cons 1.657143e-03   p_joint 4.871429e-03

Joint ci ratio: 1.446322e-01	ci left: 4.520757e-03	ci right 5.231923e-03	k: 730	n:150000
Cons ci ratio: 2.467285e-01	ci left: 1.472850e-03	ci right 1.893455e-03	k: 251	n:150000
KS ci ratio: 5.630070e-02	ci left: 3.042455e-02	ci right 3.219363e-02	k: 4695	n:150000
NFYB   150000 perm   34 sec   (4432 perm/sec)   p_kst 3.130000e-02   p_cons 1.673333e-03   p_joint 4.866667e-03

Joint ci ratio: 1.405598e-01	ci left: 4.497368e-03	ci right 5.183264e-03	k: 773	n:160000
Cons ci ratio: 2.396991e-01	ci left: 1.468834e-03	ci right 1.874566e-03	k: 266	n:160000
KS ci ratio: 5.457520e-02	ci left: 3.038433e-02	ci right 3.209522e-02	k: 4997	n:160000
NFYB   160000 perm   37 sec   (4355 perm/sec)   p_kst 3.123125e-02   p_cons 1.662500e-03   p_joint 4.831250e-03

Joint ci ratio: 1.363943e-01	ci left: 4.505390e-03	ci right 5.170493e-03	k: 821	n:170000
Cons ci ratio: 2.315987e-01	ci left: 1.487602e-03	ci right 1.882645e-03	k: 285	n:170000
KS ci ratio: 5.297856e-02	ci left: 3.037280e-02	ci right 3.203147e-02	k: 5303	n:170000
NFYB   170000 perm   40 sec   (4266 perm/sec)   p_kst 3.119412e-02   p_cons 1.676471e-03   p_joint 4.829412e-03

Joint ci ratio: 1.321973e-01	ci left: 4.539649e-03	ci right 5.187568e-03	k: 874	n:180000
Cons ci ratio: 2.239003e-01	ci left: 1.509732e-03	ci right 1.895490e-03	k: 305	n:180000
KS ci ratio: 5.145755e-02	ci left: 3.042904e-02	ci right 3.204166e-02	k: 5621	n:180000
NFYB   180000 perm   43 sec   (4197 perm/sec)   p_kst 3.122778e-02   p_cons 1.694444e-03   p_joint 4.855556e-03

Joint ci ratio: 1.278129e-01	ci left: 4.611343e-03	ci right 5.246012e-03	k: 935	n:190000
Cons ci ratio: 2.165893e-01	ci left: 1.534706e-03	ci right 1.912337e-03	k: 326	n:190000
KS ci ratio: 5.003436e-02	ci left: 3.051117e-02	ci right 3.208212e-02	k: 5945	n:190000
NFYB   190000 perm   46 sec   (4131 perm/sec)   p_kst 3.128947e-02   p_cons 1.715789e-03   p_joint 4.921053e-03

Joint ci ratio: 1.242137e-01	ci left: 4.647113e-03	ci right 5.267369e-03	k: 990	n:200000
Cons ci ratio: 2.096491e-01	ci left: 1.562103e-03	ci right 1.932578e-03	k: 348	n:200000
KS ci ratio: 4.878738e-02	ci left: 3.050658e-02	ci right 3.203705e-02	k: 6253	n:200000
NFYB   200000 perm   49 sec   (4069 perm/sec)   p_kst 3.126500e-02   p_cons 1.740000e-03   p_joint 4.950000e-03

Joint ci ratio: 1.218425e-01	ci left: 4.605815e-03	ci right 5.207976e-03	k: 1029	n:210000
Cons ci ratio: 2.044430e-01	ci left: 1.568988e-03	ci right 1.930702e-03	k: 366	n:210000
KS ci ratio: 4.764795e-02	ci left: 3.047933e-02	ci right 3.197174e-02	k: 6556	n:210000
NFYB   210000 perm   52 sec   (4010 perm/sec)   p_kst 3.121905e-02   p_cons 1.742857e-03   p_joint 4.900000e-03

Joint ci ratio: 1.195458e-01	ci left: 4.572784e-03	ci right 5.158561e-03	k: 1069	n:220000
Cons ci ratio: 2.006533e-01	ci left: 1.558079e-03	ci right 1.909803e-03	k: 380	n:220000
KS ci ratio: 4.651835e-02	ci left: 3.054034e-02	ci right 3.199932e-02	k: 6878	n:220000
NFYB   220000 perm   56 sec   (3952 perm/sec)   p_kst 3.126364e-02   p_cons 1.727273e-03   p_joint 4.859091e-03

Joint ci ratio: 1.164814e-01	ci left: 4.614484e-03	ci right 5.189407e-03	k: 1126	n:230000
Cons ci ratio: 1.973171e-01	ci left: 1.544041e-03	ci right 1.886104e-03	k: 393	n:230000
KS ci ratio: 4.553731e-02	ci left: 3.050181e-02	ci right 3.192742e-02	k: 7178	n:230000
NFYB   230000 perm   59 sec   (3894 perm/sec)   p_kst 3.120870e-02   p_cons 1.708696e-03   p_joint 4.895652e-03

Joint ci ratio: 1.140776e-01	ci left: 4.616447e-03	ci right 5.178946e-03	k: 1174	n:240000
Cons ci ratio: 1.924909e-01	ci left: 1.558974e-03	ci right 1.894909e-03	k: 413	n:240000
KS ci ratio: 4.458507e-02	ci left: 3.050802e-02	ci right 3.190333e-02	k: 7488	n:240000
NFYB   240000 perm   63 sec   (3834 perm/sec)   p_kst 3.120000e-02   p_cons 1.720833e-03   p_joint 4.891667e-03

Joint ci ratio: 1.109091e-01	ci left: 4.696147e-03	ci right 5.251425e-03	k: 1242	n:250000
Cons ci ratio: 1.862901e-01	ci left: 1.603310e-03	ci right 1.936412e-03	k: 441	n:250000
KS ci ratio: 4.367572e-02	ci left: 3.053380e-02	ci right 3.190110e-02	k: 7803	n:250000
NFYB   250000 perm   66 sec   (3779 perm/sec)   p_kst 3.121200e-02   p_cons 1.764000e-03   p_joint 4.968000e-03

Joint ci ratio: 1.090406e-01	ci left: 4.676358e-03	ci right 5.219383e-03	k: 1285	n:260000
Cons ci ratio: 1.838137e-01	ci left: 1.585658e-03	ci right 1.910226e-03	k: 453	n:260000
KS ci ratio: 4.281984e-02	ci left: 3.055787e-02	ci right 3.189876e-02	k: 8118	n:260000
NFYB   260000 perm   70 sec   (3727 perm/sec)   p_kst 3.122308e-02   p_cons 1.742308e-03   p_joint 4.942308e-03

Joint ci ratio: 1.067799e-01	ci left: 4.701369e-03	ci right 5.235268e-03	k: 1340	n:270000
Cons ci ratio: 1.797033e-01	ci left: 1.601171e-03	ci right 1.920788e-03	k: 474	n:270000
KS ci ratio: 4.203296e-02	ci left: 3.055107e-02	ci right 3.186643e-02	k: 8425	n:270000
NFYB   270000 perm   73 sec   (3675 perm/sec)   p_kst 3.120370e-02   p_cons 1.755556e-03   p_joint 4.962963e-03

Joint ci ratio: 1.053775e-01	ci left: 4.658618e-03	ci right 5.180282e-03	k: 1376	n:280000
Cons ci ratio: 1.776601e-01	ci left: 1.581513e-03	ci right 1.893231e-03	k: 485	n:280000
KS ci ratio: 4.122220e-02	ci left: 3.064043e-02	ci right 3.193359e-02	k: 8759	n:280000
NFYB   280000 perm   77 sec   (3626 perm/sec)   p_kst 3.128214e-02   p_cons 1.732143e-03   p_joint 4.914286e-03

Joint ci ratio: 1.032967e-01	ci left: 4.686043e-03	ci right 5.199789e-03	k: 1432	n:290000
Cons ci ratio: 1.748064e-01	ci left: 1.579717e-03	ci right 1.885551e-03	k: 501	n:290000
KS ci ratio: 4.045201e-02	ci left: 3.073068e-02	ci right 3.200285e-02	k: 9095	n:290000
NFYB   290000 perm   81 sec   (3578 perm/sec)   p_kst 3.136207e-02   p_cons 1.727586e-03   p_joint 4.937931e-03

Joint ci ratio: 1.017474e-01	ci left: 4.672746e-03	ci right 5.176891e-03	k: 1476	n:300000
Cons ci ratio: 1.720859e-01	ci left: 1.578078e-03	ci right 1.878346e-03	k: 517	n:300000
KS ci ratio: 3.976044e-02	ci left: 3.075900e-02	ci right 3.201008e-02	k: 9414	n:300000
NFYB   300000 perm   85 sec   (3524 perm/sec)   p_kst 3.138000e-02   p_cons 1.723333e-03   p_joint 4.920000e-03

Joint ci ratio: 1.001006e-01	ci left: 4.676087e-03	ci right 5.171947e-03	k: 1525	n:310000
Cons ci ratio: 1.698074e-01	ci left: 1.570400e-03	ci right 1.864846e-03	k: 531	n:310000
KS ci ratio: 3.918220e-02	ci left: 3.066425e-02	ci right 3.189292e-02	k: 9695	n:310000
NFYB   310000 perm   89 sec   (3473 perm/sec)   p_kst 3.127419e-02   p_cons 1.712903e-03   p_joint 4.919355e-03

Joint ci ratio: 9.906993e-02	ci left: 4.627463e-03	ci right 5.112820e-03	k: 1557	n:320000
Cons ci ratio: 1.677710e-01	ci left: 1.560234e-03	ci right 1.848911e-03	k: 544	n:320000
KS ci ratio: 3.854877e-02	ci left: 3.069938e-02	ci right 3.190913e-02	k: 10016	n:320000
NFYB   320000 perm   93 sec   (3431 perm/sec)   p_kst 3.130000e-02   p_cons 1.700000e-03   p_joint 4.865625e-03

Joint ci ratio: 9.782345e-02	ci left: 4.605462e-03	ci right 5.082085e-03	k: 1597	n:330000
Cons ci ratio: 1.661047e-01	ci left: 1.544893e-03	ci right 1.827609e-03	k: 555	n:330000
KS ci ratio: 3.796216e-02	ci left: 3.070550e-02	ci right 3.189669e-02	k: 10328	n:330000
NFYB   330000 perm   97 sec   (3385 perm/sec)   p_kst 3.129697e-02   p_cons 1.681818e-03   p_joint 4.839394e-03

Joint ci ratio: 9.635720e-02	ci left: 4.610626e-03	ci right 5.080227e-03	k: 1646	n:340000
Cons ci ratio: 1.636221e-01	ci left: 1.547393e-03	ci right 1.825917e-03	k: 572	n:340000
KS ci ratio: 3.738161e-02	ci left: 3.074346e-02	ci right 3.191749e-02	k: 10651	n:340000
NFYB   340000 perm   102 sec   (3345 perm/sec)   p_kst 3.132647e-02   p_cons 1.682353e-03   p_joint 4.841176e-03

Joint ci ratio: 9.498312e-02	ci left: 4.612755e-03	ci right 5.075501e-03	k: 1694	n:350000
Cons ci ratio: 1.613846e-01	ci left: 1.547037e-03	ci right 1.821320e-03	k: 588	n:350000
KS ci ratio: 3.683555e-02	ci left: 3.076522e-02	ci right 3.192255e-02	k: 10969	n:350000
NFYB   350000 perm   106 sec   (3305 perm/sec)   p_kst 3.134000e-02   p_cons 1.680000e-03   p_joint 4.840000e-03

Joint ci ratio: 9.380148e-02	ci left: 4.601247e-03	ci right 5.056780e-03	k: 1737	n:360000
Cons ci ratio: 1.600333e-01	ci left: 1.530723e-03	ci right 1.799623e-03	k: 598	n:360000
KS ci ratio: 3.637268e-02	ci left: 3.068677e-02	ci right 3.182634e-02	k: 11251	n:360000
NFYB   360000 perm   110 sec   (3266 perm/sec)   p_kst 3.125278e-02   p_cons 1.661111e-03   p_joint 4.825000e-03

Joint ci ratio: 9.245445e-02	ci left: 4.611517e-03	ci right 5.061156e-03	k: 1788	n:370000
Cons ci ratio: 1.574260e-01	ci left: 1.541260e-03	ci right 1.807183e-03	k: 618	n:370000
KS ci ratio: 3.588829e-02	ci left: 3.067695e-02	ci right 3.180067e-02	k: 11557	n:370000
NFYB   370000 perm   115 sec   (3229 perm/sec)   p_kst 3.123514e-02   p_cons 1.670270e-03   p_joint 4.832432e-03

Joint ci ratio: 9.116383e-02	ci left: 4.621292e-03	ci right 5.065258e-03	k: 1839	n:380000
Cons ci ratio: 1.559229e-01	ci left: 1.531040e-03	ci right 1.792442e-03	k: 630	n:380000
KS ci ratio: 3.542121e-02	ci left: 3.067036e-02	ci right 3.177891e-02	k: 11864	n:380000
NFYB   380000 perm   119 sec   (3191 perm/sec)   p_kst 3.122105e-02   p_cons 1.657895e-03   p_joint 4.839474e-03

Joint ci ratio: 9.009352e-02	ci left: 4.613059e-03	ci right 5.050758e-03	k: 1883	n:390000
Cons ci ratio: 1.548242e-01	ci left: 1.513962e-03	ci right 1.770457e-03	k: 639	n:390000
KS ci ratio: 3.496005e-02	ci left: 3.068452e-02	ci right 3.177887e-02	k: 12179	n:390000
NFYB   390000 perm   124 sec   (3155 perm/sec)   p_kst 3.122821e-02   p_cons 1.638462e-03   p_joint 4.828205e-03

Joint ci ratio: 8.899049e-02	ci left: 4.612602e-03	ci right 5.044619e-03	k: 1930	n:400000
Cons ci ratio: 1.532760e-01	ci left: 1.507359e-03	ci right 1.759948e-03	k: 652	n:400000
KS ci ratio: 3.453357e-02	ci left: 3.066832e-02	ci right 3.174848e-02	k: 12482	n:400000
NFYB   400000 perm   128 sec   (3118 perm/sec)   p_kst 3.120500e-02   p_cons 1.630000e-03   p_joint 4.825000e-03

Joint ci ratio: 8.790468e-02	ci left: 4.614583e-03	ci right 5.041242e-03	k: 1978	n:410000
Cons ci ratio: 1.520021e-01	ci left: 1.496398e-03	ci right 1.744876e-03	k: 663	n:410000
KS ci ratio: 3.410718e-02	ci left: 3.067960e-02	ci right 3.174655e-02	k: 12796	n:410000
NFYB   410000 perm   133 sec   (3082 perm/sec)   p_kst 3.120976e-02   p_cons 1.617073e-03   p_joint 4.824390e-03

Joint ci ratio: 8.703041e-02	ci left: 4.597865e-03	ci right 5.018535e-03	k: 2018	n:420000
Cons ci ratio: 1.505362e-01	ci left: 1.490550e-03	ci right 1.735455e-03	k: 676	n:420000
KS ci ratio: 3.366838e-02	ci left: 3.074001e-02	ci right 3.179504e-02	k: 13131	n:420000
NFYB   420000 perm   138 sec   (3041 perm/sec)   p_kst 3.126429e-02   p_cons 1.609524e-03   p_joint 4.804762e-03

Joint ci ratio: 8.624487e-02	ci left: 4.575118e-03	ci right 4.989738e-03	k: 2055	n:430000
Cons ci ratio: 1.495467e-01	ci left: 1.476030e-03	ci right 1.716812e-03	k: 685	n:430000
KS ci ratio: 3.325119e-02	ci left: 3.078847e-02	ci right 3.183182e-02	k: 13462	n:430000
NFYB   430000 perm   143 sec   (3006 perm/sec)   p_kst 3.130698e-02   p_cons 1.593023e-03   p_joint 4.779070e-03

Joint ci ratio: 8.507276e-02	ci left: 4.597910e-03	ci right 5.008652e-03	k: 2112	n:440000
Cons ci ratio: 1.474126e-01	ci left: 1.486250e-03	ci right 1.724935e-03	k: 705	n:440000
KS ci ratio: 3.286513e-02	ci left: 3.080549e-02	ci right 3.183706e-02	k: 13780	n:440000
NFYB   440000 perm   148 sec   (2972 perm/sec)   p_kst 3.131818e-02   p_cons 1.602273e-03   p_joint 4.800000e-03

Joint ci ratio: 8.406403e-02	ci left: 4.606672e-03	ci right 5.013078e-03	k: 2163	n:450000
Cons ci ratio: 1.457701e-01	ci left: 1.487474e-03	ci right 1.723462e-03	k: 721	n:450000
KS ci ratio: 3.247556e-02	ci left: 3.085268e-02	ci right 3.187336e-02	k: 14112	n:450000
NFYB   450000 perm   153 sec   (2940 perm/sec)   p_kst 3.136000e-02   p_cons 1.602222e-03   p_joint 4.806667e-03

Joint ci ratio: 8.312807e-02	ci left: 4.610822e-03	ci right 5.012845e-03	k: 2212	n:460000
Cons ci ratio: 1.434048e-01	ci left: 1.505425e-03	ci right 1.740054e-03	k: 745	n:460000
KS ci ratio: 3.210985e-02	ci left: 3.087848e-02	ci right 3.188830e-02	k: 14435	n:460000
NFYB   460000 perm   158 sec   (2908 perm/sec)   p_kst 3.138043e-02   p_cons 1.619565e-03   p_joint 4.808696e-03

Joint ci ratio: 8.218619e-02	ci left: 4.618988e-03	ci right 5.016941e-03	k: 2263	n:470000
Cons ci ratio: 1.421719e-01	ci left: 1.500066e-03	ci right 1.731679e-03	k: 758	n:470000
KS ci ratio: 3.177401e-02	ci left: 3.086946e-02	ci right 3.186824e-02	k: 14742	n:470000
NFYB   470000 perm   163 sec   (2876 perm/sec)   p_kst 3.136596e-02   p_cons 1.612766e-03   p_joint 4.814894e-03

Joint ci ratio: 8.132859e-02	ci left: 4.620715e-03	ci right 5.014466e-03	k: 2311	n:480000
Cons ci ratio: 1.402443e-01	ci left: 1.511020e-03	ci right 1.740897e-03	k: 779	n:480000
KS ci ratio: 3.142910e-02	ci left: 3.089809e-02	ci right 3.188674e-02	k: 15067	n:480000
NFYB   480000 perm   169 sec   (2846 perm/sec)   p_kst 3.138958e-02   p_cons 1.622917e-03   p_joint 4.814583e-03

Joint ci ratio: 8.061751e-02	ci left: 4.608392e-03	ci right 4.997499e-03	k: 2352	n:490000
Cons ci ratio: 1.387404e-01	ci left: 1.513666e-03	ci right 1.741272e-03	k: 796	n:490000
KS ci ratio: 3.107226e-02	ci left: 3.097016e-02	ci right 3.194967e-02	k: 15414	n:490000
NFYB   490000 perm   174 sec   (2815 perm/sec)   p_kst 3.145714e-02   p_cons 1.624490e-03   p_joint 4.800000e-03

Joint ci ratio: 7.987449e-02	ci left: 4.602458e-03	ci right 4.987315e-03	k: 2396	n:500000
Cons ci ratio: 1.372839e-01	ci left: 1.516218e-03	ci right 1.741620e-03	k: 813	n:500000
KS ci ratio: 3.074443e-02	ci left: 3.100567e-02	ci right 3.197577e-02	k: 15744	n:500000
NFYB   500000 perm   179 sec   (2786 perm/sec)   p_kst 3.148800e-02   p_cons 1.626000e-03   p_joint 4.792000e-03

Joint ci ratio: 7.928229e-02	ci left: 4.581395e-03	ci right 4.961519e-03	k: 2432	n:510000
Cons ci ratio: 1.362011e-01	ci left: 1.511107e-03	ci right 1.733832e-03	k: 826	n:510000
KS ci ratio: 3.046297e-02	ci left: 3.096782e-02	ci right 3.192771e-02	k: 16037	n:510000
NFYB   510000 perm   185 sec   (2758 perm/sec)   p_kst 3.144510e-02   p_cons 1.619608e-03   p_joint 4.768627e-03

Joint ci ratio: 7.843221e-02	ci left: 4.593206e-03	ci right 4.970037e-03	k: 2485	n:520000
Cons ci ratio: 1.349024e-01	ci left: 1.511773e-03	ci right 1.732301e-03	k: 842	n:520000
KS ci ratio: 3.019197e-02	ci left: 3.092574e-02	ci right 3.187565e-02	k: 16327	n:520000
NFYB   520000 perm   190 sec   (2730 perm/sec)   p_kst 3.139808e-02   p_cons 1.619231e-03   p_joint 4.778846e-03

Joint ci ratio: 7.771663e-02	ci left: 4.591639e-03	ci right 4.964749e-03	k: 2531	n:530000
Cons ci ratio: 1.334846e-01	ci left: 1.516071e-03	ci right 1.734718e-03	k: 860	n:530000
KS ci ratio: 2.990393e-02	ci left: 3.093398e-02	ci right 3.187493e-02	k: 16643	n:530000
NFYB   530000 perm   196 sec   (2702 perm/sec)   p_kst 3.140189e-02   p_cons 1.622642e-03   p_joint 4.775472e-03

Joint ci ratio: 7.694533e-02	ci left: 4.599228e-03	ci right 4.969079e-03	k: 2582	n:540000
Cons ci ratio: 1.320353e-01	ci left: 1.522012e-03	ci right 1.738946e-03	k: 879	n:540000
KS ci ratio: 2.961857e-02	ci left: 3.095299e-02	ci right 3.188538e-02	k: 16965	n:540000
NFYB   540000 perm   202 sec   (2675 perm/sec)   p_kst 3.141667e-02   p_cons 1.627778e-03   p_joint 4.781481e-03

Joint ci ratio: 7.626933e-02	ci left: 4.597639e-03	ci right 4.963971e-03	k: 2628	n:550000
Cons ci ratio: 1.312184e-01	ci left: 1.513681e-03	ci right 1.727988e-03	k: 890	n:550000
KS ci ratio: 2.934999e-02	ci left: 3.095330e-02	ci right 3.187710e-02	k: 17277	n:550000
NFYB   550000 perm   208 sec   (2649 perm/sec)   p_kst 3.141273e-02   p_cons 1.618182e-03   p_joint 4.778182e-03

Joint ci ratio: 7.565347e-02	ci left: 4.590865e-03	ci right 4.953573e-03	k: 2671	n:560000
Cons ci ratio: 1.300559e-01	ci left: 1.514288e-03	ci right 1.726635e-03	k: 906	n:560000
KS ci ratio: 2.909713e-02	ci left: 3.093590e-02	ci right 3.185110e-02	k: 17579	n:560000
NFYB   560000 perm   213 sec   (2623 perm/sec)   p_kst 3.139107e-02   p_cons 1.617857e-03   p_joint 4.769643e-03

Joint ci ratio: 7.505230e-02	ci left: 4.584340e-03	ci right 4.943529e-03	k: 2714	n:570000
Cons ci ratio: 1.290639e-01	ci left: 1.511487e-03	ci right 1.721701e-03	k: 920	n:570000
KS ci ratio: 2.883571e-02	ci left: 3.095051e-02	ci right 3.185777e-02	k: 17899	n:570000
NFYB   570000 perm   219 sec   (2598 perm/sec)   p_kst 3.140175e-02   p_cons 1.614035e-03   p_joint 4.761404e-03

Joint ci ratio: 7.449237e-02	ci left: 4.574667e-03	ci right 4.930308e-03	k: 2755	n:580000
Cons ci ratio: 1.282317e-01	ci left: 1.505450e-03	ci right 1.713372e-03	k: 932	n:580000
KS ci ratio: 2.860229e-02	ci left: 3.092013e-02	ci right 3.181904e-02	k: 18193	n:580000
NFYB   580000 perm   226 sec   (2572 perm/sec)   p_kst 3.136724e-02   p_cons 1.606897e-03   p_joint 4.750000e-03

Joint ci ratio: 7.385200e-02	ci left: 4.576977e-03	ci right 4.929608e-03	k: 2803	n:590000
Cons ci ratio: 1.269453e-01	ci left: 1.511110e-03	ci right 1.717562e-03	k: 951	n:590000
KS ci ratio: 2.832782e-02	ci left: 3.099012e-02	ci right 3.188228e-02	k: 18546	n:590000
NFYB   590000 perm   232 sec   (2547 perm/sec)   p_kst 3.143390e-02   p_cons 1.611864e-03   p_joint 4.750847e-03

Joint ci ratio: 7.311204e-02	ci left: 4.593950e-03	ci right 4.944191e-03	k: 2860	n:600000
Cons ci ratio: 1.258918e-01	ci left: 1.511748e-03	ci right 1.716446e-03	k: 967	n:600000
KS ci ratio: 2.809565e-02	ci left: 3.098333e-02	ci right 3.186787e-02	k: 18854	n:600000
NFYB   600000 perm   238 sec   (2523 perm/sec)   p_kst 3.142333e-02   p_cons 1.611667e-03   p_joint 4.766667e-03

Joint ci ratio: 7.254391e-02	ci left: 4.591066e-03	ci right 4.938253e-03	k: 2905	n:610000
Cons ci ratio: 1.249277e-01	ci left: 1.510784e-03	ci right 1.713668e-03	k: 982	n:610000
KS ci ratio: 2.788037e-02	ci left: 3.095237e-02	ci right 3.182914e-02	k: 19147	n:610000
NFYB   610000 perm   244 sec   (2499 perm/sec)   p_kst 3.138852e-02   p_cons 1.609836e-03   p_joint 4.762295e-03

Joint ci ratio: 7.192763e-02	ci left: 4.596206e-03	ci right 4.940705e-03	k: 2955	n:620000
Cons ci ratio: 1.237992e-01	ci left: 1.514546e-03	ci right 1.715963e-03	k: 1000	n:620000
KS ci ratio: 2.766408e-02	ci left: 3.093524e-02	ci right 3.180463e-02	k: 19448	n:620000
NFYB   620000 perm   251 sec   (2475 perm/sec)   p_kst 3.136774e-02   p_cons 1.612903e-03   p_joint 4.766129e-03

Joint ci ratio: 7.143432e-02	ci left: 4.587162e-03	ci right 4.928528e-03	k: 2996	n:630000
Cons ci ratio: 1.228215e-01	ci left: 1.515119e-03	ci right 1.714906e-03	k: 1016	n:630000
KS ci ratio: 2.743483e-02	ci left: 3.095811e-02	ci right 3.182081e-02	k: 19774	n:630000
NFYB   630000 perm   257 sec   (2450 perm/sec)   p_kst 3.138730e-02   p_cons 1.612698e-03   p_joint 4.755556e-03

Joint ci ratio: 7.075239e-02	ci left: 4.604503e-03	ci right 4.943754e-03	k: 3054	n:640000
Cons ci ratio: 1.216310e-01	ci left: 1.521740e-03	ci right 1.720315e-03	k: 1036	n:640000
KS ci ratio: 2.721258e-02	ci left: 3.097718e-02	ci right 3.183332e-02	k: 20098	n:640000
NFYB   640000 perm   264 sec   (2428 perm/sec)   p_kst 3.140312e-02   p_cons 1.618750e-03   p_joint 4.771875e-03

Joint ci ratio: 7.011225e-02	ci left: 4.618302e-03	ci right 4.955366e-03	k: 3110	n:650000
Cons ci ratio: 1.204744e-01	ci left: 1.528167e-03	ci right 1.725549e-03	k: 1056	n:650000
KS ci ratio: 2.698883e-02	ci left: 3.101098e-02	ci right 3.186089e-02	k: 20432	n:650000
NFYB   650000 perm   270 sec   (2406 perm/sec)   p_kst 3.143385e-02   p_cons 1.624615e-03   p_joint 4.784615e-03

Joint ci ratio: 6.954437e-02	ci left: 4.624252e-03	ci right 4.958906e-03	k: 3161	n:660000
Cons ci ratio: 1.194614e-01	ci left: 1.531467e-03	ci right 1.727494e-03	k: 1074	n:660000
KS ci ratio: 2.676318e-02	ci left: 3.106034e-02	ci right 3.190438e-02	k: 20777	n:660000
NFYB   660000 perm   277 sec   (2384 perm/sec)   p_kst 3.148030e-02   p_cons 1.627273e-03   p_joint 4.789394e-03

Joint ci ratio: 6.917419e-02	ci left: 4.605098e-03	ci right 4.936520e-03	k: 3195	n:670000
Cons ci ratio: 1.189651e-01	ci left: 1.521641e-03	ci right 1.715545e-03	k: 1083	n:670000
KS ci ratio: 2.657755e-02	ci left: 3.102966e-02	ci right 3.186693e-02	k: 21069	n:670000
NFYB   670000 perm   284 sec   (2361 perm/sec)   p_kst 3.144627e-02   p_cons 1.616418e-03   p_joint 4.768657e-03

Joint ci ratio: 6.863924e-02	ci left: 4.609638e-03	ci right 4.938720e-03	k: 3245	n:680000
Cons ci ratio: 1.181505e-01	ci left: 1.520669e-03	ci right 1.713029e-03	k: 1098	n:680000
KS ci ratio: 2.639063e-02	ci left: 3.101160e-02	ci right 3.184240e-02	k: 21369	n:680000
NFYB   680000 perm   291 sec   (2339 perm/sec)   p_kst 3.142500e-02   p_cons 1.614706e-03   p_joint 4.772059e-03

Joint ci ratio: 6.828324e-02	ci left: 4.591262e-03	ci right 4.917265e-03	k: 3279	n:690000
Cons ci ratio: 1.171945e-01	ci left: 1.523949e-03	ci right 1.715057e-03	k: 1116	n:690000
KS ci ratio: 2.619138e-02	ci left: 3.103151e-02	ci right 3.185648e-02	k: 21695	n:690000
NFYB   690000 perm   298 sec   (2319 perm/sec)   p_kst 3.144203e-02   p_cons 1.617391e-03   p_joint 4.752174e-03

Joint ci ratio: 6.779924e-02	ci left: 4.591673e-03	ci right 4.915303e-03	k: 3326	n:700000
Cons ci ratio: 1.163641e-01	ci left: 1.524368e-03	ci right 1.714080e-03	k: 1132	n:700000
KS ci ratio: 2.598622e-02	ci left: 3.107502e-02	ci right 3.189458e-02	k: 22038	n:700000
NFYB   700000 perm   305 sec   (2298 perm/sec)   p_kst 3.148286e-02   p_cons 1.617143e-03   p_joint 4.751429e-03

Joint ci ratio: 6.736552e-02	ci left: 4.586541e-03	ci right 4.907661e-03	k: 3369	n:710000
Cons ci ratio: 1.154505e-01	ci left: 1.527515e-03	ci right 1.716025e-03	k: 1150	n:710000
KS ci ratio: 2.579831e-02	ci left: 3.108793e-02	ci right 3.190181e-02	k: 22360	n:710000
NFYB   710000 perm   312 sec   (2278 perm/sec)   p_kst 3.149296e-02   p_cons 1.619718e-03   p_joint 4.745070e-03

Joint ci ratio: 6.682209e-02	ci left: 4.597948e-03	ci right 4.917168e-03	k: 3424	n:720000
Cons ci ratio: 1.147056e-01	ci left: 1.526533e-03	ci right 1.713624e-03	k: 1165	n:720000
KS ci ratio: 2.563601e-02	ci left: 3.104943e-02	ci right 3.185712e-02	k: 22645	n:720000
NFYB   720000 perm   319 sec   (2259 perm/sec)   p_kst 3.145139e-02   p_cons 1.618056e-03   p_joint 4.755556e-03

Joint ci ratio: 6.631075e-02	ci left: 4.606357e-03	ci right 4.923620e-03	k: 3477	n:730000
Cons ci ratio: 1.138302e-01	ci left: 1.529575e-03	ci right 1.715512e-03	k: 1183	n:730000
KS ci ratio: 2.545325e-02	ci left: 3.106783e-02	ci right 3.187014e-02	k: 22971	n:730000
NFYB   730000 perm   326 sec   (2239 perm/sec)   p_kst 3.146712e-02   p_cons 1.620548e-03   p_joint 4.763014e-03

Joint ci ratio: 6.585784e-02	ci left: 4.607902e-03	ci right 4.923021e-03	k: 3525	n:740000
Cons ci ratio: 1.131160e-01	ci left: 1.528600e-03	ci right 1.713175e-03	k: 1198	n:740000
KS ci ratio: 2.529341e-02	ci left: 3.104008e-02	ci right 3.183657e-02	k: 23263	n:740000
NFYB   740000 perm   333 sec   (2221 perm/sec)   p_kst 3.143649e-02   p_cons 1.618919e-03   p_joint 4.763514e-03

Joint ci ratio: 6.547854e-02	ci left: 4.600232e-03	ci right 4.912946e-03	k: 3566	n:750000
Cons ci ratio: 1.122762e-01	ci left: 1.531542e-03	ci right 1.715008e-03	k: 1216	n:750000
KS ci ratio: 2.513213e-02	ci left: 3.102368e-02	ci right 3.181461e-02	k: 23563	n:750000
NFYB   750000 perm   340 sec   (2203 perm/sec)   p_kst 3.141733e-02   p_cons 1.621333e-03   p_joint 4.754667e-03

Joint ci ratio: 6.500623e-02	ci left: 4.607008e-03	ci right 4.917838e-03	k: 3618	n:760000
Cons ci ratio: 1.113646e-01	ci left: 1.536970e-03	ci right 1.719494e-03	k: 1236	n:760000
KS ci ratio: 2.496634e-02	ci left: 3.102605e-02	ci right 3.181174e-02	k: 23877	n:760000
NFYB   760000 perm   348 sec   (2184 perm/sec)   p_kst 3.141711e-02   p_cons 1.626316e-03   p_joint 4.760526e-03

Joint ci ratio: 6.460592e-02	ci left: 4.604671e-03	ci right 4.913359e-03	k: 3663	n:770000
Cons ci ratio: 1.106071e-01	ci left: 1.538475e-03	ci right 1.719853e-03	k: 1253	n:770000
KS ci ratio: 2.480538e-02	ci left: 3.102449e-02	ci right 3.180501e-02	k: 24188	n:770000
NFYB   770000 perm   355 sec   (2166 perm/sec)   p_kst 3.141299e-02   p_cons 1.627273e-03   p_joint 4.757143e-03

Joint ci ratio: 6.416079e-02	ci left: 4.609969e-03	ci right 4.916804e-03	k: 3714	n:780000
Cons ci ratio: 1.098216e-01	ci left: 1.541192e-03	ci right 1.721516e-03	k: 1271	n:780000
KS ci ratio: 2.462933e-02	ci left: 3.106760e-02	ci right 3.184358e-02	k: 24534	n:780000
NFYB   780000 perm   363 sec   (2148 perm/sec)   p_kst 3.145385e-02   p_cons 1.629487e-03   p_joint 4.761538e-03

Joint ci ratio: 6.388686e-02	ci left: 4.591471e-03	ci right 4.895722e-03	k: 3746	n:790000
Cons ci ratio: 1.093075e-01	ci left: 1.536456e-03	ci right 1.715331e-03	k: 1283	n:790000
KS ci ratio: 2.447679e-02	ci left: 3.106056e-02	ci right 3.183149e-02	k: 24841	n:790000
NFYB   790000 perm   371 sec   (2131 perm/sec)   p_kst 3.144430e-02   p_cons 1.624051e-03   p_joint 4.741772e-03

Joint ci ratio: 6.343955e-02	ci left: 4.599274e-03	ci right 4.901829e-03	k: 3799	n:800000
Cons ci ratio: 1.086328e-01	ci left: 1.536705e-03	ci right 1.714434e-03	k: 1299	n:800000
KS ci ratio: 2.429814e-02	ci left: 3.112578e-02	ci right 3.189261e-02	k: 25206	n:800000
NFYB   800000 perm   378 sec   (2114 perm/sec)   p_kst 3.150750e-02   p_cons 1.623750e-03   p_joint 4.748750e-03

Joint ci ratio: 6.310856e-02	ci left: 4.591094e-03	ci right 4.891477e-03	k: 3839	n:810000
Cons ci ratio: 1.081351e-01	ci left: 1.532147e-03	ci right 1.708485e-03	k: 1311	n:810000
KS ci ratio: 2.416142e-02	ci left: 3.109368e-02	ci right 3.185535e-02	k: 25493	n:810000
NFYB   810000 perm   386 sec   (2097 perm/sec)   p_kst 3.147284e-02   p_cons 1.618519e-03   p_joint 4.739506e-03

Joint ci ratio: 6.277458e-02	ci left: 4.584317e-03	ci right 4.882613e-03	k: 3880	n:820000
Cons ci ratio: 1.077258e-01	ci left: 1.525328e-03	ci right 1.700174e-03	k: 1321	n:820000
KS ci ratio: 2.400392e-02	ci left: 3.112057e-02	ci right 3.187786e-02	k: 25828	n:820000
NFYB   820000 perm   394 sec   (2080 perm/sec)   p_kst 3.149756e-02   p_cons 1.610976e-03   p_joint 4.731707e-03

Joint ci ratio: 6.238195e-02	ci left: 4.587197e-03	ci right 4.883746e-03	k: 3929	n:830000
Cons ci ratio: 1.070798e-01	ci left: 1.525710e-03	ci right 1.699485e-03	k: 1337	n:830000
KS ci ratio: 2.386547e-02	ci left: 3.110610e-02	ci right 3.185862e-02	k: 26129	n:830000
NFYB   830000 perm   402 sec   (2064 perm/sec)   p_kst 3.148072e-02   p_cons 1.610843e-03   p_joint 4.733735e-03

Joint ci ratio: 6.202792e-02	ci left: 4.585326e-03	ci right 4.880010e-03	k: 3974	n:840000
Cons ci ratio: 1.064846e-01	ci left: 1.524927e-03	ci right 1.697587e-03	k: 1352	n:840000
KS ci ratio: 2.371966e-02	ci left: 3.111685e-02	ci right 3.186496e-02	k: 26451	n:840000
NFYB   840000 perm   410 sec   (2048 perm/sec)   p_kst 3.148929e-02   p_cons 1.609524e-03   p_joint 4.730952e-03

Joint ci ratio: 6.167215e-02	ci left: 4.584661e-03	ci right 4.877553e-03	k: 4020	n:850000
Cons ci ratio: 1.059381e-01	ci left: 1.523019e-03	ci right 1.694524e-03	k: 1366	n:850000
KS ci ratio: 2.358150e-02	ci left: 3.111449e-02	ci right 3.185812e-02	k: 26762	n:850000
NFYB   850000 perm   418 sec   (2032 perm/sec)   p_kst 3.148471e-02   p_cons 1.607059e-03   p_joint 4.729412e-03

Joint ci ratio: 6.130729e-02	ci left: 4.586307e-03	ci right 4.877509e-03	k: 4068	n:860000
Cons ci ratio: 1.053999e-01	ci left: 1.521158e-03	ci right 1.691529e-03	k: 1380	n:860000
KS ci ratio: 2.344170e-02	ci left: 3.112260e-02	ci right 3.186196e-02	k: 27082	n:860000
NFYB   860000 perm   426 sec   (2017 perm/sec)   p_kst 3.149070e-02   p_cons 1.604651e-03   p_joint 4.730233e-03

Joint ci ratio: 6.095627e-02	ci left: 4.586788e-03	ci right 4.876295e-03	k: 4115	n:870000
Cons ci ratio: 1.046446e-01	ci left: 1.526059e-03	ci right 1.695678e-03	k: 1400	n:870000
KS ci ratio: 2.329383e-02	ci left: 3.115796e-02	ci right 3.189344e-02	k: 27426	n:870000
NFYB   870000 perm   435 sec   (2002 perm/sec)   p_kst 3.152414e-02   p_cons 1.609195e-03   p_joint 4.729885e-03

Joint ci ratio: 6.056737e-02	ci left: 4.593978e-03	ci right 4.882024e-03	k: 4168	n:880000
Cons ci ratio: 1.041626e-01	ci left: 1.523104e-03	ci right 1.691568e-03	k: 1413	n:880000
KS ci ratio: 2.315431e-02	ci left: 3.117785e-02	ci right 3.190933e-02	k: 27757	n:880000
NFYB   880000 perm   443 sec   (1987 perm/sec)   p_kst 3.154205e-02   p_cons 1.605682e-03   p_joint 4.736364e-03

Joint ci ratio: 6.019298e-02	ci left: 4.599906e-03	ci right 4.886478e-03	k: 4220	n:890000
Cons ci ratio: 1.033974e-01	ci left: 1.528974e-03	ci right 1.696769e-03	k: 1434	n:890000
KS ci ratio: 2.301939e-02	ci left: 3.119172e-02	ci right 3.191920e-02	k: 28083	n:890000
NFYB   890000 perm   451 sec   (1973 perm/sec)   p_kst 3.155393e-02   p_cons 1.611236e-03   p_joint 4.741573e-03

Joint ci ratio: 5.980436e-02	ci left: 4.608991e-03	ci right 4.894211e-03	k: 4275	n:900000
Cons ci ratio: 1.026487e-01	ci left: 1.534717e-03	ci right 1.701850e-03	k: 1455	n:900000
KS ci ratio: 2.288472e-02	ci left: 3.121082e-02	ci right 3.193443e-02	k: 28414	n:900000
NFYB   900000 perm   459 sec   (1959 perm/sec)   p_kst 3.157111e-02   p_cons 1.616667e-03   p_joint 4.750000e-03

Joint ci ratio: 5.945076e-02	ci left: 4.613551e-03	ci right 4.897308e-03	k: 4326	n:910000
Cons ci ratio: 1.019507e-01	ci left: 1.539268e-03	ci right 1.705688e-03	k: 1475	n:910000
KS ci ratio: 2.275607e-02	ci left: 3.121967e-02	ci right 3.193936e-02	k: 28736	n:910000
NFYB   910000 perm   468 sec   (1945 perm/sec)   p_kst 3.157802e-02   p_cons 1.620879e-03   p_joint 4.753846e-03

Joint ci ratio: 5.915769e-02	ci left: 4.609450e-03	ci right 4.891509e-03	k: 4369	n:920000
Cons ci ratio: 1.015048e-01	ci left: 1.536308e-03	ci right 1.701638e-03	k: 1488	n:920000
KS ci ratio: 2.263479e-02	ci left: 3.121429e-02	ci right 3.192997e-02	k: 29045	n:920000
NFYB   920000 perm   476 sec   (1931 perm/sec)   p_kst 3.157065e-02   p_cons 1.617391e-03   p_joint 4.748913e-03

Joint ci ratio: 5.884212e-02	ci left: 4.609678e-03	ci right 4.890195e-03	k: 4416	n:930000
Cons ci ratio: 1.009638e-01	ci left: 1.536557e-03	ci right 1.700980e-03	k: 1504	n:930000
KS ci ratio: 2.251305e-02	ci left: 3.121545e-02	ci right 3.192726e-02	k: 29360	n:930000
NFYB   930000 perm   485 sec   (1917 perm/sec)   p_kst 3.156989e-02   p_cons 1.617204e-03   p_joint 4.748387e-03

Joint ci ratio: 5.849207e-02	ci left: 4.616195e-03	ci right 4.895381e-03	k: 4469	n:940000
Cons ci ratio: 1.002336e-01	ci left: 1.543027e-03	ci right 1.706878e-03	k: 1526	n:940000
KS ci ratio: 2.238469e-02	ci left: 3.123987e-02	ci right 3.194813e-02	k: 29697	n:940000
NFYB   940000 perm   494 sec   (1903 perm/sec)   p_kst 3.159255e-02   p_cons 1.623404e-03   p_joint 4.754255e-03

Joint ci ratio: 5.816758e-02	ci left: 4.619468e-03	ci right 4.897249e-03	k: 4519	n:950000
Cons ci ratio: 9.980980e-02	ci left: 1.540126e-03	ci right 1.702937e-03	k: 1539	n:950000
KS ci ratio: 2.226501e-02	ci left: 3.124599e-02	ci right 3.195055e-02	k: 30017	n:950000
NFYB   950000 perm   503 sec   (1888 perm/sec)   p_kst 3.159684e-02   p_cons 1.620000e-03   p_joint 4.756842e-03

Outputting figure to mutsig2_images.part000000000114/NFYB.2_652_950000_0.031597_0.00162_0.0047568.png
                gene_name: NFYB
               theta_stop: 0.100 
                    nperm: 950000 
                     p_ks: 0.032 
        ci_ks_bounds_left: 0.031 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.0016 
      ci_cons_bounds_left: 0.0015 
     ci_cons_bounds_right: 0.0017 
                  p_joint: 0.0048 
     ci_joint_bounds_left: 0.0046 
    ci_joint_bounds_right: 0.0049 

Current progress: 83 percent done.
NIN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.740754e-02	ci left: 1.961390e-01	ci right 2.120337e-01	k: 2040	n:10000
Cons ci ratio: 2.385065e-01	ci left: 2.315796e-02	ci right 2.952203e-02	k: 262	n:10000
KS ci ratio: 2.385131e-02	ci left: 7.209804e-01	ci right 7.384856e-01	k: 7298	n:10000
NIN   10000 perm   2 sec   (4660 perm/sec)   p_kst 7.298000e-01   p_cons 2.620000e-02   p_joint 2.040000e-01

Joint ci ratio: 3.105327e-02	ci left: 4.364987e-01	ci right 4.503178e-01	k: 8868	n:20000
Cons ci ratio: 1.711769e-01	ci left: 2.335948e-02	ci right 2.777992e-02	k: 510	n:20000
KS ci ratio: 1.683578e-02	ci left: 7.242925e-01	ci right 7.366404e-01	k: 14610	n:20000
NIN   20000 perm   5 sec   (4237 perm/sec)   p_kst 7.305000e-01   p_cons 2.550000e-02   p_joint 4.434000e-01

Joint ci ratio: 3.959396e-02	ci left: 2.413664e-01	ci right 2.511495e-01	k: 7387	n:30000
Cons ci ratio: 1.355170e-01	ci left: 2.529183e-02	ci right 2.900051e-02	k: 813	n:30000
KS ci ratio: 1.369989e-02	ci left: 7.267814e-01	ci right 7.368403e-01	k: 21955	n:30000
NIN   30000 perm   8 sec   (3996 perm/sec)   p_kst 7.318333e-01   p_cons 2.710000e-02   p_joint 2.462333e-01

Joint ci ratio: 7.416857e-02	ci left: 6.284890e-02	ci right 6.771445e-02	k: 2610	n:40000
Cons ci ratio: 1.183934e-01	ci left: 2.509359e-02	ci right 2.827562e-02	k: 1066	n:40000
KS ci ratio: 1.185643e-02	ci left: 7.277308e-01	ci right 7.364355e-01	k: 29284	n:40000
NIN   40000 perm   10 sec   (3907 perm/sec)   p_kst 7.321000e-01   p_cons 2.665000e-02   p_joint 6.525000e-02

Joint ci ratio: 2.782309e-02	ci left: 2.802094e-01	ci right 2.881357e-01	k: 14208	n:50000
Cons ci ratio: 1.048393e-01	ci left: 2.577221e-02	ci right 2.864304e-02	k: 1359	n:50000
KS ci ratio: 1.060689e-02	ci left: 7.281144e-01	ci right 7.358986e-01	k: 36601	n:50000
NIN   50000 perm   13 sec   (3831 perm/sec)   p_kst 7.320200e-01   p_cons 2.718000e-02   p_joint 2.841600e-01

Joint ci ratio: 2.997890e-02	ci left: 2.184312e-01	ci right 2.250958e-01	k: 13305	n:60000
Cons ci ratio: 9.616017e-02	ci left: 2.565257e-02	ci right 2.826013e-02	k: 1616	n:60000
KS ci ratio: 9.701735e-03	ci left: 7.276834e-01	ci right 7.347942e-01	k: 43875	n:60000
NIN   60000 perm   16 sec   (3766 perm/sec)   p_kst 7.312500e-01   p_cons 2.693333e-02   p_joint 2.217500e-01

Outputting figure to mutsig2_images.part000000000114/NIN.2_6666_60000_0.73125_0.026933_0.22175.png
                gene_name: NIN
               theta_stop: 0.096 
                    nperm: 60000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.027 
      ci_cons_bounds_left: 0.026 
     ci_cons_bounds_right: 0.028 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000114
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 114 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4398160: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000115> was used as the working directory.
Started at Wed Oct 24 16:14:39 2012
Results reported at Wed Oct 24 16:15:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000115.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000115.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 115  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000115.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     81.29 sec.
    Max Memory :      1040 MB
    Max Swap   :      3891 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
115
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 115
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 115: processing genes 10228 - 10317
Calculating significance of each gene.
Using projection method.
10228	NIPAL3	1
10229	NIPAL4	1
10230	NIPBL	5.102674e-01
10231	NIPSNAP1	1
10232	NIPSNAP3A	1
10233	NIPSNAP3B	1
10234	NISCH	1
10235	NIT1	1
10236	NIT2	1
10237	NKAIN1	2.059209e-02
10238	NKAIN2	1
10239	NKAIN3	1
10240	NKAIN4	1
10241	NKAP	1
10242	NKAPL	1
10243	NKD1	4.848268e-02
10244	NKD2	1
10245	NKG7	1
10246	NKIRAS1	1
10247	NKIRAS2	1
10248	NKRF	1
10249	NKTR	1
10250	NKX2-1	1
10251	NKX2-2	1
10252	NKX2-3	1
10253	NKX2-5	1
10254	NKX2-8	1
10255	NKX3-1	1
10256	NKX6-1	1
10257	NKX6-2	1
10258	NKX6-3	1
10259	NLE1	5.790035e-02
10260	NLGN1	1
10261	NLGN2	1
10262	NLGN3	1
10263	NLGN4X	5.037761e-02
10264	NLK	1.638289e-01
10265	NLN	2.652495e-01
10266	NLRC3	1.432492e-01
10267	NLRC4	1
10268	NLRC5	3.363708e-01
10269	NLRP1	5.577924e-01
10270	NLRP10	1
10271	NLRP11	3.354546e-01
10272	NLRP12	1
10273	NLRP13	4.473481e-01
10274	NLRP14	1
10275	NLRP2	1
10276	NLRP3	2.149305e-01
10277	NLRP4	1
10278	NLRP5	2.705474e-01
10279	NLRP6	2.730849e-01
10280	NLRP7	3.077190e-01
10281	NLRP8	3.834232e-01
10282	NLRP9	1.054532e-01
10283	NLRX1	3.605259e-01
10284	NMB	1
10285	NMBR	1
10286	NMD3	1
10287	NME1	1
10288	NME1-NME2	1
10289	NME2	1
10290	NME3	1
10291	NME4	1
10292	NME5	1
10293	NME6	1
10294	NME7	1
10295	NMI	1
10296	NMNAT1	1
10297	NMNAT2	1
10298	NMNAT3	1
10299	NMRAL1	1
10300	NMS	1
10301	NMT1	2.030643e-01
10302	NMT2	1
10303	NMU	1
10304	NMUR1	1
10305	NMUR2	1
10306	NNAT	1
10307	NNMT	1
10308	NNT	1
10309	NOB1	1
10310	NOBOX	1
10311	NOC2L	1
10312	NOC3L	1
10313	NOC4L	1
10314	NOD1	1
10315	NOD2	4.250976e-01
10316	NODAL	1
10317	NOG	1
Done

Running MutSig 2:
Scatter job 115: processing genes 10228 - 10317
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NLGN4X
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.833616e-02	ci left: 8.128353e-01	ci right 8.279776e-01	k: 8205	n:10000
KS ci ratio: 3.563461e-03	ci left: 9.899424e-01	ci right 9.935624e-01	k: 9919	n:10000
NLGN4X   10000 perm   2 sec   (5782 perm/sec)   p_kst 9.919000e-01   p_cons 8.205000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000115/NLGN4X.2_2471_10000_0.9919_0.8205_1.png
                gene_name: NLGN4X
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
NLRP9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.672674e-02	ci left: 8.387749e-01	ci right 8.530230e-01	k: 8460	n:10000
KS ci ratio: 9.971200e-03	ci left: 9.344406e-01	ci right 9.439015e-01	k: 9393	n:10000
NLRP9   10000 perm   2 sec   (6097 perm/sec)   p_kst 9.393000e-01   p_cons 8.460000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000115/NLRP9.2_3012_10000_0.9393_0.846_1.png
                gene_name: NLRP9
               theta_stop: 0.017 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.85 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000115
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 115 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1424>
Subject: Job 4398162: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1424>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000116> was used as the working directory.
Started at Wed Oct 24 16:14:43 2012
Results reported at Wed Oct 24 16:17:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000116.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000116.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 116  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000116.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    236.37 sec.
    Max Memory :      1375 MB
    Max Swap   :      3962 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
116
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 116
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 116: processing genes 10318 - 10406
Calculating significance of each gene.
Using projection method.
10318	NOL10	1
10319	NOL11	1.671067e-01
10320	NOL12	1
10321	NOL3	1
10322	NOL4	1.243740e-01
10323	NOL6	1
10324	NOL7	1
10325	NOL8	1
10326	NOL9	1
10327	NOLC1	3.325362e-01
10328	NOM1	1
10329	NOMO1	1
10330	NOMO2	6.773569e-02
10331	NOMO3	1
10332	NONO	1
10333	NOP10	1
10334	NOP14	1
10335	NOP16	1
10336	NOP2	1
10337	NOP56	1
10338	NOP58	1
10339	NOS1	2.480526e-01
10340	NOS1AP	2.544177e-01
10341	NOS2	3.364018e-01
10342	NOS3	1
10343	NOSIP	1
10344	NOSTRIN	1
10345	NOTCH1	5.798756e-03
10346	NOTCH2	8.881718e-02
10347	NOTCH2NL	1
10348	NOTCH3	1
10349	NOTCH4	3.641988e-01
10350	NOTUM	1
10351	NOV	1
10352	NOVA1	1
10353	NOVA2	1
10354	NOX1	9.437165e-02
10355	NOX3	3.513111e-02
10356	NOX4	1
10357	NOX5	1
10358	NOXA1	5.782649e-02
10359	NOXO1	1
10360	NPAS1	1
10361	NPAS2	2.099635e-01
10362	NPAS3	1
10363	NPAS4	1
10364	NPAT	1
10365	NPB	1
10366	NPBWR1	1
10367	NPBWR2	1
10368	NPC1	1
10369	NPC1L1	1
10370	NPC2	1
10371	NPDC1	1
10372	NPEPL1	1
10373	NPEPPS	1
10374	NPFF	1
10375	NPFFR1	1
10376	NPFFR2	1
10377	NPHP1	1
10378	NPHP3	1
10379	NPHP4	4.261142e-02
10380	NPHS1	4.783771e-01
10381	NPHS2	1
10382	NPIP	1
10383	NPL	1
10384	NPLOC4	1
10385	NPM1	1
10386	NPM2	1
10387	NPM3	1
10388	NPNT	1
10389	NPPA	2.044506e-02
10390	NPPB	1
10391	NPPC	1
10392	NPR1	1
10393	NPR2	1
10394	NPR3	1
10395	NPRL2	1
10396	NPRL3	1
10397	NPS	1
10398	NPSR1	1
10399	NPTN	1.454113e-01
10400	NPTX1	1
10401	NPTX2	1
10402	NPTXR	1
10403	NPVF	2.429315e-02
10404	NPW	1
10405	NPY	1
10406	NPY1R	1.883995e-01
Done

Running MutSig 2:
Scatter job 116: processing genes 10318 - 10406
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NOTCH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.318562e-01	ci left: 7.582209e-02	ci right 8.662335e-02	k: 811	n:10000
Cons ci ratio: 1.938045e-01	ci left: 3.548103e-02	ci right 4.319029e-02	k: 392	n:10000
KS ci ratio: 9.468960e-02	ci left: 1.393291e-01	ci right 1.532776e-01	k: 1462	n:10000
NOTCH1   10000 perm   3 sec   (3073 perm/sec)   p_kst 1.462000e-01   p_cons 3.920000e-02   p_joint 8.110000e-02

Joint ci ratio: 9.132389e-02	ci left: 8.048507e-02	ci right 8.823627e-02	k: 1686	n:20000
Cons ci ratio: 1.335450e-01	ci left: 3.853576e-02	ci right 4.409860e-02	k: 825	n:20000
KS ci ratio: 6.650479e-02	ci left: 1.430558e-01	ci right 1.529468e-01	k: 2959	n:20000
NOTCH1   20000 perm   10 sec   (2044 perm/sec)   p_kst 1.479500e-01   p_cons 4.125000e-02   p_joint 8.430000e-02

Joint ci ratio: 7.690508e-02	ci left: 7.662674e-02	ci right 8.278828e-02	k: 2390	n:30000
Cons ci ratio: 1.095016e-01	ci left: 3.871914e-02	ci right 4.323697e-02	k: 1228	n:30000
KS ci ratio: 5.486810e-02	ci left: 1.413960e-01	ci right 1.494062e-01	k: 4361	n:30000
NOTCH1   30000 perm   13 sec   (2224 perm/sec)   p_kst 1.453667e-01   p_cons 4.093333e-02   p_joint 7.966667e-02

Joint ci ratio: 8.028206e-02	ci left: 5.398733e-02	ci right 5.852736e-02	k: 2249	n:40000
Cons ci ratio: 9.549168e-02	ci left: 3.849139e-02	ci right 4.237569e-02	k: 1616	n:40000
KS ci ratio: 4.754600e-02	ci left: 1.417856e-01	ci right 1.487160e-01	k: 5809	n:40000
NOTCH1   40000 perm   17 sec   (2310 perm/sec)   p_kst 1.452250e-01   p_cons 4.040000e-02   p_joint 5.622500e-02

Outputting figure to mutsig2_images.part000000000116/NOTCH1.7_7804_40000_0.14522_0.0404_0.056225.png
                gene_name: NOTCH1
               theta_stop: 0.095 
                    nperm: 40000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.040 
      ci_cons_bounds_left: 0.038 
     ci_cons_bounds_right: 0.042 
                  p_joint: 0.056 
     ci_joint_bounds_left: 0.054 
    ci_joint_bounds_right: 0.059 

Current progress: 25 percent done.
NOTCH2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.965508e-03	ci left: 9.816675e-01	ci right 9.866446e-01	k: 9843	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
NOTCH2   10000 perm   3 sec   (3715 perm/sec)   p_kst 1   p_cons 9.843000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000116/NOTCH2.2_7552_10000_1_0.9843_1.png
                gene_name: NOTCH2
               theta_stop: 0.0050 
                    nperm: 10000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
NOX3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.097680e-01	ci left: 1.068582e-01	ci right 1.193681e-01	k: 1130	n:10000
Cons ci ratio: 1.194625e-01	ci left: 9.136461e-02	ci right 1.030712e-01	k: 971	n:10000
KS ci ratio: 3.777008e-02	ci left: 5.086527e-01	ci right 5.283365e-01	k: 5185	n:10000
NOX3   10000 perm   2 sec   (6326 perm/sec)   p_kst 5.185000e-01   p_cons 9.710000e-02   p_joint 1.130000e-01

Joint ci ratio: 5.065916e-02	ci left: 2.245291e-01	ci right 2.362494e-01	k: 4607	n:20000
Cons ci ratio: 8.394926e-02	ci left: 9.415843e-02	ci right 1.024588e-01	k: 1965	n:20000
KS ci ratio: 2.676292e-02	ci left: 5.105476e-01	ci right 5.244473e-01	k: 10350	n:20000
NOX3   20000 perm   4 sec   (5558 perm/sec)   p_kst 5.175000e-01   p_cons 9.825000e-02   p_joint 2.303500e-01

Outputting figure to mutsig2_images.part000000000116/NOX3.2_1759_20000_0.5175_0.09825_0.23035.png
                gene_name: NOX3
               theta_stop: 0.084 
                    nperm: 20000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.098 
      ci_cons_bounds_left: 0.094 
     ci_cons_bounds_right: 0.10 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.24 

Current progress: 75 percent done.
NPHP4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.226381e-02	ci left: 5.864060e-01	ci right 6.057380e-01	k: 5961	n:10000
KS ci ratio: 2.849127e-02	ci left: 6.448846e-01	ci right 6.636255e-01	k: 6543	n:10000
NPHP4   10000 perm   2 sec   (4784 perm/sec)   p_kst 6.543000e-01   p_cons 5.961000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000116/NPHP4.2_4397_10000_0.6543_0.5961_1.png
                gene_name: NPHP4
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000116
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 116 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4398164: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000117> was used as the working directory.
Started at Wed Oct 24 16:14:49 2012
Results reported at Wed Oct 24 16:16:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000117.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000117.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 117  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000117.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     77.69 sec.
    Max Memory :      1012 MB
    Max Swap   :      3847 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
117
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 117
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 117: processing genes 10407 - 10496
Calculating significance of each gene.
Using projection method.
10407	NPY2R	1
10408	NPY5R	1
10409	NQO1	1
10410	NQO2	1
10411	NR0B1	1
10412	NR0B2	1
10413	NR1D1	1
10414	NR1D2	1.875806e-01
10415	NR1H2	1
10416	NR1H3	1
10417	NR1H4	8.630600e-02
10418	NR1I2	1
10419	NR1I3	1
10420	NR2C1	1
10421	NR2C2	1
10422	NR2C2AP	2.401778e-02
10423	NR2E1	1.195041e-02
10424	NR2E3	1
10425	NR2F1	1
10426	NR2F2	1
10427	NR2F6	1
10428	NR3C1	1
10429	NR3C2	1
10430	NR4A1	1
10431	NR4A2	1
10432	NR4A3	1
10433	NR5A1	1
10434	NR5A2	2.467278e-01
10435	NR6A1	1.577405e-01
10436	NRAP	1
10437	NRARP	1
10438	NRAS	1
10439	NRBF2	1
10440	NRBP1	1
10441	NRBP2	1
10442	NRCAM	2.928496e-01
10443	NRD1	4.976682e-01
10444	NRF1	1.439689e-01
10445	NRG1	1
10446	NRG2	1
10447	NRG3	1
10448	NRG4	1
10449	NRGN	1
10450	NRIP1	4.151934e-03
10451	NRIP2	1
10452	NRIP3	1
10453	NRK	3.686727e-02
10454	NRL	1
10455	NRM	1
10456	NRN1	1
10457	NRN1L	1
10458	NRP1	2.988264e-01
10459	NRP2	1
10460	NRSN1	1
10461	NRSN2	1
10462	NRXN1	1
10463	NRXN2	1
10464	NRXN3	1
10465	NSA2	1
10466	NSD1	3.306974e-01
10467	NSDHL	1
10468	NSF	1
10469	NSFL1C	1
10470	NSL1	1
10471	NSMAF	1.646246e-01
10472	NSMCE1	1
10473	NSMCE2	1
10474	NSMCE4A	1
10475	NSUN2	1
10476	NSUN3	1
10477	NSUN4	1
10478	NSUN5	1
10479	NSUN6	1
10480	NSUN7	1
10481	NT5C	1
10482	NT5C1A	1
10483	NT5C1B	1
10484	NT5C2	2.626893e-01
10485	NT5C3	1
10486	NT5C3L	1
10487	NT5DC1	1
10488	NT5DC2	5.757972e-02
10489	NT5DC3	1
10490	NT5E	1
10491	NT5M	1
10492	NTAN1	1
10493	NTF3	1
10494	NTF4	1
10495	NTHL1	1
10496	NTM	1
Done

Running MutSig 2:
Scatter job 117: processing genes 10407 - 10496
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NRIP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.293718e-02	ci left: 2.706208e-01	ci right 2.883078e-01	k: 2794	n:10000
Cons ci ratio: 2.212491e-02	ci left: 7.498858e-01	ci right 7.667635e-01	k: 7584	n:10000
KS ci ratio: 8.802117e-02	ci left: 1.581661e-01	ci right 1.728293e-01	k: 1654	n:10000
NRIP1   10000 perm   2 sec   (5228 perm/sec)   p_kst 1.654000e-01   p_cons 7.584000e-01   p_joint 2.794000e-01

Outputting figure to mutsig2_images.part000000000117/NRIP1.4_3481_10000_0.1654_0.7584_0.2794.png
                gene_name: NRIP1
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.29 

Current progress: 33 percent done.
NR2E1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.414628e-02	ci left: 2.630978e-01	ci right 2.806353e-01	k: 2718	n:10000
Cons ci ratio: 1.088336e-02	ci left: 9.232741e-01	ci right 9.334747e-01	k: 9285	n:10000
KS ci ratio: 1.745679e-01	ci left: 4.379660e-02	ci right 5.226918e-02	k: 479	n:10000
NR2E1   10000 perm   1 sec   (7194 perm/sec)   p_kst 4.790000e-02   p_cons 9.285000e-01   p_joint 2.718000e-01

Joint ci ratio: 5.556674e-02	ci left: 1.936837e-01	ci right 2.048038e-01	k: 3984	n:20000
Cons ci ratio: 7.940019e-03	ci left: 9.204448e-01	ci right 9.278313e-01	k: 18484	n:20000
KS ci ratio: 1.210110e-01	ci left: 4.682585e-02	ci right 5.290587e-02	k: 996	n:20000
NR2E1   20000 perm   3 sec   (6309 perm/sec)   p_kst 4.980000e-02   p_cons 9.242000e-01   p_joint 1.992000e-01

Joint ci ratio: 4.684580e-02	ci left: 1.847815e-01	ci right 1.936787e-01	k: 5676	n:30000
Cons ci ratio: 6.511752e-03	ci left: 9.205023e-01	ci right 9.265487e-01	k: 27707	n:30000
KS ci ratio: 9.779484e-02	ci left: 4.834209e-02	ci right 5.334535e-02	k: 1524	n:30000
NR2E1   30000 perm   5 sec   (5645 perm/sec)   p_kst 5.080000e-02   p_cons 9.235667e-01   p_joint 1.892000e-01

Outputting figure to mutsig2_images.part000000000117/NR2E1.2_1194_30000_0.0508_0.92357_0.1892.png
                gene_name: NR2E1
               theta_stop: 0.098 
                    nperm: 30000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.048 
       ci_ks_bounds_right: 0.053 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 67 percent done.
NRK
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.308762e-02	ci left: 5.741659e-01	ci right 5.935853e-01	k: 5839	n:10000
KS ci ratio: 2.239042e-02	ci left: 7.454356e-01	ci right 7.624162e-01	k: 7540	n:10000
NRK   10000 perm   2 sec   (5602 perm/sec)   p_kst 7.540000e-01   p_cons 5.839000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000117/NRK.2_4865_10000_0.754_0.5839_1.png
                gene_name: NRK
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000117
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 117 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1428>
Subject: Job 4398167: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000118> was used as the working directory.
Started at Wed Oct 24 16:14:55 2012
Results reported at Wed Oct 24 16:23:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000118.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000118.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 118  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000118.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    667.82 sec.
    Max Memory :      1496 MB
    Max Swap   :      4047 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
118
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 118
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 118: processing genes 10497 - 10586
Calculating significance of each gene.
Using projection method.
10497	NTN1	8.638704e-02
10498	NTN3	1
10499	NTN4	4.696796e-02
10500	NTN5	1
10501	NTNG1	1.514942e-01
10502	NTNG2	1.116145e-03
10503	NTRK1	1
10504	NTRK2	1
10505	NTRK3	1
10506	NTS	1
10507	NTSR1	1
10508	NTSR2	1
10509	NUAK1	3.084413e-01
10510	NUAK2	1
10511	NUB1	1
10512	NUBP1	1
10513	NUBP2	1
10514	NUBPL	1.043360e-01
10515	NUCB1	2.400990e-01
10516	NUCB2	1
10517	NUCKS1	1
10518	NUDC	3.314267e-02
10519	NUDCD1	1
10520	NUDCD2	1
10521	NUDCD3	1
10522	NUDT1	4.579491e-02
10523	NUDT10	1
10524	NUDT11	1
10525	NUDT12	1
10526	NUDT13	1
10527	NUDT14	4.218624e-02
10528	NUDT15	1
10529	NUDT16	3.723872e-02
10530	NUDT16L1	1
10531	NUDT17	1
10532	NUDT18	1
10533	NUDT19	5.211192e-02
10534	NUDT2	1
10535	NUDT21	1
10536	NUDT22	1
10537	NUDT3	1
10538	NUDT4	1
10539	NUDT5	1
10540	NUDT6	1
10541	NUDT7	1
10542	NUDT8	1
10543	NUDT9	1.012650e-01
10544	NUF2	1
10545	NUFIP1	1.359516e-01
10546	NUFIP2	1
10547	NUMA1	6.022498e-01
10548	NUMB	2.541069e-01
10549	NUMBL	1
10550	NUP107	1.911722e-01
10551	NUP133	1
10552	NUP153	4.695467e-01
10553	NUP155	1
10554	NUP160	6.464366e-02
10555	NUP188	1
10556	NUP205	1
10557	NUP210	1
10558	NUP210L	4.125594e-01
10559	NUP214	1
10560	NUP35	1
10561	NUP37	1
10562	NUP43	1
10563	NUP50	1
10564	NUP54	5.742028e-02
10565	NUP62	1.886435e-01
10566	NUP62CL	1
10567	NUP85	1
10568	NUP88	1
10569	NUP93	2.145659e-01
10570	NUP98	1
10571	NUPL1	1.736211e-03
10572	NUPL2	1
10573	NUPR1	1
10574	NUS1	1
10575	NUSAP1	1
10576	NUTF2	3.623429e-02
10577	NVL	1
10578	NWD1	1
10579	NXF1	1.848402e-01
10580	NXF3	1
10581	NXF5	1
10582	NXN	1
10583	NXNL1	3.259096e-02
10584	NXNL2	1
10585	NXPH1	1
10586	NXPH2	1
Done

Running MutSig 2:
Scatter job 118: processing genes 10497 - 10586
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NTNG2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.871639e-02	ci left: 1.294361e-01	ci right 1.429766e-01	k: 1361	n:10000
Cons ci ratio: 9.353182e-02	ci left: 1.423679e-01	ci right 1.564370e-01	k: 1493	n:10000
KS ci ratio: 9.062615e-02	ci left: 1.504109e-01	ci right 1.647892e-01	k: 1575	n:10000
NTNG2   10000 perm   2 sec   (5681 perm/sec)   p_kst 1.575000e-01   p_cons 1.493000e-01   p_joint 1.361000e-01

Outputting figure to mutsig2_images.part000000000118/NTNG2.3_1621_10000_0.1575_0.1493_0.1361.png
                gene_name: NTNG2
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 20 percent done.
NUPL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.122849e-02	ci left: 3.597307e-01	ci right 3.787456e-01	k: 3692	n:10000
Cons ci ratio: 4.099902e-02	ci left: 4.676679e-01	ci right 4.873452e-01	k: 4775	n:10000
KS ci ratio: 6.866427e-02	ci left: 2.372873e-01	ci right 2.542610e-01	k: 2457	n:10000
NUPL1   10000 perm   2 sec   (5975 perm/sec)   p_kst 2.457000e-01   p_cons 4.775000e-01   p_joint 3.692000e-01

Outputting figure to mutsig2_images.part000000000118/NUPL1.3_1864_10000_0.2457_0.4775_0.3692.png
                gene_name: NUPL1
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.38 

Current progress: 40 percent done.
NUP160
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.402065e-02	ci left: 7.181531e-01	ci right 7.357145e-01	k: 7270	n:10000
Cons ci ratio: 2.935274e-02	ci left: 6.312063e-01	ci right 6.501117e-01	k: 6407	n:10000
KS ci ratio: 5.246035e-02	ci left: 3.487950e-01	ci right 3.676877e-01	k: 3582	n:10000
NUP160   10000 perm   2 sec   (4999 perm/sec)   p_kst 3.582000e-01   p_cons 6.407000e-01   p_joint 7.270000e-01

Outputting figure to mutsig2_images.part000000000118/NUP160.2_4455_10000_0.3582_0.6407_0.727.png
                gene_name: NUP160
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.73 
     ci_joint_bounds_left: 0.72 
    ci_joint_bounds_right: 0.74 

Current progress: 60 percent done.
NUP210L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.940154e-01	ci left: 7.872887e-03	ci right 1.182054e-02	k: 97	n:10000
Cons ci ratio: 7.677370e-01	ci left: 1.618501e-03	ci right 3.688296e-03	k: 25	n:10000
KS ci ratio: 1.825522e-02	ci left: 8.141562e-01	ci right 8.292559e-01	k: 8218	n:10000
NUP210L   10000 perm   2 sec   (4388 perm/sec)   p_kst 8.218000e-01   p_cons 2.500000e-03   p_joint 9.700000e-03

Joint ci ratio: 3.552752e-01	ci left: 4.977027e-03	ci right 7.170311e-03	k: 120	n:20000
Cons ci ratio: 4.970559e-01	ci left: 2.333787e-03	ci right 3.916152e-03	k: 61	n:20000
KS ci ratio: 1.284180e-02	ci left: 8.179421e-01	ci right 8.285638e-01	k: 16466	n:20000
NUP210L   20000 perm   5 sec   (3977 perm/sec)   p_kst 8.233000e-01   p_cons 3.050000e-03   p_joint 6.000000e-03

Joint ci ratio: 1.995451e-01	ci left: 1.143190e-02	ci right 1.399710e-02	k: 380	n:30000
Cons ci ratio: 3.994361e-01	ci left: 2.562755e-03	ci right 3.869722e-03	k: 95	n:30000
KS ci ratio: 1.056674e-02	ci left: 8.166480e-01	ci right 8.253564e-01	k: 24631	n:30000
NUP210L   30000 perm   8 sec   (3816 perm/sec)   p_kst 8.210333e-01   p_cons 3.166667e-03   p_joint 1.266667e-02

Joint ci ratio: 2.577298e-01	ci left: 5.009201e-03	ci right 6.513914e-03	k: 229	n:40000
Cons ci ratio: 3.445755e-01	ci left: 2.670359e-03	ci right 3.803659e-03	k: 128	n:40000
KS ci ratio: 9.194055e-03	ci left: 8.158465e-01	ci right 8.234070e-01	k: 32786	n:40000
NUP210L   40000 perm   11 sec   (3649 perm/sec)   p_kst 8.196500e-01   p_cons 3.200000e-03   p_joint 5.725000e-03

Joint ci ratio: 1.361018e-01	ci left: 1.520824e-02	ci right 1.744843e-02	k: 815	n:50000
Cons ci ratio: 2.975131e-01	ci left: 2.945803e-03	ci right 3.993152e-03	k: 172	n:50000
KS ci ratio: 8.235899e-03	ci left: 8.157982e-01	ci right 8.225647e-01	k: 40960	n:50000
NUP210L   50000 perm   14 sec   (3583 perm/sec)   p_kst 8.192000e-01   p_cons 3.440000e-03   p_joint 1.630000e-02

Joint ci ratio: 1.461367e-01	ci left: 1.098343e-02	ci right 1.273094e-02	k: 710	n:60000
Cons ci ratio: 2.746620e-01	ci left: 2.919007e-03	ci right 3.863370e-03	k: 202	n:60000
KS ci ratio: 7.519142e-03	ci left: 8.160633e-01	ci right 8.222391e-01	k: 49150	n:60000
NUP210L   60000 perm   17 sec   (3520 perm/sec)   p_kst 8.191667e-01   p_cons 3.366667e-03   p_joint 1.183333e-02

Joint ci ratio: 1.167214e-01	ci left: 1.493081e-02	ci right 1.679535e-02	k: 1109	n:70000
Cons ci ratio: 3.124968e-01	ci left: 1.892884e-03	ci right 2.606525e-03	k: 156	n:70000
KS ci ratio: 6.946477e-03	ci left: 8.169323e-01	ci right 8.226411e-01	k: 57386	n:70000
NUP210L   70000 perm   20 sec   (3464 perm/sec)   p_kst 8.198000e-01   p_cons 2.228571e-03   p_joint 1.584286e-02

Joint ci ratio: 1.052306e-01	ci left: 1.615204e-02	ci right 1.795823e-02	k: 1363	n:80000
Cons ci ratio: 2.934875e-01	ci left: 1.898837e-03	ci right 2.563088e-03	k: 177	n:80000
KS ci ratio: 6.509094e-03	ci left: 8.166033e-01	ci right 8.219485e-01	k: 65543	n:80000
NUP210L   80000 perm   23 sec   (3410 perm/sec)   p_kst 8.192875e-01   p_cons 2.212500e-03   p_joint 1.703750e-02

Joint ci ratio: 1.033125e-01	ci left: 1.493041e-02	ci right 1.656769e-02	k: 1416	n:90000
Cons ci ratio: 2.728051e-01	ci left: 1.976914e-03	ci right 2.611404e-03	k: 205	n:90000
KS ci ratio: 6.125743e-03	ci left: 8.172954e-01	ci right 8.223284e-01	k: 73784	n:90000
NUP210L   90000 perm   27 sec   (3358 perm/sec)   p_kst 8.198222e-01   p_cons 2.277778e-03   p_joint 1.573333e-02

Joint ci ratio: 9.736709e-02	ci left: 1.517281e-02	ci right 1.673545e-02	k: 1594	n:100000
Cons ci ratio: 2.610379e-01	ci left: 1.956511e-03	ci right 2.552948e-03	k: 224	n:100000
KS ci ratio: 5.798050e-03	ci left: 8.181071e-01	ci right 8.228743e-01	k: 82050	n:100000
NUP210L   100000 perm   30 sec   (3307 perm/sec)   p_kst 8.205000e-01   p_cons 2.240000e-03   p_joint 1.594000e-02

Joint ci ratio: 9.369432e-02	ci left: 1.492921e-02	ci right 1.640557e-02	k: 1722	n:110000
Cons ci ratio: 2.461636e-01	ci left: 2.017033e-03	ci right 2.591530e-03	k: 252	n:110000
KS ci ratio: 5.518664e-03	ci left: 8.187307e-01	ci right 8.232705e-01	k: 90311	n:110000
NUP210L   110000 perm   34 sec   (3256 perm/sec)   p_kst 8.210091e-01   p_cons 2.290909e-03   p_joint 1.565455e-02

Joint ci ratio: 9.408944e-02	ci left: 1.358701e-02	ci right 1.493661e-02	k: 1710	n:120000
Cons ci ratio: 2.352570e-01	ci left: 2.036892e-03	ci right 2.587601e-03	k: 276	n:120000
KS ci ratio: 5.272940e-03	ci left: 8.194303e-01	ci right 8.237708e-01	k: 98593	n:120000
NUP210L   120000 perm   37 sec   (3209 perm/sec)   p_kst 8.216083e-01   p_cons 2.300000e-03   p_joint 1.425000e-02

Joint ci ratio: 8.561724e-02	ci left: 1.518934e-02	ci right 1.655546e-02	k: 2062	n:130000
Cons ci ratio: 2.245635e-01	ci left: 2.075949e-03	ci right 2.608178e-03	k: 303	n:130000
KS ci ratio: 5.065155e-03	ci left: 8.195697e-01	ci right 8.237391e-01	k: 106816	n:130000
NUP210L   130000 perm   41 sec   (3164 perm/sec)   p_kst 8.216615e-01   p_cons 2.330769e-03   p_joint 1.586154e-02

Joint ci ratio: 8.518587e-02	ci left: 1.426487e-02	ci right 1.554105e-02	k: 2085	n:140000
Cons ci ratio: 2.185413e-01	ci left: 2.042353e-03	ci right 2.550041e-03	k: 320	n:140000
KS ci ratio: 4.886448e-03	ci left: 8.193117e-01	ci right 8.233321e-01	k: 114986	n:140000
NUP210L   140000 perm   45 sec   (3122 perm/sec)   p_kst 8.213286e-01   p_cons 2.285714e-03   p_joint 1.489286e-02

Joint ci ratio: 8.205548e-02	ci left: 1.437133e-02	ci right 1.560752e-02	k: 2247	n:150000
Cons ci ratio: 2.101924e-01	ci left: 2.070230e-03	ci right 2.562657e-03	k: 346	n:150000
KS ci ratio: 4.717033e-03	ci left: 8.196128e-01	ci right 8.234947e-01	k: 123234	n:150000
NUP210L   150000 perm   49 sec   (3077 perm/sec)   p_kst 8.215600e-01   p_cons 2.306667e-03   p_joint 1.498000e-02

Joint ci ratio: 8.023250e-02	ci left: 1.410985e-02	ci right 1.529533e-02	k: 2351	n:160000
Cons ci ratio: 2.027326e-01	ci left: 2.094944e-03	ci right 2.573375e-03	k: 372	n:160000
KS ci ratio: 4.568473e-03	ci left: 8.195959e-01	ci right 8.233550e-01	k: 131437	n:160000
NUP210L   160000 perm   53 sec   (3036 perm/sec)   p_kst 8.214813e-01   p_cons 2.325000e-03   p_joint 1.469375e-02

Joint ci ratio: 6.943014e-02	ci left: 1.776643e-02	ci right 1.905007e-02	k: 3128	n:170000
Cons ci ratio: 1.950369e-01	ci left: 2.139402e-03	ci right 2.607239e-03	k: 402	n:170000
KS ci ratio: 4.428051e-03	ci left: 8.199193e-01	ci right 8.235638e-01	k: 139697	n:170000
NUP210L   170000 perm   57 sec   (2997 perm/sec)   p_kst 8.217471e-01   p_cons 2.364706e-03   p_joint 1.840000e-02

Joint ci ratio: 1.205624e-01	ci left: 5.486730e-03	ci right 6.195994e-03	k: 1050	n:180000
Cons ci ratio: 1.894764e-01	ci left: 2.147464e-03	ci right 2.602134e-03	k: 426	n:180000
KS ci ratio: 4.304309e-03	ci left: 8.199015e-01	ci right 8.234437e-01	k: 147902	n:180000
NUP210L   180000 perm   61 sec   (2959 perm/sec)   p_kst 8.216778e-01   p_cons 2.366667e-03   p_joint 5.833333e-03

Joint ci ratio: 6.395484e-02	ci left: 1.876899e-02	ci right 2.001416e-02	k: 3683	n:190000
Cons ci ratio: 1.856076e-01	ci left: 2.124726e-03	ci right 2.564362e-03	k: 444	n:190000
KS ci ratio: 4.190543e-03	ci left: 8.198763e-01	ci right 8.233244e-01	k: 156105	n:190000
NUP210L   190000 perm   65 sec   (2920 perm/sec)   p_kst 8.216053e-01   p_cons 2.336842e-03   p_joint 1.938421e-02

Joint ci ratio: 6.227732e-02	ci left: 1.881969e-02	ci right 2.003430e-02	k: 3884	n:200000
Cons ci ratio: 1.804108e-01	ci left: 2.142537e-03	ci right 2.572090e-03	k: 470	n:200000
KS ci ratio: 4.082349e-03	ci left: 8.200705e-01	ci right 8.234301e-01	k: 164351	n:200000
NUP210L   200000 perm   69 sec   (2884 perm/sec)   p_kst 8.217550e-01   p_cons 2.350000e-03   p_joint 1.942000e-02

Joint ci ratio: 6.295365e-02	ci left: 1.755754e-02	ci right 1.870344e-02	k: 3806	n:210000
Cons ci ratio: 1.758048e-01	ci left: 2.154253e-03	ci right 2.573957e-03	k: 495	n:210000
KS ci ratio: 3.980178e-03	ci left: 8.203906e-01	ci right 8.236671e-01	k: 172627	n:210000
NUP210L   210000 perm   74 sec   (2848 perm/sec)   p_kst 8.220333e-01   p_cons 2.357143e-03   p_joint 1.812381e-02

Joint ci ratio: 6.150065e-02	ci left: 1.757387e-02	ci right 1.869342e-02	k: 3988	n:220000
Cons ci ratio: 1.725332e-01	ci left: 2.138930e-03	ci right 2.547086e-03	k: 514	n:220000
KS ci ratio: 3.889895e-03	ci left: 8.203358e-01	ci right 8.235375e-01	k: 180827	n:220000
NUP210L   220000 perm   78 sec   (2812 perm/sec)   p_kst 8.219409e-01   p_cons 2.336364e-03   p_joint 1.812727e-02

Joint ci ratio: 6.049186e-02	ci left: 1.738774e-02	ci right 1.847663e-02	k: 4123	n:230000
Cons ci ratio: 1.695968e-01	ci left: 2.120842e-03	ci right 2.517954e-03	k: 532	n:230000
KS ci ratio: 3.802211e-03	ci left: 8.205396e-01	ci right 8.236697e-01	k: 189085	n:230000
NUP210L   230000 perm   83 sec   (2775 perm/sec)   p_kst 8.221087e-01   p_cons 2.313043e-03   p_joint 1.792609e-02

Joint ci ratio: 5.884547e-02	ci left: 1.761967e-02	ci right 1.869202e-02	k: 4356	n:240000
Cons ci ratio: 1.659025e-01	ci left: 2.128276e-03	ci right 2.517233e-03	k: 556	n:240000
KS ci ratio: 3.722584e-03	ci left: 8.205389e-01	ci right 8.236033e-01	k: 197298	n:240000
NUP210L   240000 perm   87 sec   (2743 perm/sec)   p_kst 8.220750e-01   p_cons 2.316667e-03   p_joint 1.815000e-02

Joint ci ratio: 5.763420e-02	ci left: 1.764411e-02	ci right 1.869511e-02	k: 4541	n:250000
Cons ci ratio: 1.621601e-01	ci left: 2.142877e-03	ci right 2.524807e-03	k: 582	n:250000
KS ci ratio: 3.646262e-03	ci left: 8.206594e-01	ci right 8.236611e-01	k: 205541	n:250000
NUP210L   250000 perm   92 sec   (2710 perm/sec)   p_kst 8.221640e-01   p_cons 2.328000e-03   p_joint 1.816400e-02

Joint ci ratio: 1.012273e-01	ci left: 5.444219e-03	ci right 6.028421e-03	k: 1490	n:260000
Cons ci ratio: 1.583995e-01	ci left: 2.163834e-03	ci right 2.539705e-03	k: 610	n:260000
KS ci ratio: 3.572521e-03	ci left: 8.209293e-01	ci right 8.238712e-01	k: 213825	n:260000
NUP210L   260000 perm   97 sec   (2675 perm/sec)   p_kst 8.224038e-01   p_cons 2.346154e-03   p_joint 5.730769e-03

Joint ci ratio: 9.963793e-02	ci left: 5.415889e-03	ci right 5.987392e-03	k: 1538	n:270000
Cons ci ratio: 1.551324e-01	ci left: 2.176212e-03	ci right 2.545711e-03	k: 636	n:270000
KS ci ratio: 3.505162e-03	ci left: 8.210052e-01	ci right 8.238916e-01	k: 222062	n:270000
NUP210L   270000 perm   102 sec   (2642 perm/sec)   p_kst 8.224519e-01   p_cons 2.355556e-03   p_joint 5.696296e-03

Joint ci ratio: 9.799701e-02	ci left: 5.403587e-03	ci right 5.963862e-03	k: 1590	n:280000
Cons ci ratio: 1.520596e-01	ci left: 2.187779e-03	ci right 2.551215e-03	k: 662	n:280000
KS ci ratio: 3.442065e-03	ci left: 8.210259e-01	ci right 8.238603e-01	k: 230285	n:280000
NUP210L   280000 perm   107 sec   (2609 perm/sec)   p_kst 8.224464e-01   p_cons 2.364286e-03   p_joint 5.678571e-03

Joint ci ratio: 9.608233e-02	ci left: 5.432594e-03	ci right 5.984251e-03	k: 1654	n:290000
Cons ci ratio: 1.486228e-01	ci left: 2.215216e-03	ci right 2.574154e-03	k: 693	n:290000
KS ci ratio: 3.379061e-03	ci left: 8.213223e-01	ci right 8.241057e-01	k: 238588	n:290000
NUP210L   290000 perm   112 sec   (2579 perm/sec)   p_kst 8.227172e-01   p_cons 2.389655e-03   p_joint 5.703448e-03

Joint ci ratio: 9.452485e-02	ci left: 5.430471e-03	ci right 5.972478e-03	k: 1709	n:300000
Cons ci ratio: 1.461177e-01	ci left: 2.218426e-03	ci right 2.571296e-03	k: 717	n:300000
KS ci ratio: 3.322538e-03	ci left: 8.213219e-01	ci right 8.240586e-01	k: 246808	n:300000
NUP210L   300000 perm   118 sec   (2550 perm/sec)   p_kst 8.226933e-01   p_cons 2.390000e-03   p_joint 5.696667e-03

Joint ci ratio: 9.320019e-02	ci left: 5.409646e-03	ci right 5.941595e-03	k: 1758	n:310000
Cons ci ratio: 1.448152e-01	ci left: 2.187271e-03	ci right 2.531815e-03	k: 730	n:310000
KS ci ratio: 3.268110e-03	ci left: 8.213800e-01	ci right 8.240720e-01	k: 255046	n:310000
NUP210L   310000 perm   123 sec   (2521 perm/sec)   p_kst 8.227290e-01   p_cons 2.354839e-03   p_joint 5.670968e-03

Joint ci ratio: 9.162440e-02	ci left: 5.426816e-03	ci right 5.950947e-03	k: 1819	n:320000
Cons ci ratio: 1.423060e-01	ci left: 2.197251e-03	ci right 2.536861e-03	k: 756	n:320000
KS ci ratio: 3.214306e-03	ci left: 8.216136e-01	ci right 8.242618e-01	k: 263341	n:320000
NUP210L   320000 perm   128 sec   (2494 perm/sec)   p_kst 8.229406e-01   p_cons 2.362500e-03   p_joint 5.684375e-03

Joint ci ratio: 9.019829e-02	ci left: 5.434129e-03	ci right 5.950367e-03	k: 1877	n:330000
Cons ci ratio: 1.407359e-01	ci left: 2.180357e-03	ci right 2.513327e-03	k: 773	n:330000
KS ci ratio: 3.164058e-03	ci left: 8.217421e-01	ci right 8.243492e-01	k: 271606	n:330000
NUP210L   330000 perm   134 sec   (2467 perm/sec)   p_kst 8.230485e-01   p_cons 2.342424e-03   p_joint 5.687879e-03

Joint ci ratio: 8.916158e-02	ci left: 5.400807e-03	ci right 5.907674e-03	k: 1921	n:340000
Cons ci ratio: 1.386034e-01	ci left: 2.184351e-03	ci right 2.512458e-03	k: 797	n:340000
KS ci ratio: 3.118675e-03	ci left: 8.216214e-01	ci right 8.241907e-01	k: 279789	n:340000
NUP210L   340000 perm   139 sec   (2441 perm/sec)   p_kst 8.229088e-01   p_cons 2.344118e-03   p_joint 5.650000e-03

Joint ci ratio: 8.820491e-02	ci left: 5.363832e-03	ci right 5.861550e-03	k: 1963	n:350000
Cons ci ratio: 1.371515e-01	ci left: 2.168836e-03	ci right 2.490921e-03	k: 814	n:350000
KS ci ratio: 3.073501e-03	ci left: 8.216684e-01	ci right 8.242005e-01	k: 288028	n:350000
NUP210L   350000 perm   145 sec   (2416 perm/sec)   p_kst 8.229371e-01   p_cons 2.325714e-03   p_joint 5.608571e-03

Joint ci ratio: 8.706042e-02	ci left: 5.356115e-03	ci right 5.846339e-03	k: 2015	n:360000
Cons ci ratio: 1.351754e-01	ci left: 2.172986e-03	ci right 2.490665e-03	k: 838	n:360000
KS ci ratio: 3.029772e-03	ci left: 8.217576e-01	ci right 8.242539e-01	k: 296283	n:360000
NUP210L   360000 perm   151 sec   (2391 perm/sec)   p_kst 8.230083e-01   p_cons 2.327778e-03   p_joint 5.597222e-03

Joint ci ratio: 8.589672e-02	ci left: 5.356789e-03	ci right 5.840193e-03	k: 2070	n:370000
Cons ci ratio: 1.335931e-01	ci left: 2.166493e-03	ci right 2.479220e-03	k: 858	n:370000
KS ci ratio: 2.988773e-03	ci left: 8.217528e-01	ci right 8.242151e-01	k: 304505	n:370000
NUP210L   370000 perm   156 sec   (2367 perm/sec)   p_kst 8.229865e-01   p_cons 2.318919e-03   p_joint 5.594595e-03

Joint ci ratio: 8.485879e-02	ci left: 5.347164e-03	ci right 5.823580e-03	k: 2121	n:380000
Cons ci ratio: 1.320651e-01	ci left: 2.160362e-03	ci right 2.468358e-03	k: 878	n:380000
KS ci ratio: 2.947902e-03	ci left: 8.218962e-01	ci right 8.243252e-01	k: 312783	n:380000
NUP210L   380000 perm   162 sec   (2342 perm/sec)   p_kst 8.231132e-01   p_cons 2.310526e-03   p_joint 5.581579e-03

Joint ci ratio: 8.387700e-02	ci left: 5.335556e-03	ci right 5.805169e-03	k: 2171	n:390000
Cons ci ratio: 1.313966e-01	ci left: 2.127283e-03	ci right 2.428907e-03	k: 887	n:390000
KS ci ratio: 2.908867e-03	ci left: 8.220119e-01	ci right 8.244090e-01	k: 321053	n:390000
NUP210L   390000 perm   168 sec   (2315 perm/sec)   p_kst 8.232128e-01   p_cons 2.274359e-03   p_joint 5.566667e-03

Joint ci ratio: 8.281615e-02	ci left: 5.339250e-03	ci right 5.802957e-03	k: 2227	n:400000
Cons ci ratio: 1.299419e-01	ci left: 2.122466e-03	ci right 2.419818e-03	k: 907	n:400000
KS ci ratio: 2.872649e-03	ci left: 8.219891e-01	ci right 8.243562e-01	k: 329270	n:400000
NUP210L   400000 perm   175 sec   (2288 perm/sec)   p_kst 8.231750e-01   p_cons 2.267500e-03   p_joint 5.567500e-03

Joint ci ratio: 8.259845e-02	ci left: 5.237676e-03	ci right 5.691307e-03	k: 2239	n:410000
Cons ci ratio: 1.283958e-01	ci left: 2.122623e-03	ci right 2.416190e-03	k: 929	n:410000
KS ci ratio: 2.835897e-03	ci left: 8.221584e-01	ci right 8.244956e-01	k: 337565	n:410000
NUP210L   410000 perm   181 sec   (2265 perm/sec)   p_kst 8.233293e-01   p_cons 2.265854e-03   p_joint 5.460976e-03

Joint ci ratio: 8.167427e-02	ci left: 5.231903e-03	ci right 5.679723e-03	k: 2290	n:420000
Cons ci ratio: 1.276450e-01	ci left: 2.097434e-03	ci right 2.385692e-03	k: 940	n:420000
KS ci ratio: 2.802123e-03	ci left: 8.221526e-01	ci right 8.244620e-01	k: 345790	n:420000
NUP210L   420000 perm   187 sec   (2242 perm/sec)   p_kst 8.233095e-01   p_cons 2.238095e-03   p_joint 5.452381e-03

Joint ci ratio: 8.072846e-02	ci left: 5.233262e-03	ci right 5.675767e-03	k: 2344	n:430000
Cons ci ratio: 1.262443e-01	ci left: 2.095943e-03	ci right 2.380598e-03	k: 961	n:430000
KS ci ratio: 2.768775e-03	ci left: 8.222266e-01	ci right 8.245086e-01	k: 354049	n:430000
NUP210L   430000 perm   194 sec   (2219 perm/sec)   p_kst 8.233698e-01   p_cons 2.234884e-03   p_joint 5.451163e-03

Joint ci ratio: 7.986500e-02	ci left: 5.227906e-03	ci right 5.665009e-03	k: 2395	n:440000
Cons ci ratio: 1.247616e-01	ci left: 2.098940e-03	ci right 2.380407e-03	k: 984	n:440000
KS ci ratio: 2.736910e-03	ci left: 8.222632e-01	ci right 8.245189e-01	k: 362293	n:440000
NUP210L   440000 perm   200 sec   (2196 perm/sec)   p_kst 8.233932e-01   p_cons 2.236364e-03   p_joint 5.443182e-03

Joint ci ratio: 7.906115e-02	ci left: 5.218454e-03	ci right 5.650174e-03	k: 2444	n:450000
Cons ci ratio: 1.235142e-01	ci left: 2.095361e-03	ci right 2.373333e-03	k: 1004	n:450000
KS ci ratio: 2.705314e-03	ci left: 8.223851e-01	ci right 8.246151e-01	k: 370576	n:450000
NUP210L   450000 perm   207 sec   (2172 perm/sec)   p_kst 8.235022e-01   p_cons 2.231111e-03   p_joint 5.431111e-03

Joint ci ratio: 7.806110e-02	ci left: 5.239277e-03	ci right 5.666988e-03	k: 2507	n:460000
Cons ci ratio: 1.221842e-01	ci left: 2.096166e-03	ci right 2.371034e-03	k: 1026	n:460000
KS ci ratio: 2.676848e-03	ci left: 8.222775e-01	ci right 8.244837e-01	k: 378756	n:460000
NUP210L   460000 perm   214 sec   (2152 perm/sec)   p_kst 8.233826e-01   p_cons 2.230435e-03   p_joint 5.450000e-03

Joint ci ratio: 7.712823e-02	ci left: 5.255074e-03	ci right 5.678717e-03	k: 2568	n:470000
Cons ci ratio: 1.206085e-01	ci left: 2.107269e-03	ci right 2.379776e-03	k: 1053	n:470000
KS ci ratio: 2.648311e-03	ci left: 8.222790e-01	ci right 8.244617e-01	k: 386985	n:470000
NUP210L   470000 perm   220 sec   (2133 perm/sec)   p_kst 8.233723e-01   p_cons 2.240426e-03   p_joint 5.463830e-03

Joint ci ratio: 7.646225e-02	ci left: 5.237541e-03	ci right 5.655963e-03	k: 2613	n:480000
Cons ci ratio: 1.198727e-01	ci left: 2.089636e-03	ci right 2.358096e-03	k: 1066	n:480000
KS ci ratio: 2.620218e-03	ci left: 8.223308e-01	ci right 8.244903e-01	k: 395238	n:480000
NUP210L   480000 perm   227 sec   (2114 perm/sec)   p_kst 8.234125e-01   p_cons 2.220833e-03   p_joint 5.443750e-03

Joint ci ratio: 7.569880e-02	ci left: 5.236758e-03	ci right 5.650756e-03	k: 2666	n:490000
Cons ci ratio: 1.187103e-01	ci left: 2.088568e-03	ci right 2.354107e-03	k: 1087	n:490000
KS ci ratio: 2.593600e-03	ci left: 8.223130e-01	ci right 8.244505e-01	k: 403458	n:490000
NUP210L   490000 perm   234 sec   (2095 perm/sec)   p_kst 8.233837e-01   p_cons 2.218367e-03   p_joint 5.440816e-03

Joint ci ratio: 7.495777e-02	ci left: 5.236026e-03	ci right 5.645737e-03	k: 2719	n:500000
Cons ci ratio: 1.178477e-01	ci left: 2.077849e-03	ci right 2.339972e-03	k: 1103	n:500000
KS ci ratio: 2.567918e-03	ci left: 8.222800e-01	ci right 8.243962e-01	k: 411670	n:500000
NUP210L   500000 perm   241 sec   (2076 perm/sec)   p_kst 8.233400e-01   p_cons 2.206000e-03   p_joint 5.438000e-03

Joint ci ratio: 7.413065e-02	ci left: 5.250738e-03	ci right 5.656872e-03	k: 2780	n:510000
Cons ci ratio: 1.168469e-01	ci left: 2.073268e-03	ci right 2.332439e-03	k: 1122	n:510000
KS ci ratio: 2.542333e-03	ci left: 8.223231e-01	ci right 8.244183e-01	k: 419920	n:510000
NUP210L   510000 perm   248 sec   (2057 perm/sec)   p_kst 8.233725e-01   p_cons 2.200000e-03   p_joint 5.450980e-03

Joint ci ratio: 7.349953e-02	ci left: 5.240365e-03	ci right 5.642098e-03	k: 2828	n:520000
Cons ci ratio: 1.160239e-01	ci left: 2.063270e-03	ci right 2.319250e-03	k: 1138	n:520000
KS ci ratio: 2.518064e-03	ci left: 8.222991e-01	ci right 8.243742e-01	k: 428136	n:520000
NUP210L   520000 perm   255 sec   (2040 perm/sec)   p_kst 8.233385e-01   p_cons 2.188462e-03   p_joint 5.438462e-03

Joint ci ratio: 7.282067e-02	ci left: 5.239661e-03	ci right 5.637473e-03	k: 2881	n:530000
Cons ci ratio: 1.146229e-01	ci left: 2.075648e-03	ci right 2.329843e-03	k: 1166	n:530000
KS ci ratio: 2.495092e-03	ci left: 8.222043e-01	ci right 8.242601e-01	k: 436314	n:530000
NUP210L   530000 perm   262 sec   (2022 perm/sec)   p_kst 8.232340e-01   p_cons 2.200000e-03   p_joint 5.435849e-03

Joint ci ratio: 4.874342e-02	ci left: 1.154661e-02	ci right 1.212531e-02	k: 6390	n:540000
Cons ci ratio: 1.137014e-01	ci left: 2.071390e-03	ci right 2.322888e-03	k: 1185	n:540000
KS ci ratio: 2.471981e-03	ci left: 8.222021e-01	ci right 8.242389e-01	k: 444540	n:540000
NUP210L   540000 perm   270 sec   (2003 perm/sec)   p_kst 8.232222e-01   p_cons 2.194444e-03   p_joint 1.183333e-02

Joint ci ratio: 4.835223e-02	ci left: 1.152347e-02	ci right 1.209624e-02	k: 6494	n:550000
Cons ci ratio: 1.128487e-01	ci left: 2.065528e-03	ci right 2.314308e-03	k: 1203	n:550000
KS ci ratio: 2.449179e-03	ci left: 8.222384e-01	ci right 8.242564e-01	k: 452787	n:550000
NUP210L   550000 perm   277 sec   (1985 perm/sec)   p_kst 8.232491e-01   p_cons 2.187273e-03   p_joint 1.180727e-02

Joint ci ratio: 4.790791e-02	ci left: 1.153116e-02	ci right 1.209891e-02	k: 6615	n:560000
Cons ci ratio: 1.116947e-01	ci left: 2.072033e-03	ci right 2.318877e-03	k: 1228	n:560000
KS ci ratio: 2.426207e-03	ci left: 8.223683e-01	ci right 8.243677e-01	k: 461087	n:560000
NUP210L   560000 perm   285 sec   (1968 perm/sec)   p_kst 8.233696e-01   p_cons 2.192857e-03   p_joint 1.181250e-02

Joint ci ratio: 4.756500e-02	ci left: 1.149527e-02	ci right 1.205708e-02	k: 6711	n:570000
Cons ci ratio: 1.109306e-01	ci left: 2.064675e-03	ci right 2.308850e-03	k: 1245	n:570000
KS ci ratio: 2.404724e-03	ci left: 8.223900e-01	ci right 8.243717e-01	k: 469328	n:570000
NUP210L   570000 perm   292 sec   (1952 perm/sec)   p_kst 8.233825e-01   p_cons 2.184211e-03   p_joint 1.177368e-02

Joint ci ratio: 4.718029e-02	ci left: 1.148448e-02	ci right 1.204110e-02	k: 6821	n:580000
Cons ci ratio: 1.098339e-01	ci left: 2.070991e-03	ci right 2.313334e-03	k: 1270	n:580000
KS ci ratio: 2.383294e-03	ci left: 8.224732e-01	ci right 8.244374e-01	k: 477605	n:580000
NUP210L   580000 perm   300 sec   (1936 perm/sec)   p_kst 8.234569e-01   p_cons 2.189655e-03   p_joint 1.176034e-02

Joint ci ratio: 4.673318e-02	ci left: 1.150926e-02	ci right 1.206165e-02	k: 6952	n:590000
Cons ci ratio: 1.091071e-01	ci left: 2.063914e-03	ci right 2.303728e-03	k: 1287	n:590000
KS ci ratio: 2.363445e-03	ci left: 8.224279e-01	ci right 8.243757e-01	k: 485808	n:590000
NUP210L   590000 perm   307 sec   (1920 perm/sec)   p_kst 8.234034e-01   p_cons 2.181356e-03   p_joint 1.178305e-02

Joint ci ratio: 4.635487e-02	ci left: 1.150522e-02	ci right 1.205284e-02	k: 7066	n:600000
Cons ci ratio: 1.079808e-01	ci left: 2.073294e-03	ci right 2.311553e-03	k: 1314	n:600000
KS ci ratio: 2.343425e-03	ci left: 8.224661e-01	ci right 8.243974e-01	k: 494060	n:600000
NUP210L   600000 perm   315 sec   (1904 perm/sec)   p_kst 8.234333e-01   p_cons 2.190000e-03   p_joint 1.177667e-02

Joint ci ratio: 4.601154e-02	ci left: 1.148838e-02	ci right 1.203103e-02	k: 7172	n:610000
Cons ci ratio: 1.070486e-01	ci left: 2.075997e-03	ci right 2.312377e-03	k: 1337	n:610000
KS ci ratio: 2.323474e-03	ci left: 8.225573e-01	ci right 8.244724e-01	k: 502345	n:610000
NUP210L   610000 perm   323 sec   (1889 perm/sec)   p_kst 8.235164e-01   p_cons 2.191803e-03   p_joint 1.175738e-02

Joint ci ratio: 4.560287e-02	ci left: 1.150876e-02	ci right 1.204743e-02	k: 7301	n:620000
Cons ci ratio: 1.060230e-01	ci left: 2.083332e-03	ci right 2.318133e-03	k: 1363	n:620000
KS ci ratio: 2.305045e-03	ci left: 8.225164e-01	ci right 8.244161e-01	k: 510550	n:620000
NUP210L   620000 perm   331 sec   (1873 perm/sec)   p_kst 8.234677e-01   p_cons 2.198387e-03   p_joint 1.177581e-02

Joint ci ratio: 4.521722e-02	ci left: 1.152225e-02	ci right 1.205686e-02	k: 7426	n:630000
Cons ci ratio: 1.051782e-01	ci left: 2.084261e-03	ci right 2.317180e-03	k: 1385	n:630000
KS ci ratio: 2.285962e-03	ci left: 8.226152e-01	ci right 8.244993e-01	k: 518842	n:630000
NUP210L   630000 perm   339 sec   (1858 perm/sec)   p_kst 8.235587e-01   p_cons 2.198413e-03   p_joint 1.178730e-02

Joint ci ratio: 4.489235e-02	ci left: 1.150906e-02	ci right 1.203912e-02	k: 7534	n:640000
Cons ci ratio: 1.043162e-01	ci left: 2.086691e-03	ci right 2.317852e-03	k: 1408	n:640000
KS ci ratio: 2.267613e-03	ci left: 8.226765e-01	ci right 8.245456e-01	k: 527112	n:640000
NUP210L   640000 perm   347 sec   (1844 perm/sec)   p_kst 8.236125e-01   p_cons 2.200000e-03   p_joint 1.177187e-02

Joint ci ratio: 4.455669e-02	ci left: 1.150542e-02	ci right 1.203125e-02	k: 7648	n:650000
Cons ci ratio: 1.036929e-01	ci left: 2.080061e-03	ci right 2.309027e-03	k: 1425	n:650000
KS ci ratio: 2.250009e-03	ci left: 8.226958e-01	ci right 8.245505e-01	k: 535356	n:650000
NUP210L   650000 perm   355 sec   (1829 perm/sec)   p_kst 8.236246e-01   p_cons 2.192308e-03   p_joint 1.176615e-02

Joint ci ratio: 4.423421e-02	ci left: 1.149891e-02	ci right 1.202054e-02	k: 7760	n:660000
Cons ci ratio: 1.027600e-01	ci left: 2.086922e-03	ci right 2.314452e-03	k: 1451	n:660000
KS ci ratio: 2.232761e-03	ci left: 8.227208e-01	ci right 8.245612e-01	k: 543604	n:660000
NUP210L   660000 perm   364 sec   (1815 perm/sec)   p_kst 8.236424e-01   p_cons 2.198485e-03   p_joint 1.175758e-02

Joint ci ratio: 4.388481e-02	ci left: 1.151032e-02	ci right 1.202824e-02	k: 7884	n:670000
Cons ci ratio: 1.018864e-01	ci left: 2.092133e-03	ci right 2.318176e-03	k: 1476	n:670000
KS ci ratio: 2.215768e-03	ci left: 8.227629e-01	ci right 8.245895e-01	k: 551864	n:670000
NUP210L   670000 perm   372 sec   (1802 perm/sec)   p_kst 8.236776e-01   p_cons 2.202985e-03   p_joint 1.176716e-02

Joint ci ratio: 4.352156e-02	ci left: 1.153305e-02	ci right 1.204759e-02	k: 8016	n:680000
Cons ci ratio: 1.013395e-01	ci left: 2.084297e-03	ci right 2.308213e-03	k: 1492	n:680000
KS ci ratio: 2.199335e-03	ci left: 8.227804e-01	ci right 8.245934e-01	k: 560108	n:680000
NUP210L   680000 perm   380 sec   (1788 perm/sec)   p_kst 8.236882e-01   p_cons 2.194118e-03   p_joint 1.178824e-02

Joint ci ratio: 4.322359e-02	ci left: 1.152503e-02	ci right 1.203561e-02	k: 8127	n:690000
Cons ci ratio: 1.004681e-01	ci left: 2.090821e-03	ci right 2.313392e-03	k: 1518	n:690000
KS ci ratio: 2.183327e-03	ci left: 8.227886e-01	ci right 8.245884e-01	k: 568346	n:690000
NUP210L   690000 perm   389 sec   (1775 perm/sec)   p_kst 8.236899e-01   p_cons 2.200000e-03   p_joint 1.177826e-02

Joint ci ratio: 4.286326e-02	ci left: 1.155400e-02	ci right 1.206149e-02	k: 8264	n:700000
Cons ci ratio: 9.968358e-02	ci left: 2.094379e-03	ci right 2.315487e-03	k: 1542	n:700000
KS ci ratio: 2.167994e-03	ci left: 8.227523e-01	ci right 8.245393e-01	k: 576553	n:700000
NUP210L   700000 perm   397 sec   (1762 perm/sec)   p_kst 8.236471e-01   p_cons 2.202857e-03   p_joint 1.180571e-02

Outputting figure to mutsig2_images.part000000000118/NUP210L.2_5827_700000_0.82365_0.0022029_0.011806.png
                gene_name: NUP210L
               theta_stop: 0.100 
                    nperm: 700000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.0022 
      ci_cons_bounds_left: 0.0021 
     ci_cons_bounds_right: 0.0023 
                  p_joint: 0.012 
     ci_joint_bounds_left: 0.012 
    ci_joint_bounds_right: 0.012 

Current progress: 80 percent done.
NUP62
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.287760e-02	ci left: 4.454038e-01	ci right 4.650223e-01	k: 4552	n:10000
KS ci ratio: 7.397016e-03	ci left: 9.619446e-01	ci right 9.691809e-01	k: 9657	n:10000
NUP62   10000 perm   2 sec   (6665 perm/sec)   p_kst 9.657000e-01   p_cons 4.552000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000118/NUP62.2_1573_10000_0.9657_0.4552_1.png
                gene_name: NUP62
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000118
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 118 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4398170: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000119> was used as the working directory.
Started at Wed Oct 24 16:14:55 2012
Results reported at Wed Oct 24 16:17:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000119.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000119.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 119  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000119.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    161.27 sec.
    Max Memory :      1508 MB
    Max Swap   :      3999 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
119
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 119
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 119: processing genes 10587 - 10675
Calculating significance of each gene.
Using projection method.
10587	NXPH3	1
10588	NXPH4	1
10589	NXT1	1
10590	NXT2	1
10591	NYNRIN	1
10592	NYX	1
10593	OAF	1
10594	OAS1	1.267842e-02
10595	OAS2	1.593645e-01
10596	OAS3	1
10597	OASL	1
10598	OAT	1
10599	OAZ1	1
10600	OAZ2	1
10601	OAZ3	1
10602	OBFC1	1
10603	OBFC2A	1
10604	OBFC2B	1
10605	OBP2A	1
10606	OBP2B	1
10607	OBSCN	1
10608	OBSL1	2.314265e-01
10609	OC90	1
10610	OCA2	1
10611	OCEL1	1
10612	OCIAD1	1
10613	OCIAD2	1
10614	OCLM	1
10615	OCLN	1
10616	OCM	1
10617	OCM2	1
10618	OCRL	5.487013e-02
10619	ODAM	1
10620	ODC1	1.879877e-01
10621	ODF1	1
10622	ODF2	1
10623	ODF2L	1
10624	ODF3	1
10625	ODF3B	1
10626	ODF3L1	1
10627	ODF3L2	1
10628	ODF4	1
10629	ODZ1	1.066275e-02
10630	ODZ2	2.881991e-01
10631	ODZ3	1
10632	ODZ4	6.692820e-02
10633	OFD1	1
10634	OGDH	2.213914e-01
10635	OGDHL	4.257338e-01
10636	OGFOD1	1
10637	OGFOD2	1
10638	OGFR	1
10639	OGFRL1	1
10640	OGG1	1
10641	OGN	8.628682e-02
10642	OGT	1
10643	OIP5	1
10644	OIT3	1.164965e-01
10645	OLA1	1.627201e-02
10646	OLAH	1
10647	OLFM1	1
10648	OLFM2	1.276338e-02
10649	OLFM3	2.923957e-02
10650	OLFM4	1
10651	OLFML1	1
10652	OLFML2A	8.583724e-02
10653	OLFML2B	1
10654	OLFML3	1
10655	OLIG2	1
10656	OLIG3	9.119345e-02
10657	OLR1	1
10658	OMA1	1
10659	OMD	1
10660	OMG	1
10661	OMP	1
10662	ONECUT1	1
10663	ONECUT2	1
10664	OOEP	1
10665	OPA1	1.049769e-01
10666	OPA3	1
10667	OPALIN	1
10668	OPCML	1
10669	OPHN1	1
10670	OPLAH	1.338560e-01
10671	OPN1LW	1
10672	OPN1MW	1
10673	OPN1MW2	1
10674	OPN1SW	1
10675	OPN3	1
Done

Running MutSig 2:
Scatter job 119: processing genes 10587 - 10675
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ODZ1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.898406e-02	ci left: 6.370387e-01	ci right 6.558759e-01	k: 6465	n:10000
Cons ci ratio: 1.886299e-02	ci left: 8.042017e-01	ci right 8.196161e-01	k: 8120	n:10000
KS ci ratio: 4.645628e-02	ci left: 4.061158e-01	ci right 4.255332e-01	k: 4158	n:10000
ODZ1   10000 perm   3 sec   (3958 perm/sec)   p_kst 4.158000e-01   p_cons 8.120000e-01   p_joint 6.465000e-01

Outputting figure to mutsig2_images.part000000000119/ODZ1.5_8327_10000_0.4158_0.812_0.6465.png
                gene_name: ODZ1
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.82 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 11 percent done.
ODZ2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.103189e-02	ci left: 4.672683e-01	ci right 4.869450e-01	k: 4771	n:10000
Cons ci ratio: 9.134967e-02	ci left: 1.483504e-01	ci right 1.626509e-01	k: 1554	n:10000
KS ci ratio: 3.459494e-02	ci left: 5.523091e-01	ci right 5.718547e-01	k: 5621	n:10000
ODZ2   10000 perm   2 sec   (4175 perm/sec)   p_kst 5.621000e-01   p_cons 1.554000e-01   p_joint 4.771000e-01

Outputting figure to mutsig2_images.part000000000119/ODZ2.3_8414_10000_0.5621_0.1554_0.4771.png
                gene_name: ODZ2
               theta_stop: 0.091 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 22 percent done.
OAS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.572648e-02	ci left: 8.544725e-01	ci right 8.681163e-01	k: 8614	n:10000
Cons ci ratio: 1.981480e-02	ci left: 7.884733e-01	ci right 8.043536e-01	k: 7965	n:10000
KS ci ratio: 6.831423e-02	ci left: 2.391649e-01	ci right 2.561823e-01	k: 2476	n:10000
OAS1   10000 perm   1 sec   (6812 perm/sec)   p_kst 2.476000e-01   p_cons 7.965000e-01   p_joint 8.614000e-01

Outputting figure to mutsig2_images.part000000000119/OAS1.2_1424_10000_0.2476_0.7965_0.8614.png
                gene_name: OAS1
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.87 

Current progress: 33 percent done.
OAS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.520250e-02	ci left: 8.625359e-01	ci right 8.758482e-01	k: 8693	n:10000
KS ci ratio: 1.912852e-01	ci left: 3.643453e-02	ci right 4.423614e-02	k: 402	n:10000
OAS2   10000 perm   2 sec   (6414 perm/sec)   p_kst 4.020000e-02   p_cons 8.693000e-01   p_joint 1

Joint ci ratio: 2.883659e-02	ci left: 4.732542e-01	ci right 4.871515e-01	k: 9604	n:20000
Cons ci ratio: 1.071099e-02	ci left: 8.653618e-01	ci right 8.747303e-01	k: 17402	n:20000
KS ci ratio: 1.382379e-01	ci left: 3.597246e-02	ci right 4.136272e-02	k: 772	n:20000
OAS2   20000 perm   4 sec   (5675 perm/sec)   p_kst 3.860000e-02   p_cons 8.701000e-01   p_joint 4.802000e-01

Joint ci ratio: 3.045325e-02	ci left: 3.503468e-01	ci right 3.612145e-01	k: 10673	n:30000
Cons ci ratio: 8.736200e-03	ci left: 8.664794e-01	ci right 8.741154e-01	k: 26110	n:30000
KS ci ratio: 1.134582e-01	ci left: 3.609157e-02	ci right 4.046510e-02	k: 1147	n:30000
OAS2   30000 perm   6 sec   (5061 perm/sec)   p_kst 3.823333e-02   p_cons 8.703333e-01   p_joint 3.557667e-01

Joint ci ratio: 3.539020e-02	ci left: 2.305536e-01	ci right 2.388849e-01	k: 9388	n:40000
Cons ci ratio: 7.621974e-03	ci left: 8.653005e-01	ci right 8.719459e-01	k: 34746	n:40000
KS ci ratio: 9.706636e-02	ci left: 3.727033e-02	ci right 4.109694e-02	k: 1566	n:40000
OAS2   40000 perm   9 sec   (4503 perm/sec)   p_kst 3.915000e-02   p_cons 8.686500e-01   p_joint 2.347000e-01

Outputting figure to mutsig2_images.part000000000119/OAS2.2_2290_40000_0.03915_0.86865_0.2347.png
                gene_name: OAS2
               theta_stop: 0.097 
                    nperm: 40000 
                     p_ks: 0.039 
        ci_ks_bounds_left: 0.037 
       ci_ks_bounds_right: 0.041 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 44 percent done.
OCRL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.871829e-02	ci left: 6.412631e-01	ci right 6.600491e-01	k: 6507	n:10000
KS ci ratio: 6.295281e-02	ci left: 2.705218e-01	ci right 2.882069e-01	k: 2793	n:10000
OCRL   10000 perm   2 sec   (6070 perm/sec)   p_kst 2.793000e-01   p_cons 6.507000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000119/OCRL.2_2802_10000_0.2793_0.6507_1.png
                gene_name: OCRL
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 56 percent done.
ODZ4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.439863e-02	ci left: 5.551154e-01	ci right 5.746468e-01	k: 5649	n:10000
Cons ci ratio: 4.549450e-02	ci left: 4.162808e-01	ci right 4.357623e-01	k: 4260	n:10000
KS ci ratio: 3.766434e-02	ci left: 5.100533e-01	ci right 5.297351e-01	k: 5199	n:10000
ODZ4   10000 perm   2 sec   (4274 perm/sec)   p_kst 5.199000e-01   p_cons 4.260000e-01   p_joint 5.649000e-01

Outputting figure to mutsig2_images.part000000000119/ODZ4.2_8430_10000_0.5199_0.426_0.5649.png
                gene_name: ODZ4
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.57 

Current progress: 67 percent done.
OLA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.698598e-02	ci left: 3.119521e-01	ci right 3.303522e-01	k: 3211	n:10000
Cons ci ratio: 2.922539e-02	ci left: 6.332173e-01	ci right 6.520995e-01	k: 6427	n:10000
KS ci ratio: 9.018502e-02	ci left: 1.516867e-01	ci right 1.661126e-01	k: 1588	n:10000
OLA1   10000 perm   1 sec   (6712 perm/sec)   p_kst 1.588000e-01   p_cons 6.427000e-01   p_joint 3.211000e-01

Outputting figure to mutsig2_images.part000000000119/OLA1.2_1231_10000_0.1588_0.6427_0.3211.png
                gene_name: OLA1
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 78 percent done.
OLFM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.324445e-02	ci left: 5.718590e-01	ci right 5.912935e-01	k: 5816	n:10000
KS ci ratio: 2.412956e-02	ci left: 7.163357e-01	ci right 7.339330e-01	k: 7252	n:10000
OLFM2   10000 perm   1 sec   (6719 perm/sec)   p_kst 7.252000e-01   p_cons 5.816000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000119/OLFM2.2_1389_10000_0.7252_0.5816_1.png
                gene_name: OLFM2
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 89 percent done.
OPA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.947173e-02	ci left: 3.760446e-01	ci right 3.952221e-01	k: 3856	n:10000
Cons ci ratio: 3.190330e-02	ci left: 5.918258e-01	ci right 6.111151e-01	k: 6015	n:10000
KS ci ratio: 6.073045e-02	ci left: 2.850816e-01	ci right 3.030385e-01	k: 2940	n:10000
OPA1   10000 perm   2 sec   (5880 perm/sec)   p_kst 2.940000e-01   p_cons 6.015000e-01   p_joint 3.856000e-01

Outputting figure to mutsig2_images.part000000000119/OPA1.2_3168_10000_0.294_0.6015_0.3856.png
                gene_name: OPA1
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000119
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 119 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4398173: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000120> was used as the working directory.
Started at Wed Oct 24 16:14:55 2012
Results reported at Wed Oct 24 16:15:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000120.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000120.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 120  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000120.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     68.81 sec.
    Max Memory :      1037 MB
    Max Swap   :      3891 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
120
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 120
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 120: processing genes 10676 - 10765
Calculating significance of each gene.
Using projection method.
10676	OPN4	1
10677	OPN5	1
10678	OPRD1	1
10679	OPRK1	1
10680	OPRL1	9.470253e-02
10681	OPRM1	3.563097e-02
10682	OPTC	1.188750e-01
10683	OPTN	1
10684	OR10A2	1
10685	OR10A3	9.335341e-02
10686	OR10A4	1
10687	OR10A5	1
10688	OR10A6	1
10689	OR10A7	1
10690	OR10AD1	1
10691	OR10AG1	1
10692	OR10C1	7.254376e-02
10693	OR10G2	1
10694	OR10G3	1
10695	OR10G4	1
10696	OR10G7	1.555583e-01
10697	OR10G8	1
10698	OR10G9	1
10699	OR10H1	1
10700	OR10H2	1
10701	OR10H3	1
10702	OR10H4	1
10703	OR10H5	1
10704	OR10J1	1
10705	OR10J3	1
10706	OR10J5	1
10707	OR10K1	1
10708	OR10K2	1.569141e-01
10709	OR10P1	1
10710	OR10Q1	1
10711	OR10R2	1
10712	OR10S1	1
10713	OR10T2	1
10714	OR10V1	1
10715	OR10W1	1
10716	OR10X1	1
10717	OR10Z1	1
10718	OR11A1	1
10719	OR11G2	1
10720	OR11H1	1
10721	OR11H12	1
10722	OR11H4	1
10723	OR11H6	9.864752e-02
10724	OR11L1	1
10725	OR12D2	1
10726	OR12D3	1
10727	OR13A1	1
10728	OR13C2	1.638748e-01
10729	OR13C3	4.246358e-02
10730	OR13C4	1
10731	OR13C5	1
10732	OR13C8	1
10733	OR13C9	1.219955e-01
10734	OR13D1	1
10735	OR13F1	1
10736	OR13G1	1
10737	OR13H1	1
10738	OR13J1	1
10739	OR14A16	1
10740	OR14C36	1
10741	OR14I1	1
10742	OR14J1	1
10743	OR1A1	1
10744	OR1A2	1
10745	OR1B1	1
10746	OR1C1	1
10747	OR1D2	1
10748	OR1E1	1
10749	OR1E2	1
10750	OR1F1	1
10751	OR1G1	1
10752	OR1I1	1
10753	OR1J1	1
10754	OR1J2	1
10755	OR1J4	1.394003e-01
10756	OR1K1	1
10757	OR1L1	1
10758	OR1L3	1
10759	OR1L4	1
10760	OR1L6	1
10761	OR1L8	1
10762	OR1M1	1
10763	OR1N1	8.639657e-02
10764	OR1N2	1
10765	OR1Q1	1
Done

Running MutSig 2:
Scatter job 120: processing genes 10676 - 10765
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000120
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 120 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4398176: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000121> was used as the working directory.
Started at Wed Oct 24 16:15:04 2012
Results reported at Wed Oct 24 16:17:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000121.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000121.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 121  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000121.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    229.69 sec.
    Max Memory :      1070 MB
    Max Swap   :      3936 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
121
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 121
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 121: processing genes 10766 - 10855
Calculating significance of each gene.
Using projection method.
10766	OR1S1	1
10767	OR1S2	1
10768	OR2A1	1
10769	OR2A12	2.249535e-02
10770	OR2A14	1
10771	OR2A2	1
10772	OR2A25	1
10773	OR2A4	1
10774	OR2A42	1
10775	OR2A5	1
10776	OR2A7	1
10777	OR2AE1	1
10778	OR2AG1	1
10779	OR2AG2	1
10780	OR2AK2	1
10781	OR2AT4	1
10782	OR2B11	1
10783	OR2B2	1.197258e-01
10784	OR2B3	1
10785	OR2B6	1
10786	OR2C1	1
10787	OR2C3	1
10788	OR2D2	4.931891e-02
10789	OR2D3	1.134975e-01
10790	OR2F1	1
10791	OR2F2	1
10792	OR2G2	1.179670e-01
10793	OR2G3	1
10794	OR2G6	1.528512e-01
10795	OR2H1	1
10796	OR2H2	1
10797	OR2J2	1
10798	OR2J3	1.324377e-01
10799	OR2K2	1
10800	OR2L13	1
10801	OR2L2	1
10802	OR2L3	8.908142e-03
10803	OR2L8	1
10804	OR2M2	1
10805	OR2M3	1
10806	OR2M4	1
10807	OR2M5	1
10808	OR2M7	5.793315e-02
10809	OR2S2	1
10810	OR2T1	1
10811	OR2T10	1
10812	OR2T11	1
10813	OR2T12	1
10814	OR2T2	1
10815	OR2T27	1
10816	OR2T3	1
10817	OR2T33	1
10818	OR2T34	1
10819	OR2T35	1
10820	OR2T4	1.921704e-02
10821	OR2T5	1
10822	OR2T6	7.970013e-02
10823	OR2T8	1
10824	OR2V2	1.662984e-01
10825	OR2W1	1
10826	OR2W3	1
10827	OR2W5	1
10828	OR2Y1	1
10829	OR2Z1	1
10830	OR3A1	3.350014e-02
10831	OR3A2	1
10832	OR3A3	1
10833	OR4A15	1
10834	OR4A16	7.672197e-03
10835	OR4A47	1
10836	OR4A5	3.684500e-02
10837	OR4B1	1
10838	OR4C11	1
10839	OR4C12	9.601715e-02
10840	OR4C13	1
10841	OR4C15	1.445955e-01
10842	OR4C16	1
10843	OR4C3	1
10844	OR4C46	1
10845	OR4C6	1
10846	OR4D1	1
10847	OR4D10	1
10848	OR4D11	1
10849	OR4D2	1
10850	OR4D5	1
10851	OR4D6	1
10852	OR4D9	1
10853	OR4E2	1
10854	OR4F15	1
10855	OR4F17	1
Done

Running MutSig 2:
Scatter job 121: processing genes 10766 - 10855
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OR2L3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.774266e-02	ci left: 1.947597e-01	ci right 2.106139e-01	k: 2026	n:10000
Cons ci ratio: 1.279515e-01	ci left: 8.028489e-02	ci right 9.135778e-02	k: 857	n:10000
KS ci ratio: 1.037541e-02	ci left: 9.295765e-01	ci right 9.393685e-01	k: 9346	n:10000
OR2L3   10000 perm   2 sec   (4060 perm/sec)   p_kst 9.346000e-01   p_cons 8.570000e-02   p_joint 2.026000e-01

Joint ci ratio: 5.994426e-02	ci left: 1.708434e-01	ci right 1.814509e-01	k: 3522	n:20000
Cons ci ratio: 9.386888e-02	ci left: 7.642315e-02	ci right 8.399943e-02	k: 1603	n:20000
KS ci ratio: 7.406159e-03	ci left: 9.298561e-01	ci right 9.368173e-01	k: 18668	n:20000
OR2L3   20000 perm   8 sec   (2484 perm/sec)   p_kst 9.334000e-01   p_cons 8.015000e-02   p_joint 1.761000e-01

Outputting figure to mutsig2_images.part000000000121/OR2L3.2_943_20000_0.9334_0.08015_0.1761.png
                gene_name: OR2L3
               theta_stop: 0.094 
                    nperm: 20000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.080 
      ci_cons_bounds_left: 0.076 
     ci_cons_bounds_right: 0.084 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 50 percent done.
OR4A16
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.199653e-02	ci left: 5.904206e-01	ci right 6.097211e-01	k: 6001	n:10000
Cons ci ratio: 5.695986e-02	ci left: 3.121506e-01	ci right 3.305536e-01	k: 3213	n:10000
KS ci ratio: 3.657006e-02	ci left: 5.247648e-01	ci right 5.444151e-01	k: 5346	n:10000
OR4A16   10000 perm   2 sec   (6304 perm/sec)   p_kst 5.346000e-01   p_cons 3.213000e-01   p_joint 6.001000e-01

Outputting figure to mutsig2_images.part000000000121/OR4A16.2_989_10000_0.5346_0.3213_0.6001.png
                gene_name: OR4A16
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000121
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 121 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1547>
Subject: Job 4398181: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000122> was used as the working directory.
Started at Wed Oct 24 16:15:06 2012
Results reported at Wed Oct 24 16:17:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000122.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000122.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 122  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000122.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    187.63 sec.
    Max Memory :      1231 MB
    Max Swap   :      3897 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
122
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 122
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 122: processing genes 10856 - 10945
Calculating significance of each gene.
Using projection method.
10856	OR4F21	1
10857	OR4F4	1
10858	OR4F5	1
10859	OR4F6	1
10860	OR4K1	1
10861	OR4K13	1
10862	OR4K14	1.875175e-02
10863	OR4K15	1
10864	OR4K17	7.260566e-03
10865	OR4K2	1
10866	OR4K5	1
10867	OR4L1	1.113819e-01
10868	OR4M1	6.571251e-02
10869	OR4M2	1
10870	OR4N2	3.131169e-02
10871	OR4N4	1
10872	OR4N5	1
10873	OR4P4	2.748700e-02
10874	OR4Q3	1
10875	OR4S1	1
10876	OR4S2	1
10877	OR4X1	1
10878	OR4X2	1
10879	OR51A2	1
10880	OR51A4	1
10881	OR51A7	1
10882	OR51B2	1
10883	OR51B4	1
10884	OR51B5	1
10885	OR51B6	1
10886	OR51D1	1.593049e-01
10887	OR51E1	2.744028e-03
10888	OR51E2	1
10889	OR51F1	1
10890	OR51F2	1
10891	OR51G1	1
10892	OR51G2	1
10893	OR51I1	1
10894	OR51I2	1
10895	OR51L1	1
10896	OR51M1	1
10897	OR51Q1	1
10898	OR51S1	1
10899	OR51T1	1
10900	OR51V1	1
10901	OR52A1	1
10902	OR52A4	1
10903	OR52A5	1
10904	OR52B2	1.246244e-01
10905	OR52B4	1
10906	OR52B6	1
10907	OR52D1	3.011236e-02
10908	OR52E2	1
10909	OR52E4	1
10910	OR52E6	1
10911	OR52E8	1
10912	OR52H1	1
10913	OR52I1	1
10914	OR52I2	1
10915	OR52J3	1
10916	OR52K1	1
10917	OR52K2	1
10918	OR52L1	1
10919	OR52M1	1
10920	OR52N1	1.445904e-01
10921	OR52N2	1
10922	OR52N4	1.143265e-02
10923	OR52N5	1
10924	OR52R1	1
10925	OR52W1	1
10926	OR56A1	1
10927	OR56A3	1
10928	OR56A4	1
10929	OR56B1	1.053439e-01
10930	OR56B4	1
10931	OR5A1	1
10932	OR5A2	1
10933	OR5AC2	1
10934	OR5AK2	1
10935	OR5AN1	1
10936	OR5AP2	1
10937	OR5AR1	1
10938	OR5AS1	1.222586e-01
10939	OR5AU1	1
10940	OR5B12	1
10941	OR5B17	1
10942	OR5B2	1
10943	OR5B21	1
10944	OR5B3	1
10945	OR5C1	1
Done

Running MutSig 2:
Scatter job 122: processing genes 10856 - 10945
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OR4K17
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.441696e-02	ci left: 2.090529e-01	ci right 2.253122e-01	k: 2171	n:10000
Cons ci ratio: 4.659998e-02	ci left: 4.046213e-01	ci right 4.240286e-01	k: 4143	n:10000
KS ci ratio: 2.284450e-01	ci left: 2.532660e-02	ci right 3.195180e-02	k: 285	n:10000
OR4K17   10000 perm   2 sec   (5438 perm/sec)   p_kst 2.850000e-02   p_cons 4.143000e-01   p_joint 2.171000e-01

Joint ci ratio: 5.087438e-02	ci left: 2.230427e-01	ci right 2.347363e-01	k: 4577	n:20000
Cons ci ratio: 3.287626e-02	ci left: 4.086080e-01	ci right 4.223166e-01	k: 8309	n:20000
KS ci ratio: 1.633108e-01	ci left: 2.570945e-02	ci right 3.032914e-02	k: 559	n:20000
OR4K17   20000 perm   7 sec   (3011 perm/sec)   p_kst 2.795000e-02   p_cons 4.154500e-01   p_joint 2.288500e-01

Joint ci ratio: 2.805066e-02	ci left: 3.887305e-01	ci right 3.998233e-01	k: 11828	n:30000
Cons ci ratio: 2.703762e-02	ci left: 4.063892e-01	ci right 4.175612e-01	k: 12359	n:30000
KS ci ratio: 1.329373e-01	ci left: 2.629135e-02	ci right 3.006743e-02	k: 844	n:30000
OR4K17   30000 perm   9 sec   (3431 perm/sec)   p_kst 2.813333e-02   p_cons 4.119667e-01   p_joint 3.942667e-01

Joint ci ratio: 2.380004e-02	ci left: 3.992857e-01	ci right 4.089283e-01	k: 16164	n:40000
Cons ci ratio: 2.348301e-02	ci left: 4.057482e-01	ci right 4.154148e-01	k: 16423	n:40000
KS ci ratio: 1.137667e-01	ci left: 2.718282e-02	ci right 3.048606e-02	k: 1152	n:40000
OR4K17   40000 perm   11 sec   (3666 perm/sec)   p_kst 2.880000e-02   p_cons 4.105750e-01   p_joint 4.041000e-01

Joint ci ratio: 2.675700e-02	ci left: 2.963037e-01	ci right 3.043595e-01	k: 15016	n:50000
Cons ci ratio: 2.096655e-02	ci left: 4.071219e-01	ci right 4.157684e-01	k: 20572	n:50000
KS ci ratio: 1.014036e-01	ci left: 2.754653e-02	ci right 3.050848e-02	k: 1450	n:50000
OR4K17   50000 perm   13 sec   (3802 perm/sec)   p_kst 2.900000e-02   p_cons 4.114400e-01   p_joint 3.003200e-01

Joint ci ratio: 2.925515e-02	ci left: 2.269359e-01	ci right 2.336902e-01	k: 13818	n:60000
Cons ci ratio: 1.909476e-02	ci left: 4.086402e-01	ci right 4.165350e-01	k: 24755	n:60000
KS ci ratio: 9.346236e-02	ci left: 2.715051e-02	ci right 2.982869e-02	k: 1708	n:60000
OR4K17   60000 perm   15 sec   (3892 perm/sec)   p_kst 2.846667e-02   p_cons 4.125833e-01   p_joint 2.303000e-01

Outputting figure to mutsig2_images.part000000000122/OR4K17.2_1036_60000_0.028467_0.41258_0.2303.png
                gene_name: OR4K17
               theta_stop: 0.093 
                    nperm: 60000 
                     p_ks: 0.028 
        ci_ks_bounds_left: 0.027 
       ci_ks_bounds_right: 0.030 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.23 

Current progress: 50 percent done.
OR51E1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.869935e-02	ci left: 6.415648e-01	ci right 6.603472e-01	k: 6510	n:10000
KS ci ratio: 2.627951e-02	ci left: 6.807302e-01	ci right 6.989591e-01	k: 6899	n:10000
OR51E1   10000 perm   2 sec   (6483 perm/sec)   p_kst 6.899000e-01   p_cons 6.510000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000122/OR51E1.2_961_10000_0.6899_0.651_1.png
                gene_name: OR51E1
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000122
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 122 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4398184: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000123> was used as the working directory.
Started at Wed Oct 24 16:15:08 2012
Results reported at Wed Oct 24 16:16:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000123.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000123.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 123  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000123.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    143.88 sec.
    Max Memory :       978 MB
    Max Swap   :      3826 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
123
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 123
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 123: processing genes 10946 - 11034
Calculating significance of each gene.
Using projection method.
10946	OR5D13	1
10947	OR5D14	1
10948	OR5D16	7.366764e-02
10949	OR5D18	1
10950	OR5F1	1
10951	OR5H1	1.140758e-01
10952	OR5H14	1
10953	OR5H15	1
10954	OR5H2	1
10955	OR5H6	1.025101e-04
10956	OR5I1	1
10957	OR5J2	1
10958	OR5K1	1
10959	OR5K2	1
10960	OR5K3	1
10961	OR5K4	1
10962	OR5L1	1
10963	OR5L2	1.008046e-01
10964	OR5M1	1
10965	OR5M10	1
10966	OR5M11	1
10967	OR5M3	1
10968	OR5M8	1
10969	OR5M9	1
10970	OR5P2	1
10971	OR5P3	1
10972	OR5R1	1
10973	OR5T1	1
10974	OR5T2	1
10975	OR5T3	1.592918e-01
10976	OR5V1	1
10977	OR5W2	4.932717e-02
10978	OR6A2	1
10979	OR6B1	1
10980	OR6B2	1
10981	OR6B3	1
10982	OR6C1	1
10983	OR6C2	1
10984	OR6C3	1
10985	OR6C4	1
10986	OR6C6	1
10987	OR6C65	1.422610e-01
10988	OR6C68	1
10989	OR6C70	1
10990	OR6C74	1
10991	OR6C75	1
10992	OR6C76	1
10993	OR6F1	1
10994	OR6K2	1.624636e-01
10995	OR6K3	4.337341e-02
10996	OR6K6	1.091147e-01
10997	OR6M1	1
10998	OR6N1	1
10999	OR6N2	1
11000/17942 11000	OR6Q1	1
11001	OR6S1	1
11002	OR6T1	1
11003	OR6V1	1
11004	OR6X1	1
11005	OR6Y1	1
11006	OR7A10	1
11007	OR7A17	1
11008	OR7A5	1
11009	OR7C1	1
11010	OR7C2	1
11011	OR7D2	1.701000e-01
11012	OR7D4	1
11013	OR7E24	1
11014	OR7G1	6.516651e-02
11015	OR7G2	1
11016	OR7G3	1
11017	OR8A1	1
11018	OR8B12	1
11019	OR8B2	1
11020	OR8B3	1
11021	OR8B4	1
11022	OR8B8	1
11023	OR8D1	4.579699e-02
11024	OR8D2	1
11025	OR8D4	1
11026	OR8G1	1
11027	OR8G2	1
11028	OR8G5	1
11029	OR8H1	1
11030	OR8H2	3.416625e-02
11031	OR8H3	1
11032	OR8I2	1
11033	OR8J1	3.749096e-02
11034	OR8J3	1
Done

Running MutSig 2:
Scatter job 123: processing genes 10946 - 11034
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OR5H6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.079590e-03	ci left: 9.734446e-01	ci right 9.794734e-01	k: 9766	n:10000
Cons ci ratio: 2.942289e-02	ci left: 6.301003e-01	ci right 6.490183e-01	k: 6396	n:10000
KS ci ratio: 2.109147e-02	ci left: 7.671924e-01	ci right 7.836469e-01	k: 7755	n:10000
OR5H6   10000 perm   2 sec   (6074 perm/sec)   p_kst 7.755000e-01   p_cons 6.396000e-01   p_joint 9.766000e-01

Outputting figure to mutsig2_images.part000000000123/OR5H6.3_982_10000_0.7755_0.6396_0.9766.png
                gene_name: OR5H6
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 50 percent done.
OR7D2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.407835e-02	ci left: 8.794036e-01	ci right 8.919707e-01	k: 8858	n:10000
Cons ci ratio: 1.733220e-02	ci left: 8.291039e-01	ci right 8.436996e-01	k: 8365	n:10000
KS ci ratio: 8.067374e-02	ci left: 1.832380e-01	ci right 1.987424e-01	k: 1909	n:10000
OR7D2   10000 perm   1 sec   (7159 perm/sec)   p_kst 1.909000e-01   p_cons 8.365000e-01   p_joint 8.858000e-01

Outputting figure to mutsig2_images.part000000000123/OR7D2.2_943_10000_0.1909_0.8365_0.8858.png
                gene_name: OR7D2
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000123
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 123 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1430>
Subject: Job 4398188: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1430>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000124> was used as the working directory.
Started at Wed Oct 24 16:15:10 2012
Results reported at Wed Oct 24 16:17:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000124.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000124.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 124  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000124.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    197.14 sec.
    Max Memory :       688 MB
    Max Swap   :      3527 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
124
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 124
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 124: processing genes 11035 - 11124
Calculating significance of each gene.
Using projection method.
11035	OR8K1	1
11036	OR8K3	1
11037	OR8K5	1
11038	OR8S1	1
11039	OR8U8	1
11040	OR9A2	1
11041	OR9A4	1
11042	OR9G1	1
11043	OR9G4	1
11044	OR9G9	1
11045	OR9I1	1
11046	OR9K2	1
11047	OR9Q1	1
11048	OR9Q2	1
11049	ORAI1	1
11050	ORAI2	1
11051	ORAI3	1
11052	ORAOV1	1
11053	ORC1L	3.992293e-01
11054	ORC2L	1
11055	ORC3L	1
11056	ORC4L	2.031870e-01
11057	ORC5L	1
11058	ORC6L	1
11059	ORM1	8.211532e-02
11060	ORM2	1
11061	ORMDL1	1
11062	ORMDL2	1
11063	ORMDL3	1
11064	OS9	3.359662e-01
11065	OSBP	1
11066	OSBP2	1
11067	OSBPL10	1
11068	OSBPL11	3.342861e-01
11069	OSBPL1A	1
11070	OSBPL2	1.364694e-01
11071	OSBPL3	1
11072	OSBPL5	1
11073	OSBPL6	1
11074	OSBPL7	1
11075	OSBPL8	1.606607e-01
11076	OSBPL9	1
11077	OSCAR	1
11078	OSCP1	1
11079	OSGEP	1
11080	OSGEPL1	1
11081	OSGIN1	1
11082	OSGIN2	1.492558e-01
11083	OSM	1
11084	OSMR	1
11085	OSR1	1
11086	OSR2	1
11087	OSTBETA	1
11088	OSTC	1
11089	OSTF1	1
11090	OSTM1	1
11091	OSTN	1
11092	OSTalpha	1
11093	OTC	1
11094	OTOA	1
11095	OTOF	1
11096	OTOL1	1
11097	OTOP1	1.650348e-01
11098	OTOP2	1
11099	OTOP3	1
11100	OTOR	1
11101	OTOS	1
11102	OTP	1
11103	OTUB1	1
11104	OTUB2	1
11105	OTUD3	3.208725e-02
11106	OTUD4	6.925508e-02
11107	OTUD5	1
11108	OTUD6A	7.171537e-02
11109	OTUD6B	1
11110	OTUD7A	1
11111	OTUD7B	1
11112	OTX1	1
11113	OTX2	1
11114	OVCA2	1
11115	OVCH1	1.772773e-01
11116	OVCH2	1.157912e-01
11117	OVGP1	2.322956e-01
11118	OVOL1	1
11119	OVOL2	1
11120	OXA1L	1
11121	OXCT1	1
11122	OXCT2	1
11123	OXER1	1
11124	OXGR1	1
Done

Running MutSig 2:
Scatter job 124: processing genes 11035 - 11124
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OTUD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.208421e-03	ci left: 9.864298e-01	ci right 9.906784e-01	k: 9887	n:10000
Cons ci ratio: 6.684359e-02	ci left: 2.472706e-01	ci right 2.644719e-01	k: 2558	n:10000
KS ci ratio: 7.397016e-03	ci left: 9.619446e-01	ci right 9.691809e-01	k: 9657	n:10000
OTUD4   10000 perm   2 sec   (5267 perm/sec)   p_kst 9.657000e-01   p_cons 2.558000e-01   p_joint 9.887000e-01

Outputting figure to mutsig2_images.part000000000124/OTUD4.2_3234_10000_0.9657_0.2558_0.9887.png
                gene_name: OTUD4
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000124
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 124 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4398195: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000125> was used as the working directory.
Started at Wed Oct 24 16:15:10 2012
Results reported at Wed Oct 24 16:17:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000125.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000125.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 125  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000125.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    168.08 sec.
    Max Memory :      1429 MB
    Max Swap   :      3940 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
125
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 125
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 125: processing genes 11125 - 11214
Calculating significance of each gene.
Using projection method.
11125	OXNAD1	1.447750e-03
11126	OXR1	1
11127	OXSM	2.109987e-01
11128	OXSR1	1
11129	OXT	1
11130	OXTR	7.830290e-02
11131	P2RX1	1
11132	P2RX2	1
11133	P2RX3	1
11134	P2RX4	1
11135	P2RX5	1
11136	P2RX6	1
11137	P2RX7	1
11138	P2RY1	1
11139	P2RY10	1
11140	P2RY11	1
11141	P2RY12	1
11142	P2RY13	9.366586e-02
11143	P2RY14	1
11144	P2RY2	1
11145	P2RY4	6.913340e-03
11146	P2RY6	1
11147	P2RY8	1
11148	P4HA1	1
11149	P4HA2	1
11150	P4HA3	1
11151	P4HB	1
11152	P4HTM	1
11153	PA2G4	1
11154	PAAF1	1
11155	PABPC1	1
11156	PABPC1L	1
11157	PABPC3	2.774787e-01
11158	PABPC4	1
11159	PABPC5	1
11160	PABPN1	1
11161	PABPN1L	1
11162	PACRG	1
11163	PACRGL	1
11164	PACS1	1
11165	PACS2	1
11166	PACSIN1	1
11167	PACSIN2	1.626039e-01
11168	PACSIN3	1
11169	PADI1	1
11170	PADI2	1.147623e-01
11171	PADI3	1
11172	PADI4	1
11173	PADI6	1
11174	PAEP	1
11175	PAF1	7.816667e-02
11176	PAFAH1B1	1
11177	PAFAH1B2	1
11178	PAFAH1B3	1
11179	PAFAH2	1
11180	PAG1	1.231014e-01
11181	PAGE1	1
11182	PAGE2	1
11183	PAGE2B	1
11184	PAGE4	1
11185	PAGE5	1
11186	PAH	1
11187	PAICS	1
11188	PAIP1	1
11189	PAIP2	1
11190	PAIP2B	1
11191	PAK1	1
11192	PAK1IP1	1
11193	PAK2	1.097908e-01
11194	PAK3	1.319589e-01
11195	PAK4	1
11196	PAK6	2.984975e-01
11197	PAK7	1
11198	PALB2	1
11199	PALLD	1
11200	PALM	1
11201	PALM2	1
11202	PALM2-AKAP2	1
11203	PALMD	1
11204	PAM	1
11205	PAMR1	1
11206	PAN2	1
11207	PAN3	4.534511e-02
11208	PANK1	1.833170e-01
11209	PANK2	1
11210	PANK3	1.211161e-02
11211	PANK4	1
11212	PANX1	1
11213	PANX2	1
11214	PANX3	1.655252e-01
Done

Running MutSig 2:
Scatter job 125: processing genes 11125 - 11214
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OXNAD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.347668e-02	ci left: 7.272426e-01	ci right 7.446198e-01	k: 7360	n:10000
KS ci ratio: 3.998010e-03	ci left: 9.876314e-01	ci right 9.916757e-01	k: 9898	n:10000
OXNAD1   10000 perm   2 sec   (6484 perm/sec)   p_kst 9.898000e-01   p_cons 7.360000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000125/OXNAD1.2_967_10000_0.9898_0.736_1.png
                gene_name: OXNAD1
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.74 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
P2RY4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.301904e-02	ci left: 1.746777e-01	ci right 1.899078e-01	k: 1822	n:10000
Cons ci ratio: 7.098191e-02	ci left: 2.253355e-01	ci right 2.420199e-01	k: 2336	n:10000
KS ci ratio: 1.013601e-01	ci left: 1.234670e-01	ci right 1.367493e-01	k: 1300	n:10000
P2RY4   10000 perm   1 sec   (6882 perm/sec)   p_kst 1.300000e-01   p_cons 2.336000e-01   p_joint 1.822000e-01

Joint ci ratio: 6.270728e-02	ci left: 1.583001e-01	ci right 1.685980e-01	k: 3268	n:20000
Cons ci ratio: 4.949473e-02	ci left: 2.328054e-01	ci right 2.446707e-01	k: 4774	n:20000
KS ci ratio: 7.221701e-02	ci left: 1.237437e-01	ci right 1.330646e-01	k: 2567	n:20000
P2RY4   20000 perm   3 sec   (6025 perm/sec)   p_kst 1.283500e-01   p_cons 2.387000e-01   p_joint 1.634000e-01

Outputting figure to mutsig2_images.part000000000125/P2RY4.2_1102_20000_0.12835_0.2387_0.1634.png
                gene_name: P2RY4
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.16 
     ci_joint_bounds_left: 0.16 
    ci_joint_bounds_right: 0.17 

Current progress: 50 percent done.
PAN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.842512e-01	ci left: 3.929883e-02	ci right 4.736993e-02	k: 432	n:10000
Cons ci ratio: 1.112145e-01	ci left: 1.043218e-01	ci right 1.167061e-01	k: 1104	n:10000
KS ci ratio: 3.289572e-01	ci left: 1.169777e-02	ci right 1.639161e-02	k: 139	n:10000
PAN3   10000 perm   2 sec   (4305 perm/sec)   p_kst 1.390000e-02   p_cons 1.104000e-01   p_joint 4.320000e-02

Joint ci ratio: 1.293542e-01	ci left: 4.105370e-02	ci right 4.677985e-02	k: 877	n:20000
Cons ci ratio: 7.953495e-02	ci left: 1.039762e-01	ci right 1.126380e-01	k: 2165	n:20000
KS ci ratio: 2.396559e-01	ci left: 1.161730e-02	ci right 1.482653e-02	k: 263	n:20000
PAN3   20000 perm   4 sec   (4585 perm/sec)   p_kst 1.315000e-02   p_cons 1.082500e-01   p_joint 4.385000e-02

Joint ci ratio: 1.205112e-01	ci left: 3.201016e-02	ci right 3.614738e-02	k: 1021	n:30000
Cons ci ratio: 6.495163e-02	ci left: 1.047392e-01	ci right 1.118036e-01	k: 3247	n:30000
KS ci ratio: 1.971993e-01	ci left: 1.171716e-02	ci right 1.431175e-02	k: 389	n:30000
PAN3   30000 perm   7 sec   (4580 perm/sec)   p_kst 1.296667e-02   p_cons 1.082333e-01   p_joint 3.403333e-02

Joint ci ratio: 1.057670e-01	ci left: 3.144137e-02	ci right 3.497682e-02	k: 1327	n:40000
Cons ci ratio: 5.654075e-02	ci left: 1.042337e-01	ci right 1.103234e-01	k: 4290	n:40000
KS ci ratio: 1.750952e-01	ci left: 1.129070e-02	ci right 1.348094e-02	k: 494	n:40000
PAN3   40000 perm   9 sec   (4394 perm/sec)   p_kst 1.235000e-02   p_cons 1.072500e-01   p_joint 3.317500e-02

Joint ci ratio: 5.836950e-02	ci left: 8.031982e-02	ci right 8.516876e-02	k: 4136	n:50000
Cons ci ratio: 5.072941e-02	ci left: 1.039672e-01	ci right 1.093985e-01	k: 5333	n:50000
KS ci ratio: 1.559418e-01	ci left: 1.150609e-02	ci right 1.347112e-02	k: 623	n:50000
PAN3   50000 perm   13 sec   (3898 perm/sec)   p_kst 1.246000e-02   p_cons 1.066600e-01   p_joint 8.272000e-02

Joint ci ratio: 8.692454e-02	ci left: 3.135650e-02	ci right 3.422226e-02	k: 1966	n:60000
Cons ci ratio: 4.633296e-02	ci left: 1.041084e-01	ci right 1.090630e-01	k: 6394	n:60000
KS ci ratio: 1.432095e-01	ci left: 1.144946e-02	ci right 1.323151e-02	k: 739	n:60000
PAN3   60000 perm   16 sec   (3807 perm/sec)   p_kst 1.231667e-02   p_cons 1.065667e-01   p_joint 3.276667e-02

Joint ci ratio: 8.063717e-02	ci left: 3.133872e-02	ci right 3.398592e-02	k: 2285	n:70000
Cons ci ratio: 4.294705e-02	ci left: 1.040684e-01	ci right 1.086500e-01	k: 7444	n:70000
KS ci ratio: 1.330815e-01	ci left: 1.142753e-02	ci right 1.307042e-02	k: 856	n:70000
PAN3   70000 perm   19 sec   (3668 perm/sec)   p_kst 1.222857e-02   p_cons 1.063429e-01   p_joint 3.264286e-02

Joint ci ratio: 7.563254e-02	ci left: 3.125742e-02	ci right 3.372664e-02	k: 2598	n:80000
Cons ci ratio: 4.023306e-02	ci left: 1.039368e-01	ci right 1.082168e-01	k: 8485	n:80000
KS ci ratio: 1.254909e-01	ci left: 1.129330e-02	ci right 1.281739e-02	k: 963	n:80000
PAN3   80000 perm   22 sec   (3682 perm/sec)   p_kst 1.203750e-02   p_cons 1.060625e-01   p_joint 3.247500e-02

Joint ci ratio: 7.121745e-02	ci left: 3.140563e-02	ci right 3.373573e-02	k: 2930	n:90000
Cons ci ratio: 3.796715e-02	ci left: 1.038858e-01	ci right 1.079174e-01	k: 9530	n:90000
KS ci ratio: 1.184523e-01	ci left: 1.130962e-02	ci right 1.274431e-02	k: 1081	n:90000
PAN3   90000 perm   24 sec   (3700 perm/sec)   p_kst 1.201111e-02   p_cons 1.058889e-01   p_joint 3.255556e-02

Joint ci ratio: 6.750573e-02	ci left: 3.151773e-02	ci right 3.372949e-02	k: 3261	n:100000
Cons ci ratio: 3.597704e-02	ci left: 1.042076e-01	ci right 1.080353e-01	k: 10611	n:100000
KS ci ratio: 1.120545e-01	ci left: 1.141210e-02	ci right 1.277642e-02	k: 1208	n:100000
PAN3   100000 perm   27 sec   (3691 perm/sec)   p_kst 1.208000e-02   p_cons 1.061100e-01   p_joint 3.261000e-02

Joint ci ratio: 1.066735e-01	ci left: 1.147994e-02	ci right 1.278233e-02	k: 1333	n:110000
Cons ci ratio: 3.430639e-02	ci left: 1.042769e-01	ci right 1.079257e-01	k: 11670	n:110000
KS ci ratio: 1.066735e-01	ci left: 1.147994e-02	ci right 1.278233e-02	k: 1333	n:110000
PAN3   110000 perm   31 sec   (3562 perm/sec)   p_kst 1.211818e-02   p_cons 1.060909e-01   p_joint 1.211818e-02

Joint ci ratio: 1.016830e-01	ci left: 1.161090e-02	ci right 1.286284e-02	k: 1467	n:120000
Cons ci ratio: 3.289938e-02	ci left: 1.040486e-01	ci right 1.075372e-01	k: 12694	n:120000
KS ci ratio: 1.016830e-01	ci left: 1.161090e-02	ci right 1.286284e-02	k: 1467	n:120000
PAN3   120000 perm   34 sec   (3562 perm/sec)   p_kst 1.222500e-02   p_cons 1.057833e-01   p_joint 1.222500e-02

Joint ci ratio: 9.717969e-02	ci left: 1.176044e-02	ci right 1.296915e-02	k: 1606	n:130000
Cons ci ratio: 3.158934e-02	ci left: 1.042323e-01	ci right 1.075853e-01	k: 13767	n:130000
KS ci ratio: 9.717969e-02	ci left: 1.176044e-02	ci right 1.296915e-02	k: 1606	n:130000
PAN3   130000 perm   37 sec   (3554 perm/sec)   p_kst 1.235385e-02   p_cons 1.059000e-01   p_joint 1.235385e-02

Outputting figure to mutsig2_images.part000000000125/PAN3.2_2740_130000_0.012354_0.1059_0.012354.png
                gene_name: PAN3
               theta_stop: 0.097 
                    nperm: 130000 
                     p_ks: 0.012 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.012 
     ci_joint_bounds_left: 0.012 
    ci_joint_bounds_right: 0.013 

Current progress: 75 percent done.
PANK3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.186117e-02	ci left: 3.540633e-01	ci right 3.730162e-01	k: 3635	n:10000
Cons ci ratio: 2.658081e-02	ci left: 6.757928e-01	ci right 6.940994e-01	k: 6850	n:10000
KS ci ratio: 6.682605e-02	ci left: 2.473694e-01	ci right 2.645729e-01	k: 2559	n:10000
PANK3   10000 perm   1 sec   (6979 perm/sec)   p_kst 2.559000e-01   p_cons 6.850000e-01   p_joint 3.635000e-01

Outputting figure to mutsig2_images.part000000000125/PANK3.2_1141_10000_0.2559_0.685_0.3635.png
                gene_name: PANK3
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000125
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 125 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4398199: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000126> was used as the working directory.
Started at Wed Oct 24 16:15:10 2012
Results reported at Wed Oct 24 16:17:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000126.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000126.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 126  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000126.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    154.89 sec.
    Max Memory :      1597 MB
    Max Swap   :      3935 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
126
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 126
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 126: processing genes 11215 - 11303
Calculating significance of each gene.
Using projection method.
11215	PAOX	1.006660e-01
11216	PAPD4	1
11217	PAPD5	1
11218	PAPD7	1
11219	PAPL	1
11220	PAPLN	1
11221	PAPOLA	8.973206e-02
11222	PAPOLB	5.797625e-02
11223	PAPOLG	1
11224	PAPPA	1
11225	PAPPA2	2.384189e-01
11226	PAPSS1	1
11227	PAPSS2	1
11228	PAQR3	1
11229	PAQR4	1
11230	PAQR5	1
11231	PAQR6	1
11232	PAQR7	1
11233	PAQR8	1
11234	PAQR9	1
11235	PARD3	1.603660e-01
11236	PARD3B	1
11237	PARD6A	1
11238	PARD6B	1
11239	PARD6G	1
11240	PARK2	3.859325e-03
11241	PARK7	1
11242	PARL	1
11243	PARM1	1.537082e-01
11244	PARN	1.014710e-02
11245	PARP1	3.322586e-01
11246	PARP10	1
11247	PARP11	1
11248	PARP12	1
11249	PARP14	6.676595e-02
11250	PARP15	1
11251	PARP16	1
11252	PARP2	6.508267e-02
11253	PARP3	1
11254	PARP4	1
11255	PARP6	2.643802e-01
11256	PARP8	1
11257	PARP9	1
11258	PARS2	1
11259	PARVA	1
11260	PARVB	1
11261	PARVG	1
11262	PASD1	1
11263	PASK	1
11264	PATE1	1
11265	PATE2	1
11266	PATL1	1
11267	PATZ1	4.438275e-02
11268	PAWR	1
11269	PAX1	6.616136e-02
11270	PAX2	1
11271	PAX3	1
11272	PAX4	4.857480e-02
11273	PAX5	1
11274	PAX6	1
11275	PAX7	3.396247e-03
11276	PAX8	1
11277	PAX9	1
11278	PAXIP1	1
11279	PBK	1
11280	PBLD	6.476805e-02
11281	PBOV1	1
11282	PBRM1	2.147008e-01
11283	PBX1	1
11284	PBX2	1
11285	PBX3	8.488052e-02
11286	PBX4	1
11287	PBXIP1	1
11288	PC	2.761360e-01
11289	PCBD1	1
11290	PCBD2	1
11291	PCBP1	1.180971e-01
11292	PCBP2	1
11293	PCBP3	1.332276e-02
11294	PCBP4	7.707201e-02
11295	PCCA	1
11296	PCCB	1
11297	PCDH1	1
11298	PCDH10	1
11299	PCDH11X	1.906917e-01
11300	PCDH12	1
11301	PCDH15	7.435048e-02
11302	PCDH17	3.757864e-01
11303	PCDH18	1
Done

Running MutSig 2:
Scatter job 126: processing genes 11215 - 11303
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PAPPA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.519813e-02	ci left: 4.194707e-01	ci right 4.389705e-01	k: 4292	n:10000
Cons ci ratio: 4.891266e-02	ci left: 3.814188e-01	ci right 4.006447e-01	k: 3910	n:10000
KS ci ratio: 4.023461e-02	ci left: 4.770586e-01	ci right 4.967491e-01	k: 4869	n:10000
PAPPA2   10000 perm   2 sec   (4738 perm/sec)   p_kst 4.869000e-01   p_cons 3.910000e-01   p_joint 4.292000e-01

Outputting figure to mutsig2_images.part000000000126/PAPPA2.4_5517_10000_0.4869_0.391_0.4292.png
                gene_name: PAPPA2
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 14 percent done.
PARP14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.602861e-02	ci left: 2.519183e-01	ci right 2.692214e-01	k: 2605	n:10000
Cons ci ratio: 1.268230e-01	ci left: 8.164409e-02	ci right 9.279774e-02	k: 871	n:10000
KS ci ratio: 2.935912e-02	ci left: 6.311057e-01	ci right 6.500123e-01	k: 6406	n:10000
PARP14   10000 perm   3 sec   (2879 perm/sec)   p_kst 6.406000e-01   p_cons 8.710000e-02   p_joint 2.605000e-01

Joint ci ratio: 4.981684e-02	ci left: 2.304758e-01	ci right 2.423009e-01	k: 4727	n:20000
Cons ci ratio: 8.813772e-02	ci left: 8.601960e-02	ci right 9.400006e-02	k: 1799	n:20000
KS ci ratio: 2.097558e-02	ci left: 6.291368e-01	ci right 6.425237e-01	k: 12717	n:20000
PARP14   20000 perm   7 sec   (2778 perm/sec)   p_kst 6.358500e-01   p_cons 8.995000e-02   p_joint 2.363500e-01

Outputting figure to mutsig2_images.part000000000126/PARP14.4_5474_20000_0.63585_0.08995_0.23635.png
                gene_name: PARP14
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.090 
      ci_cons_bounds_left: 0.086 
     ci_cons_bounds_right: 0.094 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 29 percent done.
PCDH15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.967221e-02	ci left: 6.261796e-01	ci right 6.451413e-01	k: 6357	n:10000
Cons ci ratio: 5.730108e-02	ci left: 3.095710e-01	ci right 3.279347e-01	k: 3187	n:10000
KS ci ratio: 1.630117e-02	ci left: 8.454992e-01	ci right 8.594947e-01	k: 8526	n:10000
PCDH15   10000 perm   2 sec   (4274 perm/sec)   p_kst 8.526000e-01   p_cons 3.187000e-01   p_joint 6.357000e-01

Outputting figure to mutsig2_images.part000000000126/PCDH15.4_7659_10000_0.8526_0.3187_0.6357.png
                gene_name: PCDH15
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 43 percent done.
PARN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.787044e-02	ci left: 6.548469e-01	ci right 6.734574e-01	k: 6642	n:10000
Cons ci ratio: 4.617064e-02	ci left: 4.091051e-01	ci right 4.285422e-01	k: 4188	n:10000
KS ci ratio: 4.409049e-02	ci left: 4.316360e-01	ci right 4.511982e-01	k: 4414	n:10000
PARN   10000 perm   2 sec   (6314 perm/sec)   p_kst 4.414000e-01   p_cons 4.188000e-01   p_joint 6.642000e-01

Outputting figure to mutsig2_images.part000000000126/PARN.3_2016_10000_0.4414_0.4188_0.6642.png
                gene_name: PARN
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 57 percent done.
PARK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.075295e-01	ci left: 1.109577e-01	ci right 1.236661e-01	k: 1172	n:10000
Cons ci ratio: 1.158024e-01	ci left: 9.681653e-02	ci right 1.088160e-01	k: 1027	n:10000
KS ci ratio: 1.196764e-02	ci left: 9.091566e-01	ci right 9.202004e-01	k: 9148	n:10000
PARK2   10000 perm   2 sec   (5964 perm/sec)   p_kst 9.148000e-01   p_cons 1.027000e-01   p_joint 1.172000e-01

Joint ci ratio: 2.228831e-02	ci left: 6.004917e-01	ci right 6.140771e-01	k: 12146	n:20000
Cons ci ratio: 8.168708e-02	ci left: 9.901670e-02	ci right 1.074990e-01	k: 2064	n:20000
KS ci ratio: 8.277740e-03	ci left: 9.142646e-01	ci right 9.219133e-01	k: 18363	n:20000
PARK2   20000 perm   4 sec   (5497 perm/sec)   p_kst 9.181500e-01   p_cons 1.032000e-01   p_joint 6.073000e-01

Outputting figure to mutsig2_images.part000000000126/PARK2.2_1446_20000_0.91815_0.1032_0.6073.png
                gene_name: PARK2
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.099 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.61 

Current progress: 71 percent done.
PATZ1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.655452e-03	ci left: 9.767421e-01	ci right 9.823736e-01	k: 9797	n:10000
Cons ci ratio: 2.913638e-02	ci left: 6.346251e-01	ci right 6.534909e-01	k: 6441	n:10000
KS ci ratio: 3.935118e-02	ci left: 4.881520e-01	ci right 5.078491e-01	k: 4980	n:10000
PATZ1   10000 perm   2 sec   (5859 perm/sec)   p_kst 4.980000e-01   p_cons 6.441000e-01   p_joint 9.797000e-01

Outputting figure to mutsig2_images.part000000000126/PATZ1.2_2367_10000_0.498_0.6441_0.9797.png
                gene_name: PATZ1
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 86 percent done.
PAX7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.533935e-02	ci left: 1.376631e-01	ci right 1.515446e-01	k: 1445	n:10000
Cons ci ratio: 1.533912e-01	ci left: 5.658036e-02	ci right 6.607718e-02	k: 612	n:10000
KS ci ratio: 2.287309e-02	ci left: 7.373475e-01	ci right 7.545091e-01	k: 7460	n:10000
PAX7   10000 perm   2 sec   (6167 perm/sec)   p_kst 7.460000e-01   p_cons 6.120000e-02   p_joint 1.445000e-01

Joint ci ratio: 7.029796e-02	ci left: 1.297998e-01	ci right 1.393067e-01	k: 2690	n:20000
Cons ci ratio: 1.114503e-01	ci left: 5.499471e-02	ci right 6.153445e-02	k: 1164	n:20000
KS ci ratio: 1.647478e-02	ci left: 7.328036e-01	ci right 7.450269e-01	k: 14779	n:20000
PAX7   20000 perm   4 sec   (5465 perm/sec)   p_kst 7.389500e-01   p_cons 5.820000e-02   p_joint 1.345000e-01

Joint ci ratio: 6.009826e-02	ci left: 1.204549e-01	ci right 1.279514e-01	k: 3725	n:30000
Cons ci ratio: 9.104098e-02	ci left: 5.554431e-02	ci right 6.087498e-02	k: 1745	n:30000
KS ci ratio: 1.343249e-02	ci left: 7.344937e-01	ci right 7.444599e-01	k: 22185	n:30000
PAX7   30000 perm   6 sec   (5231 perm/sec)   p_kst 7.395000e-01   p_cons 5.816667e-02   p_joint 1.241667e-01

Outputting figure to mutsig2_images.part000000000126/PAX7.2_1715_30000_0.7395_0.058167_0.12417.png
                gene_name: PAX7
               theta_stop: 0.091 
                    nperm: 30000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.058 
      ci_cons_bounds_left: 0.056 
     ci_cons_bounds_right: 0.061 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000126
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 126 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 4398219: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000127> was used as the working directory.
Started at Wed Oct 24 16:15:19 2012
Results reported at Wed Oct 24 16:18:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000127.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000127.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 127  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000127.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    284.48 sec.
    Max Memory :      1502 MB
    Max Swap   :      3964 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
127
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 127
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 127: processing genes 11304 - 11393
Calculating significance of each gene.
Using projection method.
11304	PCDH19	1
11305	PCDH20	1
11306	PCDH7	1
11307	PCDH8	1
11308	PCDH9	1
11309	PCDHA1	1
11310	PCDHA10	2.051669e-01
11311	PCDHA11	1.894104e-01
11312	PCDHA12	8.897880e-02
11313	PCDHA13	1
11314	PCDHA2	1
11315	PCDHA3	1
11316	PCDHA4	1
11317	PCDHA5	1
11318	PCDHA6	1
11319	PCDHA7	1
11320	PCDHA8	1
11321	PCDHA9	1
11322	PCDHAC1	2.938966e-02
11323	PCDHAC2	1
11324	PCDHB1	1
11325	PCDHB10	1
11326	PCDHB11	1
11327	PCDHB12	1
11328	PCDHB13	1
11329	PCDHB14	1.616026e-01
11330	PCDHB15	2.009501e-01
11331	PCDHB16	1
11332	PCDHB2	1.093685e-02
11333	PCDHB3	2.838796e-01
11334	PCDHB4	1
11335	PCDHB5	1
11336	PCDHB6	3.618813e-01
11337	PCDHB7	1
11338	PCDHB8	3.582350e-01
11339	PCDHB9	1
11340	PCDHGA1	1.789916e-01
11341	PCDHGA10	3.497484e-01
11342	PCDHGA11	1
11343	PCDHGA12	9.755768e-02
11344	PCDHGA2	1
11345	PCDHGA3	1
11346	PCDHGA4	1
11347	PCDHGA5	1
11348	PCDHGA6	1
11349	PCDHGA7	1
11350	PCDHGA8	2.447625e-01
11351	PCDHGA9	1
11352	PCDHGB1	1
11353	PCDHGB2	1.091956e-01
11354	PCDHGB3	1
11355	PCDHGB4	1.673054e-01
11356	PCDHGB5	1
11357	PCDHGB6	1
11358	PCDHGB7	1
11359	PCDHGC3	1
11360	PCDHGC4	1
11361	PCDHGC5	1
11362	PCDP1	1
11363	PCF11	3.003643e-01
11364	PCGF1	1
11365	PCGF2	1
11366	PCGF3	1
11367	PCGF5	1
11368	PCGF6	1.007553e-01
11369	PCID2	1
11370	PCIF1	1
11371	PCK1	1
11372	PCK2	1
11373	PCLO	3.060234e-01
11374	PCM1	1
11375	PCMT1	1
11376	PCMTD1	1
11377	PCMTD2	1
11378	PCNA	1
11379	PCNP	5.032082e-02
11380	PCNT	1
11381	PCNX	1
11382	PCNXL2	2.723397e-02
11383	PCNXL3	1
11384	PCOLCE	1
11385	PCOLCE2	1
11386	PCOTH	1
11387	PCP2	2.988703e-02
11388	PCP4	1
11389	PCP4L1	1
11390	PCSK1	1
11391	PCSK2	1
11392	PCSK4	9.809654e-03
11393	PCSK5	1
Done

Running MutSig 2:
Scatter job 127: processing genes 11304 - 11393
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PCLO
Processing conservation and coverage...
64% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.355230e-01	ci left: 7.194552e-02	ci right 8.250234e-02	k: 771	n:10000
Cons ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
KS ci ratio: 1.895761e-01	ci left: 3.710237e-02	ci right 4.496786e-02	k: 409	n:10000
PCLO   10000 perm   5 sec   (2017 perm/sec)   p_kst 4.090000e-02   p_cons 1   p_joint 7.710000e-02

Joint ci ratio: 8.625504e-02	ci left: 8.954852e-02	ci right 9.767008e-02	k: 1871	n:20000
Cons ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
KS ci ratio: 1.347404e-01	ci left: 3.785835e-02	ci right 4.337623e-02	k: 811	n:20000
PCLO   20000 perm   13 sec   (1510 perm/sec)   p_kst 4.055000e-02   p_cons 1   p_joint 9.355000e-02

Joint ci ratio: 8.330529e-02	ci left: 6.586293e-02	ci right 7.162093e-02	k: 2061	n:30000
Cons ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
KS ci ratio: 1.142364e-01	ci left: 3.560529e-02	ci right 3.995148e-02	k: 1132	n:30000
PCLO   30000 perm   19 sec   (1586 perm/sec)   p_kst 3.773333e-02   p_cons 1   p_joint 6.870000e-02

Joint ci ratio: 6.111828e-02	ci left: 9.039283e-02	ci right 9.611638e-02	k: 3729	n:40000
Cons ci ratio: 9.799510e-05	ci left: 9.999078e-01	ci right 1	k: 40000	n:40000
KS ci ratio: 9.936577e-02	ci left: 3.558613e-02	ci right 3.933140e-02	k: 1497	n:40000
PCLO   40000 perm   24 sec   (1656 perm/sec)   p_kst 3.742500e-02   p_cons 1   p_joint 9.322500e-02

Outputting figure to mutsig2_images.part000000000127/PCLO.7_15546_40000_0.037425_1_0.093225.png
                gene_name: PCLO
               theta_stop: 0.099 
                    nperm: 40000 
                     p_ks: 0.037 
        ci_ks_bounds_left: 0.036 
       ci_ks_bounds_right: 0.039 
                   p_cons: 1 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1 
                  p_joint: 0.093 
     ci_joint_bounds_left: 0.090 
    ci_joint_bounds_right: 0.096 

Current progress: 14 percent done.
PCDHGB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.828189e-02	ci left: 3.875906e-01	ci right 4.068693e-01	k: 3972	n:10000
Cons ci ratio: 1.337314e-02	ci left: 8.896462e-01	ci right 9.017222e-01	k: 8958	n:10000
KS ci ratio: 9.251487e-02	ci left: 1.451135e-01	ci right 1.592898e-01	k: 1521	n:10000
PCDHGB2   10000 perm   2 sec   (5055 perm/sec)   p_kst 1.521000e-01   p_cons 8.958000e-01   p_joint 3.972000e-01

Outputting figure to mutsig2_images.part000000000127/PCDHGB2.3_2825_10000_0.1521_0.8958_0.3972.png
                gene_name: PCDHGB2
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.40 
     ci_joint_bounds_left: 0.39 
    ci_joint_bounds_right: 0.41 

Current progress: 29 percent done.
PCNXL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.042473e-02	ci left: 2.871625e-01	ci right 3.051564e-01	k: 2961	n:10000
Cons ci ratio: 8.477335e-03	ci left: 9.511695e-01	ci right 9.593627e-01	k: 9554	n:10000
KS ci ratio: 8.355196e-02	ci left: 1.728091e-01	ci right 1.879776e-01	k: 1803	n:10000
PCNXL2   10000 perm   3 sec   (3815 perm/sec)   p_kst 1.803000e-01   p_cons 9.554000e-01   p_joint 2.961000e-01

Outputting figure to mutsig2_images.part000000000127/PCNXL2.3_6550_10000_0.1803_0.9554_0.2961.png
                gene_name: PCNXL2
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.31 

Current progress: 43 percent done.
PCDHAC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.358403e-02	ci left: 2.665620e-01	ci right 2.841691e-01	k: 2753	n:10000
Cons ci ratio: 1.426573e-01	ci left: 6.517166e-02	ci right 7.528044e-02	k: 701	n:10000
KS ci ratio: 2.351896e-02	ci left: 7.265354e-01	ci right 7.439273e-01	k: 7353	n:10000
PCDHAC1   10000 perm   2 sec   (5586 perm/sec)   p_kst 7.353000e-01   p_cons 7.010000e-02   p_joint 2.753000e-01

Joint ci ratio: 6.208404e-02	ci left: 1.610153e-01	ci right 1.713820e-01	k: 3323	n:20000
Cons ci ratio: 1.037251e-01	ci left: 6.318274e-02	ci right 7.014389e-02	k: 1332	n:20000
KS ci ratio: 1.650894e-02	ci left: 7.319977e-01	ci right 7.442330e-01	k: 14763	n:20000
PCDHAC1   20000 perm   4 sec   (4921 perm/sec)   p_kst 7.381500e-01   p_cons 6.660000e-02   p_joint 1.661500e-01

Joint ci ratio: 5.929244e-02	ci left: 1.233833e-01	ci right 1.309557e-01	k: 3814	n:30000
Cons ci ratio: 8.483965e-02	ci left: 6.360800e-02	ci right 6.927632e-02	k: 1992	n:30000
KS ci ratio: 1.351965e-02	ci left: 7.319786e-01	ci right 7.419755e-01	k: 22110	n:30000
PCDHAC1   30000 perm   6 sec   (4659 perm/sec)   p_kst 7.370000e-01   p_cons 6.640000e-02   p_joint 1.271333e-01

Outputting figure to mutsig2_images.part000000000127/PCDHAC1.2_2932_30000_0.737_0.0664_0.12713.png
                gene_name: PCDHAC1
               theta_stop: 0.085 
                    nperm: 30000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.066 
      ci_cons_bounds_left: 0.064 
     ci_cons_bounds_right: 0.069 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 57 percent done.
PCDHB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.607020e-03	ci left: 9.897211e-01	ci right 9.933838e-01	k: 9917	n:10000
KS ci ratio: 3.968308e-02	ci left: 4.839539e-01	ci right 5.036497e-01	k: 4938	n:10000
PCDHB2   10000 perm   2 sec   (5728 perm/sec)   p_kst 4.938000e-01   p_cons 9.917000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000127/PCDHB2.2_2401_10000_0.4938_0.9917_1.png
                gene_name: PCDHB2
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
PCDHGA12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.995533e-02	ci left: 3.714676e-01	ci right 3.906018e-01	k: 3810	n:10000
Cons ci ratio: 2.779552e-02	ci left: 6.560548e-01	ci right 6.746488e-01	k: 6654	n:10000
KS ci ratio: 7.644396e-02	ci left: 2.001794e-01	ci right 2.161909e-01	k: 2081	n:10000
PCDHGA12   10000 perm   2 sec   (5166 perm/sec)   p_kst 2.081000e-01   p_cons 6.654000e-01   p_joint 3.810000e-01

Outputting figure to mutsig2_images.part000000000127/PCDHGA12.2_2852_10000_0.2081_0.6654_0.381.png
                gene_name: PCDHGA12
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.67 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 86 percent done.
PCSK4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.752183e-02	ci left: 8.260517e-01	ci right 8.407535e-01	k: 8335	n:10000
KS ci ratio: 4.200647e-02	ci left: 4.555849e-01	ci right 4.752352e-01	k: 4654	n:10000
PCSK4   10000 perm   2 sec   (5852 perm/sec)   p_kst 4.654000e-01   p_cons 8.335000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000127/PCSK4.2_2328_10000_0.4654_0.8335_1.png
                gene_name: PCSK4
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000127
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 127 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 4398222: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000128> was used as the working directory.
Started at Wed Oct 24 16:15:22 2012
Results reported at Wed Oct 24 16:17:55 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000128.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000128.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 128  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000128.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    175.84 sec.
    Max Memory :      1500 MB
    Max Swap   :      3927 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
128
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 128
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 128: processing genes 11394 - 11483
Calculating significance of each gene.
Using projection method.
11394	PCSK6	3.514334e-01
11395	PCSK7	1
11396	PCSK9	1
11397	PCTP	1
11398	PCYOX1	1.994708e-01
11399	PCYOX1L	1
11400	PCYT1A	1.933842e-01
11401	PCYT1B	1.156463e-01
11402	PCYT2	1
11403	PDAP1	1
11404	PDC	1
11405	PDCD1	1
11406	PDCD10	1
11407	PDCD11	1.400603e-01
11408	PDCD1LG2	1
11409	PDCD2	1
11410	PDCD2L	1
11411	PDCD4	1
11412	PDCD5	1
11413	PDCD6	1
11414	PDCD6IP	2.241825e-01
11415	PDCD7	1
11416	PDCL	1
11417	PDCL2	1
11418	PDCL3	1
11419	PDDC1	1
11420	PDE10A	1
11421	PDE11A	6.993784e-02
11422	PDE12	1
11423	PDE1A	1
11424	PDE1B	1
11425	PDE1C	8.307240e-03
11426	PDE2A	1
11427	PDE3A	2.490020e-02
11428	PDE3B	1
11429	PDE4A	2.403432e-01
11430	PDE4B	2.540968e-01
11431	PDE4C	1
11432	PDE4D	1
11433	PDE4DIP	5.421486e-01
11434	PDE5A	1
11435	PDE6A	1
11436	PDE6B	1
11437	PDE6C	1
11438	PDE6D	1
11439	PDE6G	1
11440	PDE6H	1
11441	PDE7A	1
11442	PDE7B	1
11443	PDE8A	1
11444	PDE8B	1
11445	PDE9A	1
11446	PDGFA	1
11447	PDGFB	1
11448	PDGFC	3.326262e-03
11449	PDGFD	6.210774e-02
11450	PDGFRA	1
11451	PDGFRB	2.343354e-01
11452	PDGFRL	1
11453	PDHA1	1
11454	PDHA2	2.341180e-02
11455	PDHB	1
11456	PDHX	1
11457	PDIA2	1
11458	PDIA3	1
11459	PDIA4	1
11460	PDIA5	1
11461	PDIA6	1
11462	PDIK1L	1
11463	PDILT	1
11464	PDK1	1.195362e-01
11465	PDK2	1
11466	PDK3	1
11467	PDK4	7.529267e-02
11468	PDLIM1	1
11469	PDLIM2	1
11470	PDLIM3	1
11471	PDLIM4	1
11472	PDLIM5	1.918570e-01
11473	PDLIM7	1
11474	PDP1	1
11475	PDP2	1.546982e-01
11476	PDPK1	1
11477	PDPN	1
11478	PDPR	2.977216e-02
11479	PDRG1	1
11480	PDS5A	4.379375e-01
11481	PDS5B	1
11482	PDSS1	1
11483	PDSS2	1.659433e-01
Done

Running MutSig 2:
Scatter job 128: processing genes 11394 - 11483
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PDE4DIP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.494614e-02	ci left: 2.066861e-01	ci right 2.228804e-01	k: 2147	n:10000
Cons ci ratio: 7.735548e-03	ci left: 9.586940e-01	ci right 9.662336e-01	k: 9626	n:10000
KS ci ratio: 1.075815e-01	ci left: 1.108601e-01	ci right 1.235638e-01	k: 1171	n:10000
PDE4DIP   10000 perm   2 sec   (4092 perm/sec)   p_kst 1.171000e-01   p_cons 9.626000e-01   p_joint 2.147000e-01

Joint ci ratio: 5.153164e-02	ci left: 2.185840e-01	ci right 2.301962e-01	k: 4487	n:20000
Cons ci ratio: 5.405812e-03	ci left: 9.607043e-01	ci right 9.659599e-01	k: 19268	n:20000
KS ci ratio: 7.513209e-02	ci left: 1.152809e-01	ci right 1.243300e-01	k: 2395	n:20000
PDE4DIP   20000 perm   7 sec   (2789 perm/sec)   p_kst 1.197500e-01   p_cons 9.634000e-01   p_joint 2.243500e-01

Outputting figure to mutsig2_images.part000000000128/PDE4DIP.4_8813_20000_0.11975_0.9634_0.22435.png
                gene_name: PDE4DIP
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 14 percent done.
PDCD11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.366282e-02	ci left: 5.657417e-01	ci right 5.852143e-01	k: 5755	n:10000
Cons ci ratio: 7.056164e-03	ci left: 9.650977e-01	ci right 9.720258e-01	k: 9687	n:10000
KS ci ratio: 6.550165e-02	ci left: 2.549845e-01	ci right 2.723533e-01	k: 2636	n:10000
PDCD11   10000 perm   2 sec   (4828 perm/sec)   p_kst 2.636000e-01   p_cons 9.687000e-01   p_joint 5.755000e-01

Outputting figure to mutsig2_images.part000000000128/PDCD11.2_5756_10000_0.2636_0.9687_0.5755.png
                gene_name: PDCD11
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 29 percent done.
PDE11A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 8.069985e-02	ci left: 1.831396e-01	ci right 1.986409e-01	k: 1908	n:10000
KS ci ratio: 2.972347e-02	ci left: 6.253754e-01	ci right 6.443460e-01	k: 6349	n:10000
PDE11A   10000 perm   2 sec   (5926 perm/sec)   p_kst 6.349000e-01   p_cons 1.908000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000128/PDE11A.2_3048_10000_0.6349_0.1908_1.png
                gene_name: PDE11A
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 43 percent done.
PDE1C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.221246e-02	ci left: 2.193138e-01	ci right 2.358452e-01	k: 2275	n:10000
Cons ci ratio: 1.175954e-01	ci left: 9.408985e-02	ci right 1.059443e-01	k: 999	n:10000
KS ci ratio: 8.738921e-02	ci left: 1.601305e-01	ci right 1.748638e-01	k: 1674	n:10000
PDE1C   10000 perm   2 sec   (5916 perm/sec)   p_kst 1.674000e-01   p_cons 9.990000e-02   p_joint 2.275000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 8.168708e-02	ci left: 9.901670e-02	ci right 1.074990e-01	k: 2064	n:20000
KS ci ratio: 6.125707e-02	ci left: 1.647186e-01	ci right 1.751776e-01	k: 3398	n:20000
PDE1C   20000 perm   4 sec   (5206 perm/sec)   p_kst 1.699000e-01   p_cons 1.032000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000128/PDE1C.2_1973_20000_0.1699_0.1032_1.png
                gene_name: PDE1C
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.099 
     ci_cons_bounds_right: 0.11 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 57 percent done.
PDE3A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.992472e-02	ci left: 7.866480e-01	ci right 8.025800e-01	k: 7947	n:10000
KS ci ratio: 6.138026e-02	ci left: 2.807224e-01	ci right 2.986003e-01	k: 2896	n:10000
PDE3A   10000 perm   2 sec   (5444 perm/sec)   p_kst 2.896000e-01   p_cons 7.947000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000128/PDE3A.2_3490_10000_0.2896_0.7947_1.png
                gene_name: PDE3A
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
PDGFC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.181211e-01	ci left: 9.331107e-02	ci right 1.051236e-01	k: 991	n:10000
Cons ci ratio: 2.138699e-01	ci left: 2.901644e-02	ci right 3.605933e-02	k: 324	n:10000
KS ci ratio: 4.022656e-02	ci left: 4.771585e-01	ci right 4.968491e-01	k: 4870	n:10000
PDGFC   10000 perm   2 sec   (6622 perm/sec)   p_kst 4.870000e-01   p_cons 3.240000e-02   p_joint 9.910000e-02

Joint ci ratio: 7.129614e-02	ci left: 1.265990e-01	ci right 1.360085e-01	k: 2625	n:20000
Cons ci ratio: 1.503973e-01	ci left: 3.037464e-02	ci right 3.536238e-02	k: 656	n:20000
KS ci ratio: 2.846946e-02	ci left: 4.796503e-01	ci right 4.935536e-01	k: 9732	n:20000
PDGFC   20000 perm   3 sec   (5783 perm/sec)   p_kst 4.866000e-01   p_cons 3.280000e-02   p_joint 1.312500e-01

Joint ci ratio: 5.830715e-02	ci left: 1.271025e-01	ci right 1.347692e-01	k: 3927	n:30000
Cons ci ratio: 1.236128e-01	ci left: 3.042513e-02	ci right 3.446608e-02	k: 972	n:30000
KS ci ratio: 2.330949e-02	ci left: 4.795629e-01	ci right 4.909067e-01	k: 14557	n:30000
PDGFC   30000 perm   5 sec   (5523 perm/sec)   p_kst 4.852333e-01   p_cons 3.240000e-02   p_joint 1.309000e-01

Joint ci ratio: 5.109413e-02	ci left: 1.249878e-01	ci right 1.315662e-01	k: 5130	n:40000
Cons ci ratio: 1.097172e-01	ci left: 2.922580e-02	ci right 3.264275e-02	k: 1236	n:40000
KS ci ratio: 2.029256e-02	ci left: 4.777170e-01	ci right 4.875356e-01	k: 19305	n:40000
PDGFC   40000 perm   7 sec   (5348 perm/sec)   p_kst 4.826250e-01   p_cons 3.090000e-02   p_joint 1.282500e-01

Joint ci ratio: 5.479241e-02	ci left: 9.030995e-02	ci right 9.541743e-02	k: 4642	n:50000
Cons ci ratio: 9.820806e-02	ci left: 2.936144e-02	ci right 3.241334e-02	k: 1543	n:50000
KS ci ratio: 1.815563e-02	ci left: 4.780912e-01	ci right 4.868708e-01	k: 24124	n:50000
PDGFC   50000 perm   10 sec   (5208 perm/sec)   p_kst 4.824800e-01   p_cons 3.086000e-02   p_joint 9.284000e-02

Outputting figure to mutsig2_images.part000000000128/PDGFC.2_1062_50000_0.48248_0.03086_0.09284.png
                gene_name: PDGFC
               theta_stop: 0.098 
                    nperm: 50000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.031 
      ci_cons_bounds_left: 0.029 
     ci_cons_bounds_right: 0.032 
                  p_joint: 0.093 
     ci_joint_bounds_left: 0.090 
    ci_joint_bounds_right: 0.095 

Current progress: 86 percent done.
PDPR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.743772e-01	ci left: 4.389243e-02	ci right 5.237330e-02	k: 480	n:10000
Cons ci ratio: 2.166412e-01	ci left: 2.825837e-02	ci right 3.521793e-02	k: 316	n:10000
KS ci ratio: 5.747302e-02	ci left: 3.082813e-01	ci right 3.266251e-01	k: 3174	n:10000
PDPR   10000 perm   2 sec   (5984 perm/sec)   p_kst 3.174000e-01   p_cons 3.160000e-02   p_joint 4.800000e-02

Joint ci ratio: 1.357013e-01	ci left: 3.732625e-02	ci right 4.280850e-02	k: 800	n:20000
Cons ci ratio: 1.495754e-01	ci left: 3.071190e-02	ci right 3.572501e-02	k: 663	n:20000
KS ci ratio: 4.076656e-02	ci left: 3.096583e-01	ci right 3.225952e-01	k: 6322	n:20000
PDPR   20000 perm   4 sec   (5329 perm/sec)   p_kst 3.161000e-01   p_cons 3.315000e-02   p_joint 4.000000e-02

Joint ci ratio: 1.259045e-01	ci left: 2.932611e-02	ci right 3.329867e-02	k: 938	n:30000
Cons ci ratio: 1.221922e-01	ci left: 3.113662e-02	ci right 3.522111e-02	k: 994	n:30000
KS ci ratio: 3.324861e-02	ci left: 3.113377e-01	ci right 3.218978e-01	k: 9498	n:30000
PDPR   30000 perm   6 sec   (5097 perm/sec)   p_kst 3.166000e-01   p_cons 3.313333e-02   p_joint 3.126667e-02

Joint ci ratio: 1.172691e-01	ci left: 2.557923e-02	ci right 2.878991e-02	k: 1086	n:40000
Cons ci ratio: 1.054390e-01	ci left: 3.163626e-02	ci right 3.518190e-02	k: 1335	n:40000
KS ci ratio: 2.881468e-02	ci left: 3.117437e-01	ci right 3.208829e-01	k: 12652	n:40000
PDPR   40000 perm   8 sec   (4935 perm/sec)   p_kst 3.163000e-01   p_cons 3.337500e-02   p_joint 2.715000e-02

Joint ci ratio: 1.046418e-01	ci left: 2.586966e-02	ci right 2.874558e-02	k: 1364	n:50000
Cons ci ratio: 9.501634e-02	ci left: 3.135367e-02	ci right 3.450086e-02	k: 1645	n:50000
KS ci ratio: 2.580037e-02	ci left: 3.117663e-01	ci right 3.199351e-01	k: 15792	n:50000
PDPR   50000 perm   10 sec   (4807 perm/sec)   p_kst 3.158400e-01   p_cons 3.290000e-02   p_joint 2.728000e-02

Joint ci ratio: 9.662172e-02	ci left: 2.540844e-02	ci right 2.800428e-02	k: 1601	n:60000
Cons ci ratio: 8.669695e-02	ci left: 3.151966e-02	ci right 3.439242e-02	k: 1976	n:60000
KS ci ratio: 2.353934e-02	ci left: 3.123637e-01	ci right 3.198208e-01	k: 18965	n:60000
PDPR   60000 perm   13 sec   (4700 perm/sec)   p_kst 3.160833e-01   p_cons 3.293333e-02   p_joint 2.668333e-02

Outputting figure to mutsig2_images.part000000000128/PDPR.2_2708_60000_0.31608_0.032933_0.026683.png
                gene_name: PDPR
               theta_stop: 0.097 
                    nperm: 60000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.033 
      ci_cons_bounds_left: 0.032 
     ci_cons_bounds_right: 0.034 
                  p_joint: 0.027 
     ci_joint_bounds_left: 0.025 
    ci_joint_bounds_right: 0.028 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000128
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 128 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4398225: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000129> was used as the working directory.
Started at Wed Oct 24 16:15:22 2012
Results reported at Wed Oct 24 16:17:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000129.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000129.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 129  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000129.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     78.15 sec.
    Max Memory :       689 MB
    Max Swap   :      3507 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
129
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 129
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 129: processing genes 11484 - 11573
Calculating significance of each gene.
Using projection method.
11484	PDX1	1
11485	PDXDC1	1
11486	PDXK	1
11487	PDXP	1
11488	PDYN	1
11489	PDZD11	1
11490	PDZD2	4.052296e-01
11491	PDZD3	1.984191e-01
11492	PDZD4	3.217573e-01
11493	PDZD7	1
11494	PDZD8	1
11495	PDZD9	1
11496	PDZK1	1
11497	PDZK1IP1	1
11498	PDZRN3	1
11499	PDZRN4	1
11500	PEA15	1
11501	PEAR1	1
11502	PEBP1	1
11503	PEBP4	1
11504	PECAM1	1
11505	PECI	1
11506	PECR	1
11507	PEF1	1
11508	PEG10	1
11509	PEG3	1
11510	PELI1	1
11511	PELI2	1
11512	PELI3	1.805262e-02
11513	PELO	1.211365e-01
11514	PELP1	1
11515	PEMT	1
11516	PENK	1
11517	PEPD	1
11518	PER1	1
11519	PER2	2.402318e-01
11520	PER3	4.982815e-01
11521	PERP	1.019277e-01
11522	PES1	2.363546e-01
11523	PET112L	1
11524	PEX1	4.973849e-01
11525	PEX10	1
11526	PEX11A	1
11527	PEX11B	1
11528	PEX11G	1
11529	PEX12	8.907087e-02
11530	PEX13	1
11531	PEX14	1
11532	PEX16	1
11533	PEX19	1.656362e-01
11534	PEX2	1
11535	PEX26	1
11536	PEX3	1
11537	PEX5	1
11538	PEX5L	8.541295e-03
11539	PEX6	1
11540	PEX7	1
11541	PF4	1
11542	PF4V1	1
11543	PFAS	3.486322e-01
11544	PFDN1	1
11545	PFDN2	1
11546	PFDN4	1
11547	PFDN5	1
11548	PFDN6	4.387793e-02
11549	PFKFB1	1
11550	PFKFB2	1
11551	PFKFB3	1
11552	PFKFB4	1
11553	PFKL	1
11554	PFKM	1
11555	PFKP	1
11556	PFN1	1
11557	PFN2	1
11558	PFN3	1
11559	PFN4	1
11560	PGA3	1
11561	PGA5	1
11562	PGAM1	8.599856e-02
11563	PGAM2	1
11564	PGAM4	1
11565	PGAM5	1
11566	PGAP1	1
11567	PGAP2	1
11568	PGAP3	6.304725e-02
11569	PGBD1	2.512344e-01
11570	PGBD2	1
11571	PGBD3	1
11572	PGBD4	1
11573	PGBD5	2.258810e-01
Done

Running MutSig 2:
Scatter job 129: processing genes 11484 - 11573
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PDZD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.004673e-02	ci left: 7.846201e-01	ci right 8.006090e-01	k: 7927	n:10000
KS ci ratio: 3.928043e-02	ci left: 4.890517e-01	ci right 5.087489e-01	k: 4989	n:10000
PDZD2   10000 perm   3 sec   (3575 perm/sec)   p_kst 4.989000e-01   p_cons 7.927000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000129/PDZD2.2_8616_10000_0.4989_0.7927_1.png
                gene_name: PDZD2
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
PELI3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.037083e-02	ci left: 3.675878e-01	ci right 3.866839e-01	k: 3771	n:10000
Cons ci ratio: 3.676153e-02	ci left: 5.221621e-01	ci right 5.418192e-01	k: 5320	n:10000
KS ci ratio: 5.763252e-02	ci left: 3.070909e-01	ci right 3.254162e-01	k: 3162	n:10000
PELI3   10000 perm   1 sec   (7673 perm/sec)   p_kst 3.162000e-01   p_cons 5.320000e-01   p_joint 3.771000e-01

Outputting figure to mutsig2_images.part000000000129/PELI3.2_1438_10000_0.3162_0.532_0.3771.png
                gene_name: PELI3
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 67 percent done.
PEX5L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.056855e-03	ci left: 9.449215e-01	ci right 9.536144e-01	k: 9494	n:10000
Cons ci ratio: 3.344976e-02	ci left: 5.688503e-01	ci right 5.883039e-01	k: 5786	n:10000
KS ci ratio: 2.188344e-02	ci left: 7.539324e-01	ci right 7.707145e-01	k: 7624	n:10000
PEX5L   10000 perm   1 sec   (7219 perm/sec)   p_kst 7.624000e-01   p_cons 5.786000e-01   p_joint 9.494000e-01

Outputting figure to mutsig2_images.part000000000129/PEX5L.2_1941_10000_0.7624_0.5786_0.9494.png
                gene_name: PEX5L
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000129
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 129 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1555>
Subject: Job 4398228: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1555>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000130> was used as the working directory.
Started at Wed Oct 24 16:15:24 2012
Results reported at Wed Oct 24 16:18:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000130.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000130.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 130  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000130.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    194.30 sec.
    Max Memory :      1485 MB
    Max Swap   :      4053 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
130
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 130
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 130: processing genes 11574 - 11662
Calculating significance of each gene.
Using projection method.
11574	PGC	1
11575	PGCP	1
11576	PGD	2.474984e-01
11577	PGF	1
11578	PGGT1B	1
11579	PGK1	1
11580	PGK2	1
11581	PGLS	1
11582	PGLYRP1	1
11583	PGLYRP2	1
11584	PGLYRP3	1
11585	PGLYRP4	1
11586	PGM1	1
11587	PGM2	1
11588	PGM2L1	1
11589	PGM3	1
11590	PGM5	1
11591	PGP	1
11592	PGPEP1	1
11593	PGPEP1L	1
11594	PGR	1
11595	PGRMC1	1
11596	PGRMC2	1
11597	PGS1	1
11598	PHACTR1	1
11599	PHACTR2	3.094939e-01
11600	PHACTR3	1
11601	PHACTR4	1
11602	PHAX	1
11603	PHB	1
11604	PHB2	1
11605	PHC1	8.894876e-02
11606	PHC2	7.550717e-02
11607	PHC3	1
11608	PHEX	2.395431e-01
11609	PHF1	1
11610	PHF10	1
11611	PHF11	6.636563e-02
11612	PHF12	2.252174e-02
11613	PHF13	1
11614	PHF14	1
11615	PHF15	3.392406e-01
11616	PHF16	3.119240e-01
11617	PHF17	3.257966e-01
11618	PHF19	1
11619	PHF2	2.814361e-01
11620	PHF20	1
11621	PHF20L1	1
11622	PHF21A	1.357301e-01
11623	PHF21B	1
11624	PHF23	1
11625	PHF3	2.913736e-01
11626	PHF5A	1
11627	PHF6	2.779414e-02
11628	PHF7	1
11629	PHF8	3.066992e-01
11630	PHGDH	1
11631	PHIP	4.041397e-01
11632	PHKA1	4.915890e-02
11633	PHKA2	2.558608e-01
11634	PHKB	1
11635	PHKG1	1
11636	PHKG2	1.282356e-01
11637	PHLDA1	1
11638	PHLDA2	1
11639	PHLDA3	1
11640	PHLDB1	3.490231e-01
11641	PHLDB2	1
11642	PHLDB3	3.580408e-03
11643	PHLPP1	1
11644	PHLPP2	1
11645	PHOSPHO2	1
11646	PHOX2B	1
11647	PHPT1	1
11648	PHRF1	1
11649	PHTF1	1
11650	PHTF2	1
11651	PHYH	1
11652	PHYHD1	1
11653	PHYHIP	1
11654	PHYHIPL	1
11655	PI15	1
11656	PI16	1
11657	PI3	1
11658	PI4K2A	1
11659	PI4K2B	1
11660	PI4KA	4.755319e-01
11661	PI4KB	1
11662	PIAS1	1
Done

Running MutSig 2:
Scatter job 130: processing genes 11574 - 11662
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PHEX
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.300583e-02	ci left: 7.351239e-01	ci right 7.523339e-01	k: 7438	n:10000
KS ci ratio: 1.315740e-02	ci left: 8.927222e-01	ci right 9.046444e-01	k: 8988	n:10000
PHEX   10000 perm   2 sec   (5677 perm/sec)   p_kst 8.988000e-01   p_cons 7.438000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000130/PHEX.2_2338_10000_0.8988_0.7438_1.png
                gene_name: PHEX
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.75 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 20 percent done.
PHF12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.751719e-02	ci left: 2.435138e-01	ci right 2.606309e-01	k: 2520	n:10000
Cons ci ratio: 3.255939e-02	ci left: 5.819908e-01	ci right 6.013557e-01	k: 5917	n:10000
KS ci ratio: 2.142107e-01	ci left: 2.892165e-02	ci right 3.595419e-02	k: 323	n:10000
PHF12   10000 perm   2 sec   (5404 perm/sec)   p_kst 3.230000e-02   p_cons 5.917000e-01   p_joint 2.520000e-01

Joint ci ratio: 4.455887e-02	ci left: 2.727419e-01	ci right 2.852224e-01	k: 5579	n:20000
Cons ci ratio: 2.365394e-02	ci left: 5.717206e-01	ci right 5.854565e-01	k: 11572	n:20000
KS ci ratio: 1.492271e-01	ci left: 3.085647e-02	ci right 3.588039e-02	k: 666	n:20000
PHF12   20000 perm   4 sec   (4809 perm/sec)   p_kst 3.330000e-02   p_cons 5.786000e-01   p_joint 2.789500e-01

Joint ci ratio: 2.731670e-02	ci left: 4.014334e-01	ci right 4.125846e-01	k: 12210	n:30000
Cons ci ratio: 1.938115e-02	ci left: 5.712855e-01	ci right 5.824996e-01	k: 17307	n:30000
KS ci ratio: 1.240085e-01	ci left: 3.023114e-02	ci right 3.426011e-02	k: 966	n:30000
PHF12   30000 perm   7 sec   (4603 perm/sec)   p_kst 3.220000e-02   p_cons 5.769000e-01   p_joint 4.070000e-01

Joint ci ratio: 3.848250e-02	ci left: 2.019960e-01	ci right 2.099468e-01	k: 8238	n:40000
Cons ci ratio: 1.681225e-02	ci left: 5.712393e-01	ci right 5.809497e-01	k: 23044	n:40000
KS ci ratio: 1.093076e-01	ci left: 2.944481e-02	ci right 3.287370e-02	k: 1245	n:40000
PHF12   40000 perm   9 sec   (4449 perm/sec)   p_kst 3.112500e-02   p_cons 5.761000e-01   p_joint 2.059500e-01

Joint ci ratio: 3.466319e-02	ci left: 2.001374e-01	ci right 2.072171e-01	k: 10183	n:50000
Cons ci ratio: 1.501466e-02	ci left: 5.724951e-01	ci right 5.811760e-01	k: 28842	n:50000
KS ci ratio: 9.791398e-02	ci left: 2.953716e-02	ci right 3.259761e-02	k: 1552	n:50000
PHF12   50000 perm   12 sec   (4332 perm/sec)   p_kst 3.104000e-02   p_cons 5.768400e-01   p_joint 2.036600e-01

Outputting figure to mutsig2_images.part000000000130/PHF12.2_3101_50000_0.03104_0.57684_0.20366.png
                gene_name: PHF12
               theta_stop: 0.098 
                    nperm: 50000 
                     p_ks: 0.031 
        ci_ks_bounds_left: 0.030 
       ci_ks_bounds_right: 0.033 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

Current progress: 40 percent done.
PHKA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.983253e-02	ci left: 6.236666e-01	ci right 6.426558e-01	k: 6332	n:10000
KS ci ratio: 1.236221e-02	ci left: 9.038097e-01	ci right 9.151504e-01	k: 9096	n:10000
PHKA1   10000 perm   2 sec   (5279 perm/sec)   p_kst 9.096000e-01   p_cons 6.332000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000130/PHKA1.2_3800_10000_0.9096_0.6332_1.png
                gene_name: PHKA1
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
PHLDB3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.592170e-02	ci left: 1.361934e-01	ci right 1.500152e-01	k: 1430	n:10000
Cons ci ratio: 6.417870e-02	ci left: 2.628999e-01	ci right 2.804333e-01	k: 2716	n:10000
KS ci ratio: 1.118988e-01	ci left: 1.031515e-01	ci right 1.154771e-01	k: 1092	n:10000
PHLDB3   10000 perm   2 sec   (6015 perm/sec)   p_kst 1.092000e-01   p_cons 2.716000e-01   p_joint 1.430000e-01

Joint ci ratio: 5.877315e-02	ci left: 1.765752e-01	ci right 1.873174e-01	k: 3638	n:20000
Cons ci ratio: 4.367306e-02	ci left: 2.808364e-01	ci right 2.934256e-01	k: 5742	n:20000
KS ci ratio: 7.822483e-02	ci left: 1.071696e-01	ci right 1.159437e-01	k: 2230	n:20000
PHLDB3   20000 perm   4 sec   (5293 perm/sec)   p_kst 1.115000e-01   p_cons 2.871000e-01   p_joint 1.819000e-01

Outputting figure to mutsig2_images.part000000000130/PHLDB3.2_1983_20000_0.1115_0.2871_0.1819.png
                gene_name: PHLDB3
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 80 percent done.
PHRF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.434992e-02	ci left: 1.402112e-01	ci right 1.541950e-01	k: 1471	n:10000
Cons ci ratio: 1.366775e-01	ci left: 7.078334e-02	ci right 8.126524e-02	k: 759	n:10000
KS ci ratio: 2.972347e-02	ci left: 6.253754e-01	ci right 6.443460e-01	k: 6349	n:10000
PHRF1   10000 perm   2 sec   (4768 perm/sec)   p_kst 6.349000e-01   p_cons 7.590000e-02   p_joint 1.471000e-01

Joint ci ratio: 7.013243e-02	ci left: 1.303416e-01	ci right 1.398648e-01	k: 2701	n:20000
Cons ci ratio: 9.486915e-02	ci left: 7.490680e-02	ci right 8.241624e-02	k: 1572	n:20000
KS ci ratio: 2.112301e-02	ci left: 6.258747e-01	ci right 6.392867e-01	k: 12652	n:20000
PHRF1   20000 perm   5 sec   (4263 perm/sec)   p_kst 6.326000e-01   p_cons 7.860000e-02   p_joint 1.350500e-01

Outputting figure to mutsig2_images.part000000000130/PHRF1.2_5015_20000_0.6326_0.0786_0.13505.png
                gene_name: PHRF1
               theta_stop: 0.095 
                    nperm: 20000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.079 
      ci_cons_bounds_left: 0.075 
     ci_cons_bounds_right: 0.082 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000130
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 130 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1429>
Subject: Job 4398230: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1429>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000131> was used as the working directory.
Started at Wed Oct 24 16:15:24 2012
Results reported at Wed Oct 24 19:41:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000131.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000131.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 131  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000131.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :  13204.41 sec.
    Max Memory :      5751 MB
    Max Swap   :      8238 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
131
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 131
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 131: processing genes 11663 - 11752
Calculating significance of each gene.
Using projection method.
11663	PIAS2	9.289252e-02
11664	PIAS3	3.016892e-01
11665	PIAS4	1
11666	PIBF1	1
11667	PICALM	1
11668	PICK1	1
11669	PID1	1
11670	PIF1	1
11671	PIGA	1.011288e-01
11672	PIGB	1
11673	PIGC	1
11674	PIGF	1
11675	PIGG	1
11676	PIGH	1
11677	PIGK	1
11678	PIGL	1
11679	PIGM	1
11680	PIGN	1.373439e-01
11681	PIGO	1
11682	PIGP	1
11683	PIGQ	1
11684	PIGR	1
11685	PIGS	1
11686	PIGT	1
11687	PIGU	1
11688	PIGV	1
11689	PIGW	1
11690	PIGX	1
11691	PIGY	1
11692	PIGZ	1
11693	PIH1D1	1
11694	PIH1D2	1
11695	PIK3AP1	2.674338e-01
11696	PIK3C2A	1
11697	PIK3C2B	3.620659e-01
11698	PIK3C2G	1.336178e-01
11699	PIK3C3	1.677605e-02
11700	PIK3CA	1.046509e-08
11701	PIK3CB	1
11702	PIK3CD	3.440487e-01
11703	PIK3CG	2.345687e-01
11704	PIK3IP1	1
11705	PIK3R1	1.009414e-01
11706	PIK3R2	1
11707	PIK3R3	1
11708	PIK3R4	2.562227e-01
11709	PIK3R5	1
11710	PIK3R6	1
11711	PIKFYVE	1
11712	PILRA	1
11713	PILRB	1
11714	PIM1	1
11715	PIM2	1
11716	PIM3	1
11717	PIN1	1
11718	PIN4	1
11719	PINK1	1
11720	PINX1	1
11721	PION	1.059247e-01
11722	PIP	1
11723	PIP4K2A	1
11724	PIP4K2B	1
11725	PIP4K2C	1
11726	PIP5K1A	1
11727	PIP5K1B	1
11728	PIP5K1C	1
11729	PIP5KL1	1
11730	PIPOX	1
11731	PIR	1
11732	PIRT	1
11733	PISD	1
11734	PITPNA	3.110711e-02
11735	PITPNB	1
11736	PITPNC1	1
11737	PITPNM1	1
11738	PITPNM2	1
11739	PITPNM3	1.282940e-01
11740	PITRM1	3.858136e-01
11741	PITX1	1
11742	PITX2	4.942296e-02
11743	PITX3	1.523029e-02
11744	PIWIL1	1.254283e-02
11745	PIWIL2	1
11746	PIWIL3	2.519802e-01
11747	PIWIL4	1.559941e-02
11748	PJA1	1.051670e-01
11749	PJA2	1
11750	PKD1	4.175388e-01
11751	PKD1L1	2.886340e-01
11752	PKD1L2	4.220846e-01
Done

Running MutSig 2:
Scatter job 131: processing genes 11663 - 11752
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PIK3CA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919608e+00	ci left: 0	ci right 3.688199e-04	k: 0	n:10000
Cons ci ratio: 4.846095e-01	ci left: 4.932166e-03	ci right 8.165407e-03	k: 64	n:10000
KS ci ratio: 2.771443e+00	ci left: 2.531778e-06	ci right 5.570370e-04	k: 1	n:10000
PIK3CA   10000 perm   2 sec   (4603 perm/sec)   p_kst 1.000000e-04   p_cons 6.400000e-03   p_joint 0

Joint ci ratio: 3.919804e+00	ci left: 0	ci right 1.844270e-04	k: 0	n:20000
Cons ci ratio: 3.538073e-01	ci left: 5.022594e-03	ci right 7.224712e-03	k: 121	n:20000
KS ci ratio: 2.771651e+00	ci left: 1.265890e-06	ci right 2.785503e-04	k: 1	n:20000
PIK3CA   20000 perm   8 sec   (2630 perm/sec)   p_kst 5.000000e-05   p_cons 6.050000e-03   p_joint 0

Joint ci ratio: 3.919869e+00	ci left: 0	ci right 1.229551e-04	k: 0	n:30000
Cons ci ratio: 2.896822e-01	ci left: 5.188478e-03	ci right 6.975876e-03	k: 181	n:30000
KS ci ratio: 2.771720e+00	ci left: 8.439266e-07	ci right 1.857073e-04	k: 1	n:30000
PIK3CA   30000 perm   10 sec   (2937 perm/sec)   p_kst 3.333333e-05   p_cons 6.033333e-03   p_joint 0

Joint ci ratio: 3.919902e+00	ci left: 0	ci right 9.221773e-05	k: 0	n:40000
Cons ci ratio: 2.481443e-01	ci left: 5.430825e-03	ci right 6.992166e-03	k: 247	n:40000
KS ci ratio: 2.771755e+00	ci left: 6.329450e-07	ci right 1.392831e-04	k: 1	n:40000
PIK3CA   40000 perm   13 sec   (3114 perm/sec)   p_kst 2.500000e-05   p_cons 6.175000e-03   p_joint 0

Joint ci ratio: 3.919922e+00	ci left: 0	ci right 7.377487e-05	k: 0	n:50000
Cons ci ratio: 2.245125e-01	ci left: 5.379655e-03	ci right 6.758638e-03	k: 302	n:50000
KS ci ratio: 2.771775e+00	ci left: 5.063560e-07	ci right 1.114278e-04	k: 1	n:50000
PIK3CA   50000 perm   16 sec   (3206 perm/sec)   p_kst 2.000000e-05   p_cons 6.040000e-03   p_joint 0

Joint ci ratio: 3.919935e+00	ci left: 0	ci right 6.147943e-05	k: 0	n:60000
Cons ci ratio: 2.042741e-01	ci left: 5.476804e-03	ci right 6.738354e-03	k: 365	n:60000
KS ci ratio: 2.771789e+00	ci left: 4.219634e-07	ci right 9.285719e-05	k: 1	n:60000
PIK3CA   60000 perm   18 sec   (3259 perm/sec)   p_kst 1.666667e-05   p_cons 6.083333e-03   p_joint 0

Joint ci ratio: 3.919944e+00	ci left: 0	ci right 5.269689e-05	k: 0	n:70000
Cons ci ratio: 1.869315e-01	ci left: 5.659149e-03	ci right 6.839485e-03	k: 436	n:70000
KS ci ratio: 2.771799e+00	ci left: 3.616829e-07	ci right 7.959231e-05	k: 1	n:70000
PIK3CA   70000 perm   21 sec   (3281 perm/sec)   p_kst 1.428571e-05   p_cons 6.228571e-03   p_joint 0

Joint ci ratio: 3.919951e+00	ci left: 0	ci right 4.610993e-05	k: 0	n:80000
Cons ci ratio: 1.720099e-01	ci left: 5.895018e-03	ci right 7.016225e-03	k: 515	n:80000
KS ci ratio: 2.771807e+00	ci left: 3.164725e-07	ci right 6.964355e-05	k: 1	n:80000
PIK3CA   80000 perm   24 sec   (3288 perm/sec)   p_kst 1.250000e-05   p_cons 6.437500e-03   p_joint 0

Joint ci ratio: 3.919956e+00	ci left: 0	ci right 4.098671e-05	k: 0	n:90000
Cons ci ratio: 1.615436e-01	ci left: 5.974726e-03	ci right 7.035236e-03	k: 584	n:90000
KS ci ratio: 2.771812e+00	ci left: 2.813089e-07	ci right 6.190558e-05	k: 1	n:90000
PIK3CA   90000 perm   27 sec   (3283 perm/sec)   p_kst 1.111111e-05   p_cons 6.488889e-03   p_joint 0

Joint ci ratio: 3.919961e+00	ci left: 0	ci right 3.688811e-05	k: 0	n:100000
Cons ci ratio: 1.530170e-01	ci left: 6.020908e-03	ci right 7.028036e-03	k: 651	n:100000
KS ci ratio: 2.771817e+00	ci left: 2.531780e-07	ci right 5.571516e-05	k: 1	n:100000
PIK3CA   100000 perm   31 sec   (3267 perm/sec)   p_kst 1.000000e-05   p_cons 6.510000e-03   p_joint 0

Joint ci ratio: 3.919964e+00	ci left: 0	ci right 3.353471e-05	k: 0	n:110000
Cons ci ratio: 1.452048e-01	ci left: 6.103707e-03	ci right 7.068039e-03	k: 723	n:110000
KS ci ratio: 2.771821e+00	ci left: 2.301619e-07	ci right 5.065025e-05	k: 1	n:110000
PIK3CA   110000 perm   34 sec   (3248 perm/sec)   p_kst 9.090909e-06   p_cons 6.572727e-03   p_joint 0

Joint ci ratio: 3.919967e+00	ci left: 0	ci right 3.074019e-05	k: 0	n:120000
Cons ci ratio: 1.392734e-01	ci left: 6.101385e-03	ci right 7.022705e-03	k: 786	n:120000
KS ci ratio: 2.771824e+00	ci left: 2.109817e-07	ci right 4.642948e-05	k: 1	n:120000
PIK3CA   120000 perm   37 sec   (3226 perm/sec)   p_kst 8.333333e-06   p_cons 6.550000e-03   p_joint 0

Joint ci ratio: 3.919970e+00	ci left: 0	ci right 2.837559e-05	k: 0	n:130000
Cons ci ratio: 1.549345e-01	ci left: 4.520253e-03	ci right 5.286703e-03	k: 636	n:130000
KS ci ratio: 2.771827e+00	ci left: 1.947524e-07	ci right 4.285804e-05	k: 1	n:130000
PIK3CA   130000 perm   41 sec   (3199 perm/sec)   p_kst 7.692308e-06   p_cons 4.892308e-03   p_joint 0

Joint ci ratio: 3.919972e+00	ci left: 0	ci right 2.634879e-05	k: 0	n:140000
Cons ci ratio: 1.492986e-01	ci left: 4.534060e-03	ci right 5.272389e-03	k: 685	n:140000
KS ci ratio: 2.771829e+00	ci left: 1.808415e-07	ci right 3.979680e-05	k: 1	n:140000
PIK3CA   140000 perm   44 sec   (3169 perm/sec)   p_kst 7.142857e-06   p_cons 4.892857e-03   p_joint 0

Joint ci ratio: 3.919974e+00	ci left: 0	ci right 2.459223e-05	k: 0	n:150000
Cons ci ratio: 1.441377e-01	ci left: 4.552891e-03	ci right 5.266453e-03	k: 735	n:150000
KS ci ratio: 2.771831e+00	ci left: 1.687854e-07	ci right 3.714372e-05	k: 1	n:150000
PIK3CA   150000 perm   48 sec   (3136 perm/sec)   p_kst 6.666667e-06   p_cons 4.900000e-03   p_joint 0

Joint ci ratio: 3.919976e+00	ci left: 0	ci right 2.305523e-05	k: 0	n:160000
Cons ci ratio: 1.390338e-01	ci left: 4.599918e-03	ci right 5.293207e-03	k: 790	n:160000
KS ci ratio: 2.771833e+00	ci left: 1.582363e-07	ci right 3.482227e-05	k: 1	n:160000
PIK3CA   160000 perm   52 sec   (3104 perm/sec)   p_kst 6.250000e-06   p_cons 4.937500e-03   p_joint 0

Joint ci ratio: 3.919977e+00	ci left: 0	ci right 2.169906e-05	k: 0	n:170000
Cons ci ratio: 1.349987e-01	ci left: 4.602010e-03	ci right 5.273867e-03	k: 838	n:170000
KS ci ratio: 2.771834e+00	ci left: 1.489283e-07	ci right 3.277393e-05	k: 1	n:170000
PIK3CA   170000 perm   55 sec   (3074 perm/sec)   p_kst 5.882353e-06   p_cons 4.929412e-03   p_joint 0

Joint ci ratio: 3.919978e+00	ci left: 0	ci right 2.049356e-05	k: 0	n:180000
Cons ci ratio: 1.314447e-01	ci left: 4.593380e-03	ci right 5.244944e-03	k: 884	n:180000
KS ci ratio: 2.771835e+00	ci left: 1.406545e-07	ci right 3.095318e-05	k: 1	n:180000
PIK3CA   180000 perm   59 sec   (3042 perm/sec)   p_kst 5.555556e-06   p_cons 4.911111e-03   p_joint 0

Joint ci ratio: 3.919979e+00	ci left: 0	ci right 1.941497e-05	k: 0	n:190000
Cons ci ratio: 1.282266e-01	ci left: 4.580771e-03	ci right 5.213428e-03	k: 929	n:190000
KS ci ratio: 2.771837e+00	ci left: 1.332516e-07	ci right 2.932409e-05	k: 1	n:190000
PIK3CA   190000 perm   63 sec   (3008 perm/sec)   p_kst 5.263158e-06   p_cons 4.889474e-03   p_joint 0

Joint ci ratio: 3.919980e+00	ci left: 0	ci right 1.844423e-05	k: 0	n:200000
Cons ci ratio: 1.251693e-01	ci left: 4.574442e-03	ci right 5.190043e-03	k: 975	n:200000
KS ci ratio: 2.771838e+00	ci left: 1.265890e-07	ci right 2.785790e-05	k: 1	n:200000
PIK3CA   200000 perm   67 sec   (2978 perm/sec)   p_kst 5.000000e-06   p_cons 4.875000e-03   p_joint 0

Joint ci ratio: 3.919981e+00	ci left: 0	ci right 1.756594e-05	k: 0	n:210000
Cons ci ratio: 1.471780e-01	ci left: 3.118830e-03	ci right 3.618843e-03	k: 706	n:210000
KS ci ratio: 2.771839e+00	ci left: 1.205610e-07	ci right 2.653135e-05	k: 1	n:210000
PIK3CA   210000 perm   71 sec   (2947 perm/sec)   p_kst 4.761905e-06   p_cons 3.361905e-03   p_joint 0

Joint ci ratio: 3.919982e+00	ci left: 0	ci right 1.676749e-05	k: 0	n:220000
Cons ci ratio: 1.434706e-01	ci left: 3.139134e-03	ci right 3.628640e-03	k: 743	n:220000
KS ci ratio: 2.771840e+00	ci left: 1.150809e-07	ci right 2.532539e-05	k: 1	n:220000
PIK3CA   220000 perm   75 sec   (2916 perm/sec)   p_kst 4.545455e-06   p_cons 3.377273e-03   p_joint 0

Joint ci ratio: 3.919983e+00	ci left: 0	ci right 1.603848e-05	k: 0	n:230000
Cons ci ratio: 1.403912e-01	ci left: 3.141034e-03	ci right 3.619443e-03	k: 776	n:230000
KS ci ratio: 2.771841e+00	ci left: 1.100774e-07	ci right 2.422430e-05	k: 1	n:230000
PIK3CA   230000 perm   80 sec   (2883 perm/sec)   p_kst 4.347826e-06   p_cons 3.373913e-03   p_joint 0

Joint ci ratio: 3.919984e+00	ci left: 0	ci right 1.537021e-05	k: 0	n:240000
Cons ci ratio: 1.378438e-01	ci left: 3.126783e-03	ci right 3.593671e-03	k: 805	n:240000
KS ci ratio: 2.771841e+00	ci left: 1.054909e-07	ci right 2.321496e-05	k: 1	n:240000
PIK3CA   240000 perm   84 sec   (2852 perm/sec)   p_kst 4.166667e-06   p_cons 3.354167e-03   p_joint 0

Joint ci ratio: 3.919984e+00	ci left: 0	ci right 1.475541e-05	k: 0	n:250000
Cons ci ratio: 1.351867e-01	ci left: 3.125340e-03	ci right 3.582294e-03	k: 837	n:250000
KS ci ratio: 2.771842e+00	ci left: 1.012712e-07	ci right 2.228637e-05	k: 1	n:250000
PIK3CA   250000 perm   89 sec   (2820 perm/sec)   p_kst 4.000000e-06   p_cons 3.348000e-03   p_joint 0

Joint ci ratio: 3.919985e+00	ci left: 0	ci right 1.418790e-05	k: 0	n:260000
Cons ci ratio: 1.317689e-01	ci left: 3.168719e-03	ci right 3.619386e-03	k: 881	n:260000
KS ci ratio: 2.771843e+00	ci left: 9.737618e-08	ci right 2.142921e-05	k: 1	n:260000
PIK3CA   260000 perm   93 sec   (2791 perm/sec)   p_kst 3.846154e-06   p_cons 3.388462e-03   p_joint 0

Joint ci ratio: 3.919985e+00	ci left: 0	ci right 1.366242e-05	k: 0	n:270000
Cons ci ratio: 1.293712e-01	ci left: 3.169590e-03	ci right 3.611547e-03	k: 914	n:270000
KS ci ratio: 2.771843e+00	ci left: 9.376965e-08	ci right 2.063554e-05	k: 1	n:270000
PIK3CA   270000 perm   98 sec   (2760 perm/sec)   p_kst 3.703704e-06   p_cons 3.385185e-03   p_joint 0

Joint ci ratio: 3.919986e+00	ci left: 0	ci right 1.317448e-05	k: 0	n:280000
Cons ci ratio: 1.270325e-01	ci left: 3.173925e-03	ci right 3.607883e-03	k: 948	n:280000
KS ci ratio: 2.771844e+00	ci left: 9.042074e-08	ci right 1.989856e-05	k: 1	n:280000
PIK3CA   280000 perm   103 sec   (2730 perm/sec)   p_kst 3.571429e-06   p_cons 3.385714e-03   p_joint 0

Joint ci ratio: 3.919986e+00	ci left: 0	ci right 1.272019e-05	k: 0	n:290000
Cons ci ratio: 1.251360e-01	ci left: 3.161324e-03	ci right 3.586628e-03	k: 977	n:290000
KS ci ratio: 2.771844e+00	ci left: 8.730278e-08	ci right 1.921241e-05	k: 1	n:290000
PIK3CA   290000 perm   107 sec   (2700 perm/sec)   p_kst 3.448276e-06   p_cons 3.368966e-03   p_joint 0

Joint ci ratio: 3.919987e+00	ci left: 0	ci right 1.229619e-05	k: 0	n:300000
Cons ci ratio: 1.235067e-01	ci left: 3.139915e-03	ci right 3.556437e-03	k: 1003	n:300000
KS ci ratio: 2.771845e+00	ci left: 8.439269e-08	ci right 1.857200e-05	k: 1	n:300000
PIK3CA   300000 perm   112 sec   (2671 perm/sec)   p_kst 3.333333e-06   p_cons 3.343333e-03   p_joint 0

Joint ci ratio: 3.919987e+00	ci left: 0	ci right 1.189954e-05	k: 0	n:310000
Cons ci ratio: 1.205958e-01	ci left: 3.191872e-03	ci right 3.604595e-03	k: 1052	n:310000
KS ci ratio: 2.771845e+00	ci left: 8.167035e-08	ci right 1.797291e-05	k: 1	n:310000
PIK3CA   310000 perm   117 sec   (2642 perm/sec)   p_kst 3.225806e-06   p_cons 3.393548e-03   p_joint 0

Joint ci ratio: 3.919988e+00	ci left: 0	ci right 1.152768e-05	k: 0	n:320000
Cons ci ratio: 1.188595e-01	ci left: 3.186099e-03	ci right 3.591727e-03	k: 1083	n:320000
KS ci ratio: 2.771846e+00	ci left: 7.911815e-08	ci right 1.741126e-05	k: 1	n:320000
PIK3CA   320000 perm   123 sec   (2612 perm/sec)   p_kst 3.125000e-06   p_cons 3.384375e-03   p_joint 0

Joint ci ratio: 3.919988e+00	ci left: 0	ci right 1.117836e-05	k: 0	n:330000
Cons ci ratio: 1.169857e-01	ci left: 3.192483e-03	ci right 3.592074e-03	k: 1118	n:330000
KS ci ratio: 2.771846e+00	ci left: 7.672063e-08	ci right 1.688365e-05	k: 1	n:330000
PIK3CA   330000 perm   128 sec   (2584 perm/sec)   p_kst 3.030303e-06   p_cons 3.387879e-03   p_joint 0

Joint ci ratio: 3.919988e+00	ci left: 0	ci right 1.084959e-05	k: 0	n:340000
Cons ci ratio: 1.152981e-01	ci left: 3.192826e-03	ci right 3.586302e-03	k: 1151	n:340000
KS ci ratio: 2.771846e+00	ci left: 7.446414e-08	ci right 1.638708e-05	k: 1	n:340000
PIK3CA   340000 perm   133 sec   (2556 perm/sec)   p_kst 2.941176e-06   p_cons 3.385294e-03   p_joint 0

Joint ci ratio: 3.919989e+00	ci left: 0	ci right 1.053960e-05	k: 0	n:350000
Cons ci ratio: 1.139714e-01	ci left: 3.176532e-03	ci right 3.563192e-03	k: 1178	n:350000
KS ci ratio: 2.771847e+00	ci left: 7.233659e-08	ci right 1.591888e-05	k: 1	n:350000
PIK3CA   350000 perm   138 sec   (2528 perm/sec)   p_kst 2.857143e-06   p_cons 3.365714e-03   p_joint 0

Joint ci ratio: 3.919989e+00	ci left: 0	ci right 1.024683e-05	k: 0	n:360000
Cons ci ratio: 1.122699e-01	ci left: 3.185466e-03	ci right 3.567041e-03	k: 1214	n:360000
KS ci ratio: 2.771847e+00	ci left: 7.032724e-08	ci right 1.547669e-05	k: 1	n:360000
PIK3CA   360000 perm   144 sec   (2502 perm/sec)   p_kst 2.777778e-06   p_cons 3.372222e-03   p_joint 0

Joint ci ratio: 3.919989e+00	ci left: 0	ci right 9.969895e-06	k: 0	n:370000
Cons ci ratio: 1.113592e-01	ci left: 3.151911e-03	ci right 3.526204e-03	k: 1234	n:370000
KS ci ratio: 2.771847e+00	ci left: 6.842651e-08	ci right 1.505840e-05	k: 1	n:370000
PIK3CA   370000 perm   149 sec   (2476 perm/sec)   p_kst 2.702703e-06   p_cons 3.335135e-03   p_joint 0

Joint ci ratio: 3.919990e+00	ci left: 0	ci right 9.707530e-06	k: 0	n:380000
Cons ci ratio: 1.096406e-01	ci left: 3.168763e-03	ci right 3.538874e-03	k: 1273	n:380000
KS ci ratio: 2.771848e+00	ci left: 6.662581e-08	ci right 1.466213e-05	k: 1	n:380000
PIK3CA   380000 perm   155 sec   (2450 perm/sec)   p_kst 2.631579e-06   p_cons 3.350000e-03   p_joint 0

Joint ci ratio: 3.919990e+00	ci left: 0	ci right 9.458621e-06	k: 0	n:390000
Cons ci ratio: 1.082893e-01	ci left: 3.167327e-03	ci right 3.532421e-03	k: 1305	n:390000
KS ci ratio: 2.771848e+00	ci left: 6.491745e-08	ci right 1.428618e-05	k: 1	n:390000
PIK3CA   390000 perm   161 sec   (2425 perm/sec)   p_kst 2.564103e-06   p_cons 3.346154e-03   p_joint 0

Joint ci ratio: 3.919990e+00	ci left: 0	ci right 9.222156e-06	k: 0	n:400000
Cons ci ratio: 1.069066e-01	ci left: 3.170857e-03	ci right 3.531397e-03	k: 1339	n:400000
KS ci ratio: 2.263202e+00	ci left: 6.055238e-07	ci right 1.806160e-05	k: 2	n:400000
PIK3CA   400000 perm   167 sec   (2400 perm/sec)   p_kst 5.000000e-06   p_cons 3.347500e-03   p_joint 0

Joint ci ratio: 3.919990e+00	ci left: 0	ci right 8.997226e-06	k: 0	n:410000
Cons ci ratio: 1.059631e-01	ci left: 3.150496e-03	ci right 3.505361e-03	k: 1363	n:410000
KS ci ratio: 2.263202e+00	ci left: 5.907549e-07	ci right 1.762108e-05	k: 2	n:410000
PIK3CA   410000 perm   173 sec   (2376 perm/sec)   p_kst 4.878049e-06   p_cons 3.324390e-03   p_joint 0

Joint ci ratio: 3.919991e+00	ci left: 0	ci right 8.783008e-06	k: 0	n:420000
Cons ci ratio: 1.046290e-01	ci left: 3.156623e-03	ci right 3.507427e-03	k: 1398	n:420000
KS ci ratio: 2.263202e+00	ci left: 5.766893e-07	ci right 1.720153e-05	k: 2	n:420000
PIK3CA   420000 perm   178 sec   (2353 perm/sec)   p_kst 4.761905e-06   p_cons 3.328571e-03   p_joint 0

Joint ci ratio: 3.919991e+00	ci left: 0	ci right 8.578753e-06	k: 0	n:430000
Cons ci ratio: 1.030919e-01	ci left: 3.178352e-03	ci right 3.526068e-03	k: 1440	n:430000
KS ci ratio: 2.263203e+00	ci left: 5.632779e-07	ci right 1.680150e-05	k: 2	n:430000
PIK3CA   430000 perm   185 sec   (2329 perm/sec)   p_kst 4.651163e-06   p_cons 3.348837e-03   p_joint 0

Joint ci ratio: 3.919991e+00	ci left: 0	ci right 8.383782e-06	k: 0	n:440000
Cons ci ratio: 1.018621e-01	ci left: 3.183624e-03	ci right 3.527513e-03	k: 1475	n:440000
KS ci ratio: 2.263203e+00	ci left: 5.504761e-07	ci right 1.641965e-05	k: 2	n:440000
PIK3CA   440000 perm   191 sec   (2306 perm/sec)   p_kst 4.545455e-06   p_cons 3.352273e-03   p_joint 0

Joint ci ratio: 3.919991e+00	ci left: 0	ci right 8.197476e-06	k: 0	n:450000
Cons ci ratio: 1.007422e-01	ci left: 3.184352e-03	ci right 3.524314e-03	k: 1508	n:450000
KS ci ratio: 2.263203e+00	ci left: 5.382433e-07	ci right 1.605477e-05	k: 2	n:450000
PIK3CA   450000 perm   197 sec   (2283 perm/sec)   p_kst 4.444444e-06   p_cons 3.351111e-03   p_joint 0

Joint ci ratio: 3.919991e+00	ci left: 0	ci right 8.019271e-06	k: 0	n:460000
Cons ci ratio: 9.965848e-02	ci left: 3.185068e-03	ci right 3.521235e-03	k: 1541	n:460000
KS ci ratio: 2.263203e+00	ci left: 5.265423e-07	ci right 1.570575e-05	k: 2	n:460000
PIK3CA   460000 perm   204 sec   (2260 perm/sec)   p_kst 4.347826e-06   p_cons 3.350000e-03   p_joint 0

Joint ci ratio: 3.919992e+00	ci left: 0	ci right 7.848649e-06	k: 0	n:470000
Cons ci ratio: 9.857758e-02	ci left: 3.187848e-03	ci right 3.520448e-03	k: 1575	n:470000
KS ci ratio: 1.959990e+00	ci left: 1.316326e-06	ci right 1.865366e-05	k: 3	n:470000
PIK3CA   470000 perm   210 sec   (2238 perm/sec)   p_kst 6.382979e-06   p_cons 3.351064e-03   p_joint 0

Joint ci ratio: 3.919992e+00	ci left: 0	ci right 7.685136e-06	k: 0	n:480000
Cons ci ratio: 9.740976e-02	ci left: 3.198662e-03	ci right 3.528211e-03	k: 1613	n:480000
KS ci ratio: 1.959990e+00	ci left: 1.288902e-06	ci right 1.826504e-05	k: 3	n:480000
PIK3CA   480000 perm   217 sec   (2217 perm/sec)   p_kst 6.250000e-06   p_cons 3.360417e-03   p_joint 0

Joint ci ratio: 3.919992e+00	ci left: 0	ci right 7.528297e-06	k: 0	n:490000
Cons ci ratio: 9.645840e-02	ci left: 3.197106e-03	ci right 3.523096e-03	k: 1645	n:490000
KS ci ratio: 1.959990e+00	ci left: 1.262598e-06	ci right 1.789229e-05	k: 3	n:490000
PIK3CA   490000 perm   223 sec   (2196 perm/sec)   p_kst 6.122449e-06   p_cons 3.357143e-03   p_joint 0

Joint ci ratio: 3.919992e+00	ci left: 0	ci right 7.377732e-06	k: 0	n:500000
Cons ci ratio: 9.590786e-02	ci left: 3.170248e-03	ci right 3.491550e-03	k: 1664	n:500000
KS ci ratio: 1.959990e+00	ci left: 1.237346e-06	ci right 1.753445e-05	k: 3	n:500000
PIK3CA   500000 perm   230 sec   (2175 perm/sec)   p_kst 6.000000e-06   p_cons 3.328000e-03   p_joint 0

Joint ci ratio: 3.919992e+00	ci left: 0	ci right 7.233071e-06	k: 0	n:510000
Cons ci ratio: 9.488729e-02	ci left: 3.176991e-03	ci right 3.495359e-03	k: 1700	n:510000
KS ci ratio: 1.959990e+00	ci left: 1.213084e-06	ci right 1.719063e-05	k: 3	n:510000
PIK3CA   510000 perm   237 sec   (2154 perm/sec)   p_kst 5.882353e-06   p_cons 3.333333e-03   p_joint 0

Joint ci ratio: 3.919992e+00	ci left: 0	ci right 7.093974e-06	k: 0	n:520000
Cons ci ratio: 9.403450e-02	ci left: 3.174102e-03	ci right 3.489165e-03	k: 1731	n:520000
KS ci ratio: 1.959991e+00	ci left: 1.189756e-06	ci right 1.686005e-05	k: 3	n:520000
PIK3CA   520000 perm   244 sec   (2135 perm/sec)   p_kst 5.769231e-06   p_cons 3.328846e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.960126e-06	k: 0	n:530000
Cons ci ratio: 9.323084e-02	ci left: 3.169491e-03	ci right 3.481261e-03	k: 1761	n:530000
KS ci ratio: 1.753067e+00	ci left: 2.056353e-06	ci right 1.932364e-05	k: 4	n:530000
PIK3CA   530000 perm   251 sec   (2115 perm/sec)   p_kst 7.547170e-06   p_cons 3.322642e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.831235e-06	k: 0	n:540000
Cons ci ratio: 9.229254e-02	ci left: 3.175917e-03	ci right 3.485005e-03	k: 1797	n:540000
KS ci ratio: 1.753068e+00	ci left: 2.018273e-06	ci right 1.896580e-05	k: 4	n:540000
PIK3CA   540000 perm   258 sec   (2095 perm/sec)   p_kst 7.407407e-06   p_cons 3.327778e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.707031e-06	k: 0	n:550000
Cons ci ratio: 9.148216e-02	ci left: 3.175018e-03	ci right 3.481160e-03	k: 1829	n:550000
KS ci ratio: 1.753068e+00	ci left: 1.981577e-06	ci right 1.862096e-05	k: 4	n:550000
PIK3CA   550000 perm   265 sec   (2075 perm/sec)   p_kst 7.272727e-06   p_cons 3.325455e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.587263e-06	k: 0	n:560000
Cons ci ratio: 9.057083e-02	ci left: 3.182889e-03	ci right 3.486571e-03	k: 1866	n:560000
KS ci ratio: 1.753068e+00	ci left: 1.946191e-06	ci right 1.828845e-05	k: 4	n:560000
PIK3CA   560000 perm   272 sec   (2057 perm/sec)   p_kst 7.142857e-06   p_cons 3.332143e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.471697e-06	k: 0	n:570000
Cons ci ratio: 8.987585e-02	ci left: 3.176778e-03	ci right 3.477428e-03	k: 1895	n:570000
KS ci ratio: 1.753068e+00	ci left: 1.912048e-06	ci right 1.796760e-05	k: 4	n:570000
PIK3CA   570000 perm   280 sec   (2038 perm/sec)   p_kst 7.017544e-06   p_cons 3.324561e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.360117e-06	k: 0	n:580000
Cons ci ratio: 8.917339e-02	ci left: 3.172571e-03	ci right 3.470355e-03	k: 1925	n:580000
KS ci ratio: 1.753068e+00	ci left: 1.879081e-06	ci right 1.765782e-05	k: 4	n:580000
PIK3CA   580000 perm   287 sec   (2020 perm/sec)   p_kst 6.896552e-06   p_cons 3.318966e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.252319e-06	k: 0	n:590000
Cons ci ratio: 8.814867e-02	ci left: 3.193381e-03	ci right 3.489496e-03	k: 1970	n:590000
KS ci ratio: 1.753068e+00	ci left: 1.847232e-06	ci right 1.735853e-05	k: 4	n:590000
PIK3CA   590000 perm   295 sec   (2003 perm/sec)   p_kst 6.779661e-06   p_cons 3.338983e-03   p_joint 0

Joint ci ratio: 3.919993e+00	ci left: 0	ci right 6.148114e-06	k: 0	n:600000
Cons ci ratio: 8.746371e-02	ci left: 3.190689e-03	ci right 3.484138e-03	k: 2001	n:600000
KS ci ratio: 1.753069e+00	ci left: 1.816445e-06	ci right 1.706923e-05	k: 4	n:600000
PIK3CA   600000 perm   302 sec   (1986 perm/sec)   p_kst 6.666667e-06   p_cons 3.335000e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 6.047325e-06	k: 0	n:610000
Cons ci ratio: 8.675168e-02	ci left: 3.191303e-03	ci right 3.482298e-03	k: 2034	n:610000
KS ci ratio: 1.753069e+00	ci left: 1.786667e-06	ci right 1.678940e-05	k: 4	n:610000
PIK3CA   610000 perm   310 sec   (1969 perm/sec)   p_kst 6.557377e-06   p_cons 3.334426e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.949788e-06	k: 0	n:620000
Cons ci ratio: 8.595256e-02	ci left: 3.199798e-03	ci right 3.488745e-03	k: 2072	n:620000
KS ci ratio: 1.753069e+00	ci left: 1.757850e-06	ci right 1.651861e-05	k: 4	n:620000
PIK3CA   620000 perm   318 sec   (1952 perm/sec)   p_kst 6.451613e-06   p_cons 3.341935e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.855347e-06	k: 0	n:630000
Cons ci ratio: 8.525621e-02	ci left: 3.201820e-03	ci right 3.488491e-03	k: 2106	n:630000
KS ci ratio: 1.753069e+00	ci left: 1.729948e-06	ci right 1.625641e-05	k: 4	n:630000
PIK3CA   630000 perm   325 sec   (1936 perm/sec)   p_kst 6.349206e-06   p_cons 3.342857e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.763858e-06	k: 0	n:640000
Cons ci ratio: 8.463602e-02	ci left: 3.199200e-03	ci right 3.483450e-03	k: 2137	n:640000
KS ci ratio: 1.753069e+00	ci left: 1.702917e-06	ci right 1.600240e-05	k: 4	n:640000
PIK3CA   640000 perm   333 sec   (1919 perm/sec)   p_kst 6.250000e-06   p_cons 3.339063e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.675183e-06	k: 0	n:650000
Cons ci ratio: 8.402918e-02	ci left: 3.196668e-03	ci right 3.478556e-03	k: 2168	n:650000
KS ci ratio: 1.753069e+00	ci left: 1.676718e-06	ci right 1.575621e-05	k: 4	n:650000
PIK3CA   650000 perm   341 sec   (1904 perm/sec)   p_kst 6.153846e-06   p_cons 3.335385e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.589196e-06	k: 0	n:660000
Cons ci ratio: 8.334024e-02	ci left: 3.201638e-03	ci right 3.481537e-03	k: 2204	n:660000
KS ci ratio: 1.753069e+00	ci left: 1.651314e-06	ci right 1.551749e-05	k: 4	n:660000
PIK3CA   660000 perm   350 sec   (1888 perm/sec)   p_kst 6.060606e-06   p_cons 3.339394e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.505775e-06	k: 0	n:670000
Cons ci ratio: 8.274210e-02	ci left: 3.200622e-03	ci right 3.478327e-03	k: 2236	n:670000
KS ci ratio: 1.753069e+00	ci left: 1.626667e-06	ci right 1.528588e-05	k: 4	n:670000
PIK3CA   670000 perm   358 sec   (1872 perm/sec)   p_kst 5.970149e-06   p_cons 3.337313e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.424808e-06	k: 0	n:680000
Cons ci ratio: 8.213849e-02	ci left: 3.201083e-03	ci right 3.476705e-03	k: 2269	n:680000
KS ci ratio: 1.753070e+00	ci left: 1.602745e-06	ci right 1.506109e-05	k: 4	n:680000
PIK3CA   680000 perm   366 sec   (1857 perm/sec)   p_kst 5.882353e-06   p_cons 3.336765e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.346188e-06	k: 0	n:690000
Cons ci ratio: 8.165470e-02	ci left: 3.193019e-03	ci right 3.466250e-03	k: 2296	n:690000
KS ci ratio: 1.753070e+00	ci left: 1.579517e-06	ci right 1.484282e-05	k: 4	n:690000
PIK3CA   690000 perm   375 sec   (1842 perm/sec)   p_kst 5.797101e-06   p_cons 3.327536e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.269814e-06	k: 0	n:700000
Cons ci ratio: 8.109187e-02	ci left: 3.192188e-03	ci right 3.463377e-03	k: 2328	n:700000
KS ci ratio: 1.753070e+00	ci left: 1.556953e-06	ci right 1.463078e-05	k: 4	n:700000
PIK3CA   700000 perm   383 sec   (1827 perm/sec)   p_kst 5.714286e-06   p_cons 3.325714e-03   p_joint 0

Joint ci ratio: 3.919994e+00	ci left: 0	ci right 5.195591e-06	k: 0	n:710000
Cons ci ratio: 8.059192e-02	ci left: 3.187247e-03	ci right 3.456268e-03	k: 2357	n:710000
KS ci ratio: 1.753070e+00	ci left: 1.535024e-06	ci right 1.442471e-05	k: 4	n:710000
PIK3CA   710000 perm   392 sec   (1813 perm/sec)   p_kst 5.633803e-06   p_cons 3.319718e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 5.123431e-06	k: 0	n:720000
Cons ci ratio: 8.000028e-02	ci left: 3.190615e-03	ci right 3.457851e-03	k: 2392	n:720000
KS ci ratio: 1.753070e+00	ci left: 1.513704e-06	ci right 1.422437e-05	k: 4	n:720000
PIK3CA   720000 perm   400 sec   (1798 perm/sec)   p_kst 5.555556e-06   p_cons 3.322222e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 5.053247e-06	k: 0	n:730000
Cons ci ratio: 7.953660e-02	ci left: 3.184498e-03	ci right 3.449604e-03	k: 2420	n:730000
KS ci ratio: 1.753070e+00	ci left: 1.492968e-06	ci right 1.402951e-05	k: 4	n:730000
PIK3CA   730000 perm   409 sec   (1784 perm/sec)   p_kst 5.479452e-06   p_cons 3.315068e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.984960e-06	k: 0	n:740000
Cons ci ratio: 7.898387e-02	ci left: 3.186500e-03	ci right 3.449844e-03	k: 2454	n:740000
KS ci ratio: 1.753070e+00	ci left: 1.472793e-06	ci right 1.383993e-05	k: 4	n:740000
PIK3CA   740000 perm   418 sec   (1770 perm/sec)   p_kst 5.405405e-06   p_cons 3.316216e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.918494e-06	k: 0	n:750000
Cons ci ratio: 7.842671e-02	ci left: 3.189762e-03	ci right 3.451431e-03	k: 2489	n:750000
KS ci ratio: 1.753070e+00	ci left: 1.453156e-06	ci right 1.365539e-05	k: 4	n:750000
PIK3CA   750000 perm   427 sec   (1756 perm/sec)   p_kst 5.333333e-06   p_cons 3.318667e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.853777e-06	k: 0	n:760000
Cons ci ratio: 7.783479e-02	ci left: 3.196815e-03	ci right 3.456994e-03	k: 2527	n:760000
KS ci ratio: 1.753070e+00	ci left: 1.434035e-06	ci right 1.347572e-05	k: 4	n:760000
PIK3CA   760000 perm   436 sec   (1742 perm/sec)   p_kst 5.263158e-06   p_cons 3.325000e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.790741e-06	k: 0	n:770000
Cons ci ratio: 7.727118e-02	ci left: 3.202418e-03	ci right 3.461081e-03	k: 2564	n:770000
KS ci ratio: 1.753070e+00	ci left: 1.415411e-06	ci right 1.330071e-05	k: 4	n:770000
PIK3CA   770000 perm   445 sec   (1729 perm/sec)   p_kst 5.194805e-06   p_cons 3.329870e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.729321e-06	k: 0	n:780000
Cons ci ratio: 4.744203e-02	ci left: 8.471019e-03	ci right 8.883924e-03	k: 6767	n:780000
KS ci ratio: 1.753071e+00	ci left: 1.397265e-06	ci right 1.313019e-05	k: 4	n:780000
PIK3CA   780000 perm   455 sec   (1716 perm/sec)   p_kst 5.128205e-06   p_cons 8.675641e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.669457e-06	k: 0	n:790000
Cons ci ratio: 4.717473e-02	ci left: 8.460106e-03	ci right 8.870092e-03	k: 6844	n:790000
KS ci ratio: 1.753071e+00	ci left: 1.379578e-06	ci right 1.296399e-05	k: 4	n:790000
PIK3CA   790000 perm   464 sec   (1704 perm/sec)   p_kst 5.063291e-06   p_cons 8.663291e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.611089e-06	k: 0	n:800000
Cons ci ratio: 4.686411e-02	ci left: 8.466768e-03	ci right 8.874302e-03	k: 6935	n:800000
KS ci ratio: 1.753071e+00	ci left: 1.362333e-06	ci right 1.280194e-05	k: 4	n:800000
PIK3CA   800000 perm   473 sec   (1691 perm/sec)   p_kst 5.000000e-06   p_cons 8.668750e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.554162e-06	k: 0	n:810000
Cons ci ratio: 4.656958e-02	ci left: 8.469613e-03	ci right 8.874653e-03	k: 7023	n:810000
KS ci ratio: 1.753071e+00	ci left: 1.345514e-06	ci right 1.264389e-05	k: 4	n:810000
PIK3CA   810000 perm   483 sec   (1678 perm/sec)   p_kst 4.938272e-06   p_cons 8.670370e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.498623e-06	k: 0	n:820000
Cons ci ratio: 4.635951e-02	ci left: 8.443464e-03	ci right 8.845384e-03	k: 7087	n:820000
KS ci ratio: 1.753071e+00	ci left: 1.329106e-06	ci right 1.248969e-05	k: 4	n:820000
PIK3CA   820000 perm   492 sec   (1666 perm/sec)   p_kst 4.878049e-06   p_cons 8.642683e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.444423e-06	k: 0	n:830000
Cons ci ratio: 4.603229e-02	ci left: 8.462019e-03	ci right 8.861903e-03	k: 7188	n:830000
KS ci ratio: 1.753071e+00	ci left: 1.313092e-06	ci right 1.233922e-05	k: 4	n:830000
PIK3CA   830000 perm   502 sec   (1654 perm/sec)   p_kst 4.819277e-06   p_cons 8.660241e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.391514e-06	k: 0	n:840000
Cons ci ratio: 4.577211e-02	ci left: 8.457779e-03	ci right 8.855144e-03	k: 7270	n:840000
KS ci ratio: 1.753071e+00	ci left: 1.297460e-06	ci right 1.219232e-05	k: 4	n:840000
PIK3CA   840000 perm   512 sec   (1642 perm/sec)   p_kst 4.761905e-06   p_cons 8.654762e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.339849e-06	k: 0	n:850000
Cons ci ratio: 4.547888e-02	ci left: 8.467603e-03	ci right 8.862815e-03	k: 7364	n:850000
KS ci ratio: 1.600327e+00	ci left: 1.909987e-06	ci right 1.372740e-05	k: 5	n:850000
PIK3CA   850000 perm   522 sec   (1630 perm/sec)   p_kst 5.882353e-06   p_cons 8.663529e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.289386e-06	k: 0	n:860000
Cons ci ratio: 4.522179e-02	ci left: 8.465709e-03	ci right 8.858541e-03	k: 7448	n:860000
KS ci ratio: 1.600327e+00	ci left: 1.887777e-06	ci right 1.356778e-05	k: 5	n:860000
PIK3CA   860000 perm   532 sec   (1616 perm/sec)   p_kst 5.813953e-06   p_cons 8.660465e-03   p_joint 0

Joint ci ratio: 3.919995e+00	ci left: 0	ci right 4.240082e-06	k: 0	n:870000
Cons ci ratio: 4.492993e-02	ci left: 8.478641e-03	ci right 8.869468e-03	k: 7545	n:870000
KS ci ratio: 1.600327e+00	ci left: 1.866079e-06	ci right 1.341182e-05	k: 5	n:870000
PIK3CA   870000 perm   542 sec   (1604 perm/sec)   p_kst 5.747126e-06   p_cons 8.672414e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 4.191900e-06	k: 0	n:880000
Cons ci ratio: 4.468495e-02	ci left: 8.475554e-03	ci right 8.864054e-03	k: 7628	n:880000
KS ci ratio: 1.600327e+00	ci left: 1.844873e-06	ci right 1.325942e-05	k: 5	n:880000
PIK3CA   880000 perm   552 sec   (1593 perm/sec)   p_kst 5.681818e-06   p_cons 8.668182e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 4.144800e-06	k: 0	n:890000
Cons ci ratio: 4.436855e-02	ci left: 8.501434e-03	ci right 8.888291e-03	k: 7737	n:890000
KS ci ratio: 1.600327e+00	ci left: 1.824144e-06	ci right 1.311044e-05	k: 5	n:890000
PIK3CA   890000 perm   563 sec   (1582 perm/sec)   p_kst 5.617978e-06   p_cons 8.693258e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 4.098747e-06	k: 0	n:900000
Cons ci ratio: 4.409848e-02	ci left: 8.511363e-03	ci right 8.896254e-03	k: 7832	n:900000
KS ci ratio: 1.600327e+00	ci left: 1.803876e-06	ci right 1.296477e-05	k: 5	n:900000
PIK3CA   900000 perm   574 sec   (1569 perm/sec)   p_kst 5.555556e-06   p_cons 8.702222e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 4.053705e-06	k: 0	n:910000
Cons ci ratio: 4.383606e-02	ci left: 8.519993e-03	ci right 8.902924e-03	k: 7926	n:910000
KS ci ratio: 1.600327e+00	ci left: 1.784053e-06	ci right 1.282230e-05	k: 5	n:910000
PIK3CA   910000 perm   584 sec   (1558 perm/sec)   p_kst 5.494505e-06   p_cons 8.709890e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 4.009644e-06	k: 0	n:920000
Cons ci ratio: 4.355090e-02	ci left: 8.539195e-03	ci right 8.920430e-03	k: 8030	n:920000
KS ci ratio: 1.600327e+00	ci left: 1.764661e-06	ci right 1.268292e-05	k: 5	n:920000
PIK3CA   920000 perm   595 sec   (1547 perm/sec)   p_kst 5.434783e-06   p_cons 8.728261e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.966529e-06	k: 0	n:930000
Cons ci ratio: 4.329540e-02	ci left: 8.548418e-03	ci right 8.927770e-03	k: 8125	n:930000
KS ci ratio: 1.600327e+00	ci left: 1.745687e-06	ci right 1.254655e-05	k: 5	n:930000
PIK3CA   930000 perm   605 sec   (1537 perm/sec)   p_kst 5.376344e-06   p_cons 8.736559e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.924332e-06	k: 0	n:940000
Cons ci ratio: 4.307342e-02	ci left: 8.545874e-03	ci right 8.923120e-03	k: 8209	n:940000
KS ci ratio: 1.600327e+00	ci left: 1.727115e-06	ci right 1.241308e-05	k: 5	n:940000
PIK3CA   940000 perm   616 sec   (1527 perm/sec)   p_kst 5.319149e-06   p_cons 8.732979e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.883023e-06	k: 0	n:950000
Cons ci ratio: 4.285482e-02	ci left: 8.543388e-03	ci right 8.918564e-03	k: 8293	n:950000
KS ci ratio: 1.600327e+00	ci left: 1.708935e-06	ci right 1.228241e-05	k: 5	n:950000
PIK3CA   950000 perm   627 sec   (1516 perm/sec)   p_kst 5.263158e-06   p_cons 8.729474e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.842575e-06	k: 0	n:960000
Cons ci ratio: 4.265750e-02	ci left: 8.533745e-03	ci right 8.906729e-03	k: 8370	n:960000
KS ci ratio: 1.600327e+00	ci left: 1.691134e-06	ci right 1.215447e-05	k: 5	n:960000
PIK3CA   960000 perm   637 sec   (1506 perm/sec)   p_kst 5.208333e-06   p_cons 8.718750e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.802961e-06	k: 0	n:970000
Cons ci ratio: 4.246034e-02	ci left: 8.525324e-03	ci right 8.896176e-03	k: 8448	n:970000
KS ci ratio: 1.600328e+00	ci left: 1.673699e-06	ci right 1.202917e-05	k: 5	n:970000
PIK3CA   970000 perm   648 sec   (1496 perm/sec)   p_kst 5.154639e-06   p_cons 8.709278e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.764156e-06	k: 0	n:980000
Cons ci ratio: 4.226839e-02	ci left: 8.516069e-03	ci right 8.884803e-03	k: 8525	n:980000
KS ci ratio: 1.600328e+00	ci left: 1.656621e-06	ci right 1.190642e-05	k: 5	n:980000
PIK3CA   980000 perm   659 sec   (1486 perm/sec)   p_kst 5.102041e-06   p_cons 8.698980e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.726134e-06	k: 0	n:990000
Cons ci ratio: 4.205684e-02	ci left: 8.516001e-03	ci right 8.882842e-03	k: 8611	n:990000
KS ci ratio: 1.600328e+00	ci left: 1.639887e-06	ci right 1.178615e-05	k: 5	n:990000
PIK3CA   990000 perm   670 sec   (1477 perm/sec)   p_kst 5.050505e-06   p_cons 8.697980e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.688873e-06	k: 0	n:1000000
Cons ci ratio: 4.184357e-02	ci left: 8.517918e-03	ci right 8.882936e-03	k: 8699	n:1000000
KS ci ratio: 1.600328e+00	ci left: 1.623488e-06	ci right 1.166829e-05	k: 5	n:1000000
PIK3CA   1000000 perm   682 sec   (1467 perm/sec)   p_kst 5.000000e-06   p_cons 8.699000e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.652349e-06	k: 0	n:1010000
Cons ci ratio: 4.164548e-02	ci left: 8.514903e-03	ci right 8.878023e-03	k: 8782	n:1010000
KS ci ratio: 1.600328e+00	ci left: 1.607414e-06	ci right 1.155277e-05	k: 5	n:1010000
PIK3CA   1010000 perm   693 sec   (1458 perm/sec)   p_kst 4.950495e-06   p_cons 8.695050e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.616542e-06	k: 0	n:1020000
Cons ci ratio: 4.144781e-02	ci left: 8.512920e-03	ci right 8.874192e-03	k: 8866	n:1020000
KS ci ratio: 1.600328e+00	ci left: 1.591655e-06	ci right 1.143950e-05	k: 5	n:1020000
PIK3CA   1020000 perm   704 sec   (1448 perm/sec)   p_kst 4.901961e-06   p_cons 8.692157e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.581430e-06	k: 0	n:1030000
Cons ci ratio: 4.123666e-02	ci left: 8.517707e-03	ci right 8.877297e-03	k: 8957	n:1030000
KS ci ratio: 1.600328e+00	ci left: 1.576202e-06	ci right 1.132844e-05	k: 5	n:1030000
PIK3CA   1030000 perm   716 sec   (1439 perm/sec)   p_kst 4.854369e-06   p_cons 8.696117e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.546993e-06	k: 0	n:1040000
Cons ci ratio: 4.105618e-02	ci left: 8.510986e-03	ci right 8.868682e-03	k: 9036	n:1040000
KS ci ratio: 1.600328e+00	ci left: 1.561046e-06	ci right 1.121951e-05	k: 5	n:1040000
PIK3CA   1040000 perm   727 sec   (1430 perm/sec)   p_kst 4.807692e-06   p_cons 8.688462e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.513212e-06	k: 0	n:1050000
Cons ci ratio: 4.084868e-02	ci left: 8.516651e-03	ci right 8.872734e-03	k: 9128	n:1050000
KS ci ratio: 1.600328e+00	ci left: 1.546179e-06	ci right 1.111266e-05	k: 5	n:1050000
PIK3CA   1050000 perm   739 sec   (1421 perm/sec)   p_kst 4.761905e-06   p_cons 8.693333e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.480069e-06	k: 0	n:1060000
Cons ci ratio: 4.065542e-02	ci left: 8.517545e-03	ci right 8.871940e-03	k: 9215	n:1060000
KS ci ratio: 1.600328e+00	ci left: 1.531593e-06	ci right 1.100783e-05	k: 5	n:1060000
PIK3CA   1060000 perm   751 sec   (1412 perm/sec)   p_kst 4.716981e-06   p_cons 8.693396e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.447545e-06	k: 0	n:1070000
Cons ci ratio: 4.046268e-02	ci left: 8.519351e-03	ci right 8.872102e-03	k: 9303	n:1070000
KS ci ratio: 1.600328e+00	ci left: 1.517279e-06	ci right 1.090495e-05	k: 5	n:1070000
PIK3CA   1070000 perm   762 sec   (1403 perm/sec)   p_kst 4.672897e-06   p_cons 8.694393e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.415623e-06	k: 0	n:1080000
Cons ci ratio: 4.022946e-02	ci left: 8.539461e-03	ci right 8.890960e-03	k: 9411	n:1080000
KS ci ratio: 1.600328e+00	ci left: 1.503230e-06	ci right 1.080398e-05	k: 5	n:1080000
PIK3CA   1080000 perm   774 sec   (1395 perm/sec)   p_kst 4.629630e-06   p_cons 8.713889e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.384287e-06	k: 0	n:1090000
Cons ci ratio: 4.004694e-02	ci left: 8.539224e-03	ci right 8.889082e-03	k: 9497	n:1090000
KS ci ratio: 1.600328e+00	ci left: 1.489439e-06	ci right 1.070486e-05	k: 5	n:1090000
PIK3CA   1090000 perm   786 sec   (1386 perm/sec)   p_kst 4.587156e-06   p_cons 8.712844e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.353521e-06	k: 0	n:1100000
Cons ci ratio: 3.985639e-02	ci left: 8.543496e-03	ci right 8.891825e-03	k: 9588	n:1100000
KS ci ratio: 1.600328e+00	ci left: 1.475898e-06	ci right 1.060754e-05	k: 5	n:1100000
PIK3CA   1100000 perm   798 sec   (1378 perm/sec)   p_kst 4.545455e-06   p_cons 8.716364e-03   p_joint 0

Joint ci ratio: 3.919996e+00	ci left: 0	ci right 3.323309e-06	k: 0	n:1110000
Cons ci ratio: 3.964376e-02	ci left: 8.558400e-03	ci right 8.905433e-03	k: 9691	n:1110000
KS ci ratio: 1.600328e+00	ci left: 1.462602e-06	ci right 1.051198e-05	k: 5	n:1110000
PIK3CA   1110000 perm   810 sec   (1370 perm/sec)   p_kst 4.504505e-06   p_cons 8.730631e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.293637e-06	k: 0	n:1120000
Cons ci ratio: 3.946295e-02	ci left: 8.560664e-03	ci right 8.906170e-03	k: 9780	n:1120000
KS ci ratio: 1.481615e+00	ci left: 1.965979e-06	ci right 1.166021e-05	k: 6	n:1120000
PIK3CA   1120000 perm   822 sec   (1362 perm/sec)   p_kst 5.357143e-06   p_cons 8.732143e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.264490e-06	k: 0	n:1130000
Cons ci ratio: 3.927857e-02	ci left: 8.565521e-03	ci right 8.909571e-03	k: 9872	n:1130000
KS ci ratio: 1.481615e+00	ci left: 1.948581e-06	ci right 1.155702e-05	k: 6	n:1130000
PIK3CA   1130000 perm   836 sec   (1352 perm/sec)   p_kst 5.309735e-06   p_cons 8.736283e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.235854e-06	k: 0	n:1140000
Cons ci ratio: 3.912053e-02	ci left: 8.559872e-03	ci right 8.902280e-03	k: 9952	n:1140000
KS ci ratio: 1.481616e+00	ci left: 1.931489e-06	ci right 1.145564e-05	k: 6	n:1140000
PIK3CA   1140000 perm   849 sec   (1343 perm/sec)   p_kst 5.263158e-06   p_cons 8.729825e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.207716e-06	k: 0	n:1150000
Cons ci ratio: 3.898594e-02	ci left: 8.544851e-03	ci right 8.885457e-03	k: 10021	n:1150000
KS ci ratio: 1.481616e+00	ci left: 1.914693e-06	ci right 1.135603e-05	k: 6	n:1150000
PIK3CA   1150000 perm   861 sec   (1336 perm/sec)   p_kst 5.217391e-06   p_cons 8.713913e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.180063e-06	k: 0	n:1160000
Cons ci ratio: 3.882944e-02	ci left: 8.540336e-03	ci right 8.879365e-03	k: 10102	n:1160000
KS ci ratio: 1.481616e+00	ci left: 1.898187e-06	ci right 1.125813e-05	k: 6	n:1160000
PIK3CA   1160000 perm   873 sec   (1328 perm/sec)   p_kst 5.172414e-06   p_cons 8.708621e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.152883e-06	k: 0	n:1170000
Cons ci ratio: 3.863848e-02	ci left: 8.551985e-03	ci right 8.889770e-03	k: 10202	n:1170000
KS ci ratio: 1.481616e+00	ci left: 1.881963e-06	ci right 1.116191e-05	k: 6	n:1170000
PIK3CA   1170000 perm   886 sec   (1321 perm/sec)   p_kst 5.128205e-06   p_cons 8.719658e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.126164e-06	k: 0	n:1180000
Cons ci ratio: 3.849556e-02	ci left: 8.543296e-03	ci right 8.879461e-03	k: 10278	n:1180000
KS ci ratio: 1.481616e+00	ci left: 1.866014e-06	ci right 1.106732e-05	k: 6	n:1180000
PIK3CA   1180000 perm   899 sec   (1313 perm/sec)   p_kst 5.084746e-06   p_cons 8.710169e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.099894e-06	k: 0	n:1190000
Cons ci ratio: 3.833181e-02	ci left: 8.544743e-03	ci right 8.879504e-03	k: 10366	n:1190000
KS ci ratio: 1.481616e+00	ci left: 1.850333e-06	ci right 1.097432e-05	k: 6	n:1190000
PIK3CA   1190000 perm   912 sec   (1305 perm/sec)   p_kst 5.042017e-06   p_cons 8.710924e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.074061e-06	k: 0	n:1200000
Cons ci ratio: 3.816645e-02	ci left: 8.547820e-03	ci right 8.881225e-03	k: 10456	n:1200000
KS ci ratio: 1.481616e+00	ci left: 1.834914e-06	ci right 1.088286e-05	k: 6	n:1200000
PIK3CA   1200000 perm   924 sec   (1298 perm/sec)   p_kst 5.000000e-06   p_cons 8.713333e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.048656e-06	k: 0	n:1210000
Cons ci ratio: 3.802504e-02	ci left: 8.541025e-03	ci right 8.872904e-03	k: 10534	n:1210000
KS ci ratio: 1.481616e+00	ci left: 1.819749e-06	ci right 1.079292e-05	k: 6	n:1210000
PIK3CA   1210000 perm   940 sec   (1287 perm/sec)   p_kst 4.958678e-06   p_cons 8.705785e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 3.023667e-06	k: 0	n:1220000
Cons ci ratio: 3.788700e-02	ci left: 8.533532e-03	ci right 8.863889e-03	k: 10611	n:1220000
KS ci ratio: 1.481616e+00	ci left: 1.804833e-06	ci right 1.070446e-05	k: 6	n:1220000
PIK3CA   1220000 perm   953 sec   (1280 perm/sec)   p_kst 4.918033e-06   p_cons 8.697541e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.999084e-06	k: 0	n:1230000
Cons ci ratio: 3.774154e-02	ci left: 8.530189e-03	ci right 8.859122e-03	k: 10693	n:1230000
KS ci ratio: 1.481616e+00	ci left: 1.790160e-06	ci right 1.061743e-05	k: 6	n:1230000
PIK3CA   1230000 perm   967 sec   (1272 perm/sec)   p_kst 4.878049e-06   p_cons 8.693496e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.974898e-06	k: 0	n:1240000
Cons ci ratio: 3.758016e-02	ci left: 8.534893e-03	ci right 8.862570e-03	k: 10785	n:1240000
KS ci ratio: 1.481616e+00	ci left: 1.775723e-06	ci right 1.053180e-05	k: 6	n:1240000
PIK3CA   1240000 perm   980 sec   (1265 perm/sec)   p_kst 4.838710e-06   p_cons 8.697581e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.951099e-06	k: 0	n:1250000
Cons ci ratio: 3.743993e-02	ci left: 8.530806e-03	ci right 8.857077e-03	k: 10866	n:1250000
KS ci ratio: 1.481616e+00	ci left: 1.761517e-06	ci right 1.044755e-05	k: 6	n:1250000
PIK3CA   1250000 perm   993 sec   (1259 perm/sec)   p_kst 4.800000e-06   p_cons 8.692800e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.927678e-06	k: 0	n:1260000
Cons ci ratio: 3.729954e-02	ci left: 8.527572e-03	ci right 8.852470e-03	k: 10948	n:1260000
KS ci ratio: 1.481616e+00	ci left: 1.747537e-06	ci right 1.036463e-05	k: 6	n:1260000
PIK3CA   1260000 perm   1006 sec   (1252 perm/sec)   p_kst 4.761905e-06   p_cons 8.688889e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.904625e-06	k: 0	n:1270000
Cons ci ratio: 3.712509e-02	ci left: 8.540774e-03	ci right 8.864622e-03	k: 11051	n:1270000
KS ci ratio: 1.481616e+00	ci left: 1.733777e-06	ci right 1.028302e-05	k: 6	n:1270000
PIK3CA   1270000 perm   1020 sec   (1245 perm/sec)   p_kst 4.724409e-06   p_cons 8.701575e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.881933e-06	k: 0	n:1280000
Cons ci ratio: 3.698317e-02	ci left: 8.539841e-03	ci right 8.862388e-03	k: 11136	n:1280000
KS ci ratio: 1.481616e+00	ci left: 1.720232e-06	ci right 1.020269e-05	k: 6	n:1280000
PIK3CA   1280000 perm   1034 sec   (1238 perm/sec)   p_kst 4.687500e-06   p_cons 8.700000e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.859592e-06	k: 0	n:1290000
Cons ci ratio: 3.683956e-02	ci left: 8.540460e-03	ci right 8.861752e-03	k: 11223	n:1290000
KS ci ratio: 1.481616e+00	ci left: 1.706897e-06	ci right 1.012360e-05	k: 6	n:1290000
PIK3CA   1290000 perm   1048 sec   (1231 perm/sec)   p_kst 4.651163e-06   p_cons 8.700000e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.837596e-06	k: 0	n:1300000
Cons ci ratio: 3.667309e-02	ci left: 8.552505e-03	ci right 8.872766e-03	k: 11325	n:1300000
KS ci ratio: 1.481616e+00	ci left: 1.693767e-06	ci right 1.004572e-05	k: 6	n:1300000
PIK3CA   1300000 perm   1061 sec   (1225 perm/sec)   p_kst 4.615385e-06   p_cons 8.711538e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.815935e-06	k: 0	n:1310000
Cons ci ratio: 3.654920e-02	ci left: 8.545459e-03	ci right 8.864352e-03	k: 11402	n:1310000
KS ci ratio: 1.481616e+00	ci left: 1.680837e-06	ci right 9.969037e-06	k: 6	n:1310000
PIK3CA   1310000 perm   1075 sec   (1218 perm/sec)   p_kst 4.580153e-06   p_cons 8.703817e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.794602e-06	k: 0	n:1320000
Cons ci ratio: 3.640737e-02	ci left: 8.547530e-03	ci right 8.865237e-03	k: 11491	n:1320000
KS ci ratio: 1.481616e+00	ci left: 1.668103e-06	ci right 9.893514e-06	k: 6	n:1320000
PIK3CA   1320000 perm   1089 sec   (1212 perm/sec)   p_kst 4.545455e-06   p_cons 8.705303e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.773590e-06	k: 0	n:1330000
Cons ci ratio: 3.627982e-02	ci left: 8.543612e-03	ci right 8.860037e-03	k: 11572	n:1330000
KS ci ratio: 1.481616e+00	ci left: 1.655561e-06	ci right 9.819127e-06	k: 6	n:1330000
PIK3CA   1330000 perm   1103 sec   (1206 perm/sec)   p_kst 4.511278e-06   p_cons 8.700752e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.752891e-06	k: 0	n:1340000
Cons ci ratio: 3.616456e-02	ci left: 8.534576e-03	ci right 8.849642e-03	k: 11646	n:1340000
KS ci ratio: 1.481616e+00	ci left: 1.643206e-06	ci right 9.745850e-06	k: 6	n:1340000
PIK3CA   1340000 perm   1117 sec   (1200 perm/sec)   p_kst 4.477612e-06   p_cons 8.691045e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.732500e-06	k: 0	n:1350000
Cons ci ratio: 3.603954e-02	ci left: 8.530815e-03	ci right 8.844631e-03	k: 11727	n:1350000
KS ci ratio: 1.481616e+00	ci left: 1.631034e-06	ci right 9.673659e-06	k: 6	n:1350000
PIK3CA   1350000 perm   1131 sec   (1194 perm/sec)   p_kst 4.444444e-06   p_cons 8.686667e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.712408e-06	k: 0	n:1360000
Cons ci ratio: 3.589588e-02	ci left: 8.536585e-03	ci right 8.849336e-03	k: 11821	n:1360000
KS ci ratio: 1.481616e+00	ci left: 1.619042e-06	ci right 9.602530e-06	k: 6	n:1360000
PIK3CA   1360000 perm   1146 sec   (1187 perm/sec)   p_kst 4.411765e-06   p_cons 8.691912e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.692609e-06	k: 0	n:1370000
Cons ci ratio: 3.577361e-02	ci left: 8.532868e-03	ci right 8.844396e-03	k: 11902	n:1370000
KS ci ratio: 1.481616e+00	ci left: 1.607224e-06	ci right 9.532438e-06	k: 6	n:1370000
PIK3CA   1370000 perm   1160 sec   (1181 perm/sec)   p_kst 4.379562e-06   p_cons 8.687591e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.673097e-06	k: 0	n:1380000
Cons ci ratio: 3.564209e-02	ci left: 8.534235e-03	ci right 8.844644e-03	k: 11990	n:1380000
KS ci ratio: 1.481616e+00	ci left: 1.595577e-06	ci right 9.463363e-06	k: 6	n:1380000
PIK3CA   1380000 perm   1175 sec   (1174 perm/sec)   p_kst 4.347826e-06   p_cons 8.688406e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.653867e-06	k: 0	n:1390000
Cons ci ratio: 3.552090e-02	ci left: 8.531305e-03	ci right 8.840531e-03	k: 12072	n:1390000
KS ci ratio: 1.481616e+00	ci left: 1.584098e-06	ci right 9.395281e-06	k: 6	n:1390000
PIK3CA   1390000 perm   1190 sec   (1168 perm/sec)   p_kst 4.316547e-06   p_cons 8.684892e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.634910e-06	k: 0	n:1400000
Cons ci ratio: 3.541565e-02	ci left: 8.521339e-03	ci right 8.829270e-03	k: 12144	n:1400000
KS ci ratio: 1.481617e+00	ci left: 1.572783e-06	ci right 9.328172e-06	k: 6	n:1400000
PIK3CA   1400000 perm   1204 sec   (1162 perm/sec)   p_kst 4.285714e-06   p_cons 8.674286e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.616223e-06	k: 0	n:1410000
Cons ci ratio: 3.530549e-02	ci left: 8.514328e-03	ci right 8.821029e-03	k: 12220	n:1410000
KS ci ratio: 1.481617e+00	ci left: 1.561629e-06	ci right 9.262015e-06	k: 6	n:1410000
PIK3CA   1410000 perm   1219 sec   (1157 perm/sec)   p_kst 4.255319e-06   p_cons 8.666667e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.597799e-06	k: 0	n:1420000
Cons ci ratio: 3.516032e-02	ci left: 8.524869e-03	ci right 8.830661e-03	k: 12321	n:1420000
KS ci ratio: 1.481617e+00	ci left: 1.550631e-06	ci right 9.196790e-06	k: 6	n:1420000
PIK3CA   1420000 perm   1234 sec   (1151 perm/sec)   p_kst 4.225352e-06   p_cons 8.676761e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.579633e-06	k: 0	n:1430000
Cons ci ratio: 3.502688e-02	ci left: 8.530412e-03	ci right 8.835219e-03	k: 12415	n:1430000
KS ci ratio: 1.481617e+00	ci left: 1.539788e-06	ci right 9.132477e-06	k: 6	n:1430000
PIK3CA   1430000 perm   1249 sec   (1145 perm/sec)   p_kst 4.195804e-06   p_cons 8.681818e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.561719e-06	k: 0	n:1440000
Cons ci ratio: 3.491889e-02	ci left: 8.524177e-03	ci right 8.827804e-03	k: 12492	n:1440000
KS ci ratio: 1.481617e+00	ci left: 1.529095e-06	ci right 9.069057e-06	k: 6	n:1440000
PIK3CA   1440000 perm   1264 sec   (1139 perm/sec)   p_kst 4.166667e-06   p_cons 8.675000e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.544052e-06	k: 0	n:1450000
Cons ci ratio: 3.478260e-02	ci left: 8.532388e-03	ci right 8.835097e-03	k: 12590	n:1450000
KS ci ratio: 1.481617e+00	ci left: 1.518549e-06	ci right 9.006512e-06	k: 6	n:1450000
PIK3CA   1450000 perm   1280 sec   (1133 perm/sec)   p_kst 4.137931e-06   p_cons 8.682759e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.526627e-06	k: 0	n:1460000
Cons ci ratio: 3.467684e-02	ci left: 8.526228e-03	ci right 8.827780e-03	k: 12667	n:1460000
KS ci ratio: 1.481617e+00	ci left: 1.508148e-06	ci right 8.944824e-06	k: 6	n:1460000
PIK3CA   1460000 perm   1295 sec   (1128 perm/sec)   p_kst 4.109589e-06   p_cons 8.676027e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.509439e-06	k: 0	n:1470000
Cons ci ratio: 3.455428e-02	ci left: 8.528921e-03	ci right 8.829482e-03	k: 12757	n:1470000
KS ci ratio: 1.481617e+00	ci left: 1.497889e-06	ci right 8.883975e-06	k: 6	n:1470000
PIK3CA   1470000 perm   1310 sec   (1122 perm/sec)   p_kst 4.081633e-06   p_cons 8.678231e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.492483e-06	k: 0	n:1480000
Cons ci ratio: 3.444517e-02	ci left: 8.525551e-03	ci right 8.825025e-03	k: 12838	n:1480000
KS ci ratio: 1.481617e+00	ci left: 1.487768e-06	ci right 8.823948e-06	k: 6	n:1480000
PIK3CA   1480000 perm   1326 sec   (1116 perm/sec)   p_kst 4.054054e-06   p_cons 8.674324e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.475755e-06	k: 0	n:1490000
Cons ci ratio: 3.434246e-02	ci left: 8.519566e-03	ci right 8.817919e-03	k: 12915	n:1490000
KS ci ratio: 1.481617e+00	ci left: 1.477783e-06	ci right 8.764727e-06	k: 6	n:1490000
PIK3CA   1490000 perm   1342 sec   (1111 perm/sec)   p_kst 4.026846e-06   p_cons 8.667785e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.459250e-06	k: 0	n:1500000
Cons ci ratio: 3.419688e-02	ci left: 8.535475e-03	ci right 8.833094e-03	k: 13025	n:1500000
KS ci ratio: 1.481617e+00	ci left: 1.467931e-06	ci right 8.706296e-06	k: 6	n:1500000
PIK3CA   1500000 perm   1357 sec   (1105 perm/sec)   p_kst 4.000000e-06   p_cons 8.683333e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.442964e-06	k: 0	n:1510000
Cons ci ratio: 3.408193e-02	ci left: 8.536729e-03	ci right 8.833372e-03	k: 13113	n:1510000
KS ci ratio: 1.481617e+00	ci left: 1.458209e-06	ci right 8.648638e-06	k: 6	n:1510000
PIK3CA   1510000 perm   1373 sec   (1100 perm/sec)   p_kst 3.973510e-06   p_cons 8.684106e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.426891e-06	k: 0	n:1520000
Cons ci ratio: 3.396036e-02	ci left: 8.541883e-03	ci right 8.837625e-03	k: 13207	n:1520000
KS ci ratio: 1.306662e+00	ci left: 2.272261e-06	ci right 1.037049e-05	k: 8	n:1520000
PIK3CA   1520000 perm   1389 sec   (1094 perm/sec)   p_kst 5.263158e-06   p_cons 8.688816e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.411029e-06	k: 0	n:1530000
Cons ci ratio: 3.384392e-02	ci left: 8.545027e-03	ci right 8.839844e-03	k: 13298	n:1530000
KS ci ratio: 1.306662e+00	ci left: 2.257409e-06	ci right 1.030271e-05	k: 8	n:1530000
PIK3CA   1530000 perm   1405 sec   (1089 perm/sec)   p_kst 5.228758e-06   p_cons 8.691503e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.395373e-06	k: 0	n:1540000
Cons ci ratio: 3.371471e-02	ci left: 8.555215e-03	ci right 8.849235e-03	k: 13400	n:1540000
KS ci ratio: 1.306662e+00	ci left: 2.242751e-06	ci right 1.023581e-05	k: 8	n:1540000
PIK3CA   1540000 perm   1421 sec   (1084 perm/sec)   p_kst 5.194805e-06   p_cons 8.701299e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.379919e-06	k: 0	n:1550000
Cons ci ratio: 3.361335e-02	ci left: 8.551838e-03	ci right 8.844841e-03	k: 13481	n:1550000
KS ci ratio: 1.306662e+00	ci left: 2.228281e-06	ci right 1.016977e-05	k: 8	n:1550000
PIK3CA   1550000 perm   1438 sec   (1078 perm/sec)   p_kst 5.161290e-06   p_cons 8.697419e-03   p_joint 0

Joint ci ratio: 3.919997e+00	ci left: 0	ci right 2.364664e-06	k: 0	n:1560000
Cons ci ratio: 3.350417e-02	ci left: 8.552955e-03	ci right 8.845027e-03	k: 13569	n:1560000
KS ci ratio: 1.306662e+00	ci left: 2.213998e-06	ci right 1.010458e-05	k: 8	n:1560000
PIK3CA   1560000 perm   1453 sec   (1073 perm/sec)   p_kst 5.128205e-06   p_cons 8.698077e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.349602e-06	k: 0	n:1570000
Cons ci ratio: 3.339358e-02	ci left: 8.555323e-03	ci right 8.846493e-03	k: 13659	n:1570000
KS ci ratio: 1.239609e+00	ci left: 2.621260e-06	ci right 1.088201e-05	k: 9	n:1570000
PIK3CA   1570000 perm   1470 sec   (1068 perm/sec)   p_kst 5.732484e-06   p_cons 8.700000e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.334731e-06	k: 0	n:1580000
Cons ci ratio: 3.329874e-02	ci left: 8.550131e-03	ci right 8.840282e-03	k: 13737	n:1580000
KS ci ratio: 1.239609e+00	ci left: 2.604670e-06	ci right 1.081314e-05	k: 9	n:1580000
PIK3CA   1580000 perm   1486 sec   (1063 perm/sec)   p_kst 5.696203e-06   p_cons 8.694304e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.320047e-06	k: 0	n:1590000
Cons ci ratio: 3.317565e-02	ci left: 8.559975e-03	ci right 8.849366e-03	k: 13839	n:1590000
KS ci ratio: 1.181920e+00	ci left: 3.015972e-06	ci right 1.156623e-05	k: 10	n:1590000
PIK3CA   1590000 perm   1505 sec   (1057 perm/sec)   p_kst 6.289308e-06   p_cons 8.703774e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.305547e-06	k: 0	n:1600000
Cons ci ratio: 3.307426e-02	ci left: 8.559160e-03	ci right 8.847622e-03	k: 13924	n:1600000
KS ci ratio: 1.181920e+00	ci left: 2.997122e-06	ci right 1.149394e-05	k: 10	n:1600000
PIK3CA   1600000 perm   1522 sec   (1052 perm/sec)   p_kst 6.250000e-06   p_cons 8.702500e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.291227e-06	k: 0	n:1610000
Cons ci ratio: 3.297261e-02	ci left: 8.558973e-03	ci right 8.846525e-03	k: 14010	n:1610000
KS ci ratio: 1.131602e+00	ci left: 3.410663e-06	ci right 1.222484e-05	k: 11	n:1610000
PIK3CA   1610000 perm   1538 sec   (1047 perm/sec)   p_kst 6.832298e-06   p_cons 8.701863e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.277083e-06	k: 0	n:1620000
Cons ci ratio: 3.286837e-02	ci left: 8.560626e-03	ci right 8.847307e-03	k: 14099	n:1620000
KS ci ratio: 1.131602e+00	ci left: 3.389610e-06	ci right 1.214937e-05	k: 11	n:1620000
PIK3CA   1620000 perm   1554 sec   (1042 perm/sec)   p_kst 6.790123e-06   p_cons 8.703086e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.263114e-06	k: 0	n:1630000
Cons ci ratio: 3.276627e-02	ci left: 8.561652e-03	ci right 8.847460e-03	k: 14187	n:1630000
KS ci ratio: 1.131602e+00	ci left: 3.368815e-06	ci right 1.207484e-05	k: 11	n:1630000
PIK3CA   1630000 perm   1571 sec   (1037 perm/sec)   p_kst 6.748466e-06   p_cons 8.703681e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.249314e-06	k: 0	n:1640000
Cons ci ratio: 3.266396e-02	ci left: 8.563271e-03	ci right 8.848224e-03	k: 14276	n:1640000
KS ci ratio: 1.131602e+00	ci left: 3.348273e-06	ci right 1.200121e-05	k: 11	n:1640000
PIK3CA   1640000 perm   1588 sec   (1033 perm/sec)   p_kst 6.707317e-06   p_cons 8.704878e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.235682e-06	k: 0	n:1650000
Cons ci ratio: 3.255917e-02	ci left: 8.566675e-03	ci right 8.850811e-03	k: 14368	n:1650000
KS ci ratio: 1.131602e+00	ci left: 3.327981e-06	ci right 1.192848e-05	k: 11	n:1650000
PIK3CA   1650000 perm   1605 sec   (1028 perm/sec)   p_kst 6.666667e-06   p_cons 8.707879e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.222214e-06	k: 0	n:1660000
Cons ci ratio: 3.245992e-02	ci left: 8.567650e-03	ci right 8.850935e-03	k: 14456	n:1660000
KS ci ratio: 1.131602e+00	ci left: 3.307932e-06	ci right 1.185662e-05	k: 11	n:1660000
PIK3CA   1660000 perm   1621 sec   (1024 perm/sec)   p_kst 6.626506e-06   p_cons 8.708434e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.208907e-06	k: 0	n:1670000
Cons ci ratio: 3.236493e-02	ci left: 8.566833e-03	ci right 8.849246e-03	k: 14541	n:1670000
KS ci ratio: 1.131602e+00	ci left: 3.288124e-06	ci right 1.178562e-05	k: 11	n:1670000
PIK3CA   1670000 perm   1638 sec   (1019 perm/sec)   p_kst 6.586826e-06   p_cons 8.707186e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.195759e-06	k: 0	n:1680000
Cons ci ratio: 3.228303e-02	ci left: 8.559531e-03	ci right 8.840976e-03	k: 14615	n:1680000
KS ci ratio: 1.131602e+00	ci left: 3.268552e-06	ci right 1.171547e-05	k: 11	n:1680000
PIK3CA   1680000 perm   1656 sec   (1015 perm/sec)   p_kst 6.547619e-06   p_cons 8.699405e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.182767e-06	k: 0	n:1690000
Cons ci ratio: 3.218296e-02	ci left: 8.562295e-03	ci right 8.842943e-03	k: 14706	n:1690000
KS ci ratio: 1.131602e+00	ci left: 3.249212e-06	ci right 1.164615e-05	k: 11	n:1690000
PIK3CA   1690000 perm   1673 sec   (1010 perm/sec)   p_kst 6.508876e-06   p_cons 8.701775e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.169927e-06	k: 0	n:1700000
Cons ci ratio: 3.209366e-02	ci left: 8.559776e-03	ci right 8.839549e-03	k: 14788	n:1700000
KS ci ratio: 1.131602e+00	ci left: 3.230099e-06	ci right 1.157764e-05	k: 11	n:1700000
PIK3CA   1700000 perm   1689 sec   (1006 perm/sec)   p_kst 6.470588e-06   p_cons 8.698824e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.157237e-06	k: 0	n:1710000
Cons ci ratio: 3.201596e-02	ci left: 8.551486e-03	ci right 8.830299e-03	k: 14860	n:1710000
KS ci ratio: 1.131602e+00	ci left: 3.211209e-06	ci right 1.150993e-05	k: 11	n:1710000
PIK3CA   1710000 perm   1707 sec   (1002 perm/sec)   p_kst 6.432749e-06   p_cons 8.690058e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.144695e-06	k: 0	n:1720000
Cons ci ratio: 3.190651e-02	ci left: 8.560597e-03	ci right 8.838735e-03	k: 14962	n:1720000
KS ci ratio: 1.131602e+00	ci left: 3.192539e-06	ci right 1.144302e-05	k: 11	n:1720000
PIK3CA   1720000 perm   1724 sec   (998 perm/sec)   p_kst 6.395349e-06   p_cons 8.698837e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.132298e-06	k: 0	n:1730000
Cons ci ratio: 3.180776e-02	ci left: 8.564443e-03	ci right 8.841829e-03	k: 15055	n:1730000
KS ci ratio: 1.131602e+00	ci left: 3.174085e-06	ci right 1.137687e-05	k: 11	n:1730000
PIK3CA   1730000 perm   1742 sec   (993 perm/sec)   p_kst 6.358382e-06   p_cons 8.702312e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.120043e-06	k: 0	n:1740000
Cons ci ratio: 3.169831e-02	ci left: 8.574519e-03	ci right 8.851258e-03	k: 15159	n:1740000
KS ci ratio: 1.131602e+00	ci left: 3.155843e-06	ci right 1.131149e-05	k: 11	n:1740000
PIK3CA   1740000 perm   1759 sec   (989 perm/sec)   p_kst 6.321839e-06   p_cons 8.712069e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.107929e-06	k: 0	n:1750000
Cons ci ratio: 3.160879e-02	ci left: 8.574275e-03	ci right 8.850211e-03	k: 15245	n:1750000
KS ci ratio: 1.131602e+00	ci left: 3.137810e-06	ci right 1.124685e-05	k: 11	n:1750000
PIK3CA   1750000 perm   1777 sec   (985 perm/sec)   p_kst 6.285714e-06   p_cons 8.711429e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.095952e-06	k: 0	n:1760000
Cons ci ratio: 3.151899e-02	ci left: 8.574600e-03	ci right 8.849748e-03	k: 15332	n:1760000
KS ci ratio: 1.131602e+00	ci left: 3.119981e-06	ci right 1.118295e-05	k: 11	n:1760000
PIK3CA   1760000 perm   1795 sec   (980 perm/sec)   p_kst 6.250000e-06   p_cons 8.711364e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.084111e-06	k: 0	n:1770000
Cons ci ratio: 3.143304e-02	ci left: 8.573240e-03	ci right 8.847581e-03	k: 15416	n:1770000
KS ci ratio: 1.131602e+00	ci left: 3.102354e-06	ci right 1.111977e-05	k: 11	n:1770000
PIK3CA   1770000 perm   1813 sec   (976 perm/sec)   p_kst 6.214689e-06   p_cons 8.709605e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.072402e-06	k: 0	n:1780000
Cons ci ratio: 3.134778e-02	ci left: 8.571896e-03	ci right 8.845436e-03	k: 15500	n:1780000
KS ci ratio: 1.131602e+00	ci left: 3.084925e-06	ci right 1.105730e-05	k: 11	n:1780000
PIK3CA   1780000 perm   1831 sec   (972 perm/sec)   p_kst 6.179775e-06   p_cons 8.707865e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.060824e-06	k: 0	n:1790000
Cons ci ratio: 3.127232e-02	ci left: 8.565579e-03	ci right 8.838249e-03	k: 15575	n:1790000
KS ci ratio: 1.131602e+00	ci left: 3.067691e-06	ci right 1.099553e-05	k: 11	n:1790000
PIK3CA   1790000 perm   1849 sec   (968 perm/sec)   p_kst 6.145251e-06   p_cons 8.701117e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.049375e-06	k: 0	n:1800000
Cons ci ratio: 3.117833e-02	ci left: 8.569807e-03	ci right 8.841777e-03	k: 15669	n:1800000
KS ci ratio: 1.131602e+00	ci left: 3.050648e-06	ci right 1.093444e-05	k: 11	n:1800000
PIK3CA   1800000 perm   1867 sec   (964 perm/sec)   p_kst 6.111111e-06   p_cons 8.705000e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.038053e-06	k: 0	n:1810000
Cons ci ratio: 3.108815e-02	ci left: 8.572346e-03	ci right 8.843595e-03	k: 15760	n:1810000
KS ci ratio: 1.131602e+00	ci left: 3.033794e-06	ci right 1.087403e-05	k: 11	n:1810000
PIK3CA   1810000 perm   1886 sec   (960 perm/sec)   p_kst 6.077348e-06   p_cons 8.707182e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.026855e-06	k: 0	n:1820000
Cons ci ratio: 3.098989e-02	ci left: 8.579764e-03	ci right 8.850374e-03	k: 15860	n:1820000
KS ci ratio: 1.087208e+00	ci left: 3.406914e-06	ci right 1.151733e-05	k: 12	n:1820000
PIK3CA   1820000 perm   1904 sec   (956 perm/sec)   p_kst 6.593407e-06   p_cons 8.714286e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.015779e-06	k: 0	n:1830000
Cons ci ratio: 3.091209e-02	ci left: 8.576257e-03	ci right 8.846066e-03	k: 15940	n:1830000
KS ci ratio: 1.087208e+00	ci left: 3.388297e-06	ci right 1.145439e-05	k: 12	n:1830000
PIK3CA   1830000 perm   1923 sec   (952 perm/sec)   p_kst 6.557377e-06   p_cons 8.710383e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 2.004824e-06	k: 0	n:1840000
Cons ci ratio: 3.082129e-02	ci left: 8.580340e-03	ci right 8.849470e-03	k: 16034	n:1840000
KS ci ratio: 1.087208e+00	ci left: 3.369882e-06	ci right 1.139214e-05	k: 12	n:1840000
PIK3CA   1840000 perm   1941 sec   (948 perm/sec)   p_kst 6.521739e-06   p_cons 8.714130e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.993987e-06	k: 0	n:1850000
Cons ci ratio: 3.073417e-02	ci left: 8.582771e-03	ci right 8.851203e-03	k: 16125	n:1850000
KS ci ratio: 1.087208e+00	ci left: 3.351667e-06	ci right 1.133056e-05	k: 12	n:1850000
PIK3CA   1850000 perm   1960 sec   (944 perm/sec)   p_kst 6.486486e-06   p_cons 8.716216e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.983267e-06	k: 0	n:1860000
Cons ci ratio: 3.066305e-02	ci left: 8.576640e-03	ci right 8.844248e-03	k: 16200	n:1860000
KS ci ratio: 1.087208e+00	ci left: 3.333647e-06	ci right 1.126964e-05	k: 12	n:1860000
PIK3CA   1860000 perm   1981 sec   (939 perm/sec)   p_kst 6.451613e-06   p_cons 8.709677e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.972661e-06	k: 0	n:1870000
Cons ci ratio: 3.059052e-02	ci left: 8.571636e-03	ci right 8.838445e-03	k: 16277	n:1870000
KS ci ratio: 1.087208e+00	ci left: 3.315820e-06	ci right 1.120938e-05	k: 12	n:1870000
PIK3CA   1870000 perm   2000 sec   (935 perm/sec)   p_kst 6.417112e-06   p_cons 8.704278e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.962168e-06	k: 0	n:1880000
Cons ci ratio: 3.051757e-02	ci left: 8.567214e-03	ci right 8.833239e-03	k: 16355	n:1880000
KS ci ratio: 1.087208e+00	ci left: 3.298182e-06	ci right 1.114975e-05	k: 12	n:1880000
PIK3CA   1880000 perm   2019 sec   (931 perm/sec)   p_kst 6.382979e-06   p_cons 8.699468e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.951786e-06	k: 0	n:1890000
Cons ci ratio: 3.045261e-02	ci left: 8.558639e-03	ci right 8.823822e-03	k: 16425	n:1890000
KS ci ratio: 1.087208e+00	ci left: 3.280732e-06	ci right 1.109076e-05	k: 12	n:1890000
PIK3CA   1890000 perm   2038 sec   (927 perm/sec)   p_kst 6.349206e-06   p_cons 8.690476e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.941514e-06	k: 0	n:1900000
Cons ci ratio: 3.037507e-02	ci left: 8.557468e-03	ci right 8.821927e-03	k: 16509	n:1900000
KS ci ratio: 1.087208e+00	ci left: 3.263465e-06	ci right 1.103239e-05	k: 12	n:1900000
PIK3CA   1900000 perm   2057 sec   (924 perm/sec)   p_kst 6.315789e-06   p_cons 8.688947e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.931349e-06	k: 0	n:1910000
Cons ci ratio: 3.031286e-02	ci left: 8.547996e-03	ci right 8.811612e-03	k: 16577	n:1910000
KS ci ratio: 1.087208e+00	ci left: 3.246378e-06	ci right 1.097463e-05	k: 12	n:1910000
PIK3CA   1910000 perm   2077 sec   (920 perm/sec)   p_kst 6.282723e-06   p_cons 8.679058e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.921290e-06	k: 0	n:1920000
Cons ci ratio: 3.021717e-02	ci left: 8.557749e-03	ci right 8.820819e-03	k: 16682	n:1920000
KS ci ratio: 1.087208e+00	ci left: 3.229470e-06	ci right 1.091747e-05	k: 12	n:1920000
PIK3CA   1920000 perm   2096 sec   (916 perm/sec)   p_kst 6.250000e-06   p_cons 8.688542e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.911335e-06	k: 0	n:1930000
Cons ci ratio: 3.014776e-02	ci left: 8.553004e-03	ci right 8.815313e-03	k: 16759	n:1930000
KS ci ratio: 1.087208e+00	ci left: 3.212737e-06	ci right 1.086090e-05	k: 12	n:1930000
PIK3CA   1930000 perm   2115 sec   (912 perm/sec)   p_kst 6.217617e-06   p_cons 8.683420e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.901482e-06	k: 0	n:1940000
Cons ci ratio: 3.006351e-02	ci left: 8.557005e-03	ci right 8.818691e-03	k: 16853	n:1940000
KS ci ratio: 1.087208e+00	ci left: 3.196177e-06	ci right 1.080492e-05	k: 12	n:1940000
PIK3CA   1940000 perm   2134 sec   (909 perm/sec)   p_kst 6.185567e-06   p_cons 8.687113e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.891731e-06	k: 0	n:1950000
Cons ci ratio: 2.999962e-02	ci left: 8.549769e-03	ci right 8.810668e-03	k: 16925	n:1950000
KS ci ratio: 1.087208e+00	ci left: 3.179786e-06	ci right 1.074951e-05	k: 12	n:1950000
PIK3CA   1950000 perm   2154 sec   (905 perm/sec)   p_kst 6.153846e-06   p_cons 8.679487e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.882080e-06	k: 0	n:1960000
Cons ci ratio: 2.992991e-02	ci left: 8.546151e-03	ci right 8.806324e-03	k: 17004	n:1960000
KS ci ratio: 1.087209e+00	ci left: 3.163563e-06	ci right 1.069466e-05	k: 12	n:1960000
PIK3CA   1960000 perm   2173 sec   (902 perm/sec)   p_kst 6.122449e-06   p_cons 8.675510e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.872526e-06	k: 0	n:1970000
Cons ci ratio: 2.985628e-02	ci left: 8.545091e-03	ci right 8.804580e-03	k: 17088	n:1970000
KS ci ratio: 1.087209e+00	ci left: 3.147504e-06	ci right 1.064037e-05	k: 12	n:1970000
PIK3CA   1970000 perm   2193 sec   (898 perm/sec)   p_kst 6.091371e-06   p_cons 8.674112e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.863069e-06	k: 0	n:1980000
Cons ci ratio: 2.977707e-02	ci left: 8.547551e-03	ci right 8.806415e-03	k: 17179	n:1980000
KS ci ratio: 1.087209e+00	ci left: 3.131607e-06	ci right 1.058664e-05	k: 12	n:1980000
PIK3CA   1980000 perm   2213 sec   (895 perm/sec)   p_kst 6.060606e-06   p_cons 8.676263e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.853707e-06	k: 0	n:1990000
Cons ci ratio: 2.970630e-02	ci left: 8.545498e-03	ci right 8.803674e-03	k: 17261	n:1990000
KS ci ratio: 1.087209e+00	ci left: 3.115871e-06	ci right 1.053344e-05	k: 12	n:1990000
PIK3CA   1990000 perm   2233 sec   (891 perm/sec)   p_kst 6.030151e-06   p_cons 8.673869e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.844438e-06	k: 0	n:2000000
Cons ci ratio: 2.962483e-02	ci left: 8.549918e-03	ci right 8.807507e-03	k: 17356	n:2000000
KS ci ratio: 1.087209e+00	ci left: 3.100291e-06	ci right 1.048077e-05	k: 12	n:2000000
PIK3CA   2000000 perm   2253 sec   (888 perm/sec)   p_kst 6.000000e-06   p_cons 8.678000e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.835262e-06	k: 0	n:2010000
Cons ci ratio: 2.954745e-02	ci left: 8.552320e-03	ci right 8.809297e-03	k: 17447	n:2010000
KS ci ratio: 1.087209e+00	ci left: 3.084867e-06	ci right 1.042863e-05	k: 12	n:2010000
PIK3CA   2010000 perm   2273 sec   (884 perm/sec)   p_kst 5.970149e-06   p_cons 8.680100e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.826176e-06	k: 0	n:2020000
Cons ci ratio: 2.947151e-02	ci left: 8.554208e-03	ci right 8.810570e-03	k: 17537	n:2020000
KS ci ratio: 1.047660e+00	ci left: 3.426713e-06	ci right 1.100512e-05	k: 13	n:2020000
PIK3CA   2020000 perm   2293 sec   (881 perm/sec)   p_kst 6.435644e-06   p_cons 8.681683e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.817180e-06	k: 0	n:2030000
Cons ci ratio: 2.940289e-02	ci left: 8.552166e-03	ci right 8.807860e-03	k: 17619	n:2030000
KS ci ratio: 1.047660e+00	ci left: 3.409833e-06	ci right 1.095091e-05	k: 13	n:2030000
PIK3CA   2030000 perm   2313 sec   (878 perm/sec)   p_kst 6.403941e-06   p_cons 8.679310e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.808273e-06	k: 0	n:2040000
Cons ci ratio: 2.933809e-02	ci left: 8.548197e-03	ci right 8.803200e-03	k: 17697	n:2040000
KS ci ratio: 1.047660e+00	ci left: 3.393118e-06	ci right 1.089723e-05	k: 13	n:2040000
PIK3CA   2040000 perm   2333 sec   (874 perm/sec)   p_kst 6.372549e-06   p_cons 8.675000e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.799452e-06	k: 0	n:2050000
Cons ci ratio: 2.925214e-02	ci left: 8.556860e-03	ci right 8.811361e-03	k: 17801	n:2050000
KS ci ratio: 1.047660e+00	ci left: 3.376566e-06	ci right 1.084407e-05	k: 13	n:2050000
PIK3CA   2050000 perm   2353 sec   (871 perm/sec)   p_kst 6.341463e-06   p_cons 8.683415e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.790717e-06	k: 0	n:2060000
Cons ci ratio: 2.918998e-02	ci left: 8.551945e-03	ci right 8.805750e-03	k: 17877	n:2060000
KS ci ratio: 1.047660e+00	ci left: 3.360175e-06	ci right 1.079143e-05	k: 13	n:2060000
PIK3CA   2060000 perm   2374 sec   (868 perm/sec)   p_kst 6.310680e-06   p_cons 8.678155e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.782066e-06	k: 0	n:2070000
Cons ci ratio: 2.912739e-02	ci left: 8.547558e-03	ci right 8.800680e-03	k: 17954	n:2070000
KS ci ratio: 1.047660e+00	ci left: 3.343943e-06	ci right 1.073930e-05	k: 13	n:2070000
PIK3CA   2070000 perm   2394 sec   (865 perm/sec)   p_kst 6.280193e-06   p_cons 8.673430e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.773498e-06	k: 0	n:2080000
Cons ci ratio: 2.906032e-02	ci left: 8.546077e-03	ci right 8.798563e-03	k: 18037	n:2080000
KS ci ratio: 1.047660e+00	ci left: 3.327866e-06	ci right 1.068767e-05	k: 13	n:2080000
PIK3CA   2080000 perm   2415 sec   (861 perm/sec)   p_kst 6.250000e-06   p_cons 8.671635e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.765013e-06	k: 0	n:2090000
Cons ci ratio: 2.899049e-02	ci left: 8.546512e-03	ci right 8.798393e-03	k: 18124	n:2090000
KS ci ratio: 1.047660e+00	ci left: 3.311943e-06	ci right 1.063653e-05	k: 13	n:2090000
PIK3CA   2090000 perm   2436 sec   (858 perm/sec)   p_kst 6.220096e-06   p_cons 8.671770e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.756608e-06	k: 0	n:2100000
Cons ci ratio: 2.892036e-02	ci left: 8.547415e-03	ci right 8.798704e-03	k: 18212	n:2100000
KS ci ratio: 1.047660e+00	ci left: 3.296172e-06	ci right 1.058588e-05	k: 13	n:2100000
PIK3CA   2100000 perm   2456 sec   (855 perm/sec)   p_kst 6.190476e-06   p_cons 8.672381e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.748283e-06	k: 0	n:2110000
Cons ci ratio: 2.883723e-02	ci left: 8.556311e-03	ci right 8.807126e-03	k: 18317	n:2110000
KS ci ratio: 1.047660e+00	ci left: 3.280550e-06	ci right 1.053571e-05	k: 13	n:2110000
PIK3CA   2110000 perm   2477 sec   (852 perm/sec)   p_kst 6.161137e-06   p_cons 8.681043e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.740036e-06	k: 0	n:2120000
Cons ci ratio: 2.877609e-02	ci left: 8.552478e-03	ci right 8.802641e-03	k: 18395	n:2120000
KS ci ratio: 1.047660e+00	ci left: 3.265076e-06	ci right 1.048601e-05	k: 13	n:2120000
PIK3CA   2120000 perm   2498 sec   (849 perm/sec)   p_kst 6.132075e-06   p_cons 8.676887e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.731867e-06	k: 0	n:2130000
Cons ci ratio: 2.870045e-02	ci left: 8.557538e-03	ci right 8.807181e-03	k: 18492	n:2130000
KS ci ratio: 1.047660e+00	ci left: 3.249747e-06	ci right 1.043678e-05	k: 13	n:2130000
PIK3CA   2130000 perm   2519 sec   (846 perm/sec)   p_kst 6.103286e-06   p_cons 8.681690e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.723774e-06	k: 0	n:2140000
Cons ci ratio: 2.863396e-02	ci left: 8.557449e-03	ci right 8.806500e-03	k: 18578	n:2140000
KS ci ratio: 1.047660e+00	ci left: 3.234561e-06	ci right 1.038801e-05	k: 13	n:2140000
PIK3CA   2140000 perm   2540 sec   (842 perm/sec)   p_kst 6.074766e-06   p_cons 8.681308e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.715756e-06	k: 0	n:2150000
Cons ci ratio: 2.856792e-02	ci left: 8.557361e-03	ci right 8.805826e-03	k: 18664	n:2150000
KS ci ratio: 1.047660e+00	ci left: 3.219517e-06	ci right 1.033970e-05	k: 13	n:2150000
PIK3CA   2150000 perm   2562 sec   (839 perm/sec)   p_kst 6.046512e-06   p_cons 8.680930e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.707813e-06	k: 0	n:2160000
Cons ci ratio: 2.849927e-02	ci left: 8.559113e-03	ci right 8.807022e-03	k: 18754	n:2160000
KS ci ratio: 1.047660e+00	ci left: 3.204611e-06	ci right 1.029183e-05	k: 13	n:2160000
PIK3CA   2160000 perm   2583 sec   (836 perm/sec)   p_kst 6.018519e-06   p_cons 8.682407e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.699943e-06	k: 0	n:2170000
Cons ci ratio: 2.842275e-02	ci left: 8.565883e-03	ci right 8.813311e-03	k: 18855	n:2170000
KS ci ratio: 1.047660e+00	ci left: 3.189844e-06	ci right 1.024440e-05	k: 13	n:2170000
PIK3CA   2170000 perm   2605 sec   (833 perm/sec)   p_kst 5.990783e-06   p_cons 8.688940e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.692145e-06	k: 0	n:2180000
Cons ci ratio: 2.836193e-02	ci left: 8.563482e-03	ci right 8.810303e-03	k: 18936	n:2180000
KS ci ratio: 1.012136e+00	ci left: 3.510981e-06	ci right 1.077503e-05	k: 14	n:2180000
PIK3CA   2180000 perm   2626 sec   (830 perm/sec)   p_kst 6.422018e-06   p_cons 8.686239e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.684418e-06	k: 0	n:2190000
Cons ci ratio: 2.828576e-02	ci left: 8.570625e-03	ci right 8.816978e-03	k: 19038	n:2190000
KS ci ratio: 1.012136e+00	ci left: 3.494950e-06	ci right 1.072583e-05	k: 14	n:2190000
PIK3CA   2190000 perm   2648 sec   (827 perm/sec)   p_kst 6.392694e-06   p_cons 8.693151e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.676762e-06	k: 0	n:2200000
Cons ci ratio: 2.822061e-02	ci left: 8.571385e-03	ci right 8.817183e-03	k: 19126	n:2200000
KS ci ratio: 1.012136e+00	ci left: 3.479063e-06	ci right 1.067708e-05	k: 14	n:2200000
PIK3CA   2200000 perm   2669 sec   (824 perm/sec)   p_kst 6.363636e-06   p_cons 8.693636e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.669175e-06	k: 0	n:2210000
Cons ci ratio: 2.815295e-02	ci left: 8.573936e-03	ci right 8.819209e-03	k: 19218	n:2210000
KS ci ratio: 1.012136e+00	ci left: 3.463321e-06	ci right 1.062877e-05	k: 14	n:2210000
PIK3CA   2210000 perm   2691 sec   (821 perm/sec)   p_kst 6.334842e-06   p_cons 8.695928e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.661656e-06	k: 0	n:2220000
Cons ci ratio: 2.809679e-02	ci left: 8.569756e-03	ci right 8.814411e-03	k: 19295	n:2220000
KS ci ratio: 1.012136e+00	ci left: 3.447720e-06	ci right 1.058089e-05	k: 14	n:2220000
PIK3CA   2220000 perm   2713 sec   (818 perm/sec)   p_kst 6.306306e-06   p_cons 8.691441e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.654205e-06	k: 0	n:2230000
Cons ci ratio: 2.803366e-02	ci left: 8.570066e-03	ci right 8.814172e-03	k: 19382	n:2230000
KS ci ratio: 1.012136e+00	ci left: 3.432260e-06	ci right 1.053344e-05	k: 14	n:2230000
PIK3CA   2230000 perm   2735 sec   (815 perm/sec)   p_kst 6.278027e-06   p_cons 8.691480e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.646820e-06	k: 0	n:2240000
Cons ci ratio: 2.796878e-02	ci left: 8.571704e-03	ci right 8.815283e-03	k: 19472	n:2240000
KS ci ratio: 1.012136e+00	ci left: 3.416937e-06	ci right 1.048642e-05	k: 14	n:2240000
PIK3CA   2240000 perm   2757 sec   (813 perm/sec)   p_kst 6.250000e-06   p_cons 8.692857e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.639501e-06	k: 0	n:2250000
Cons ci ratio: 2.790220e-02	ci left: 8.574652e-03	ci right 8.817726e-03	k: 19565	n:2250000
KS ci ratio: 1.012136e+00	ci left: 3.401751e-06	ci right 1.043981e-05	k: 14	n:2250000
PIK3CA   2250000 perm   2779 sec   (810 perm/sec)   p_kst 6.222222e-06   p_cons 8.695556e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.632246e-06	k: 0	n:2260000
Cons ci ratio: 2.783465e-02	ci left: 8.578454e-03	ci right 8.821037e-03	k: 19660	n:2260000
KS ci ratio: 1.012136e+00	ci left: 3.386699e-06	ci right 1.039362e-05	k: 14	n:2260000
PIK3CA   2260000 perm   2801 sec   (807 perm/sec)   p_kst 6.194690e-06   p_cons 8.699115e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.625056e-06	k: 0	n:2270000
Cons ci ratio: 2.778108e-02	ci left: 8.573911e-03	ci right 8.815891e-03	k: 19736	n:2270000
KS ci ratio: 1.012136e+00	ci left: 3.371779e-06	ci right 1.034783e-05	k: 14	n:2270000
PIK3CA   2270000 perm   2823 sec   (804 perm/sec)   p_kst 6.167401e-06   p_cons 8.694273e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.617928e-06	k: 0	n:2280000
Cons ci ratio: 2.772499e-02	ci left: 8.571150e-03	ci right 8.812556e-03	k: 19816	n:2280000
KS ci ratio: 1.012136e+00	ci left: 3.356991e-06	ci right 1.030244e-05	k: 14	n:2280000
PIK3CA   2280000 perm   2845 sec   (801 perm/sec)   p_kst 6.140351e-06   p_cons 8.691228e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.610863e-06	k: 0	n:2290000
Cons ci ratio: 2.766784e-02	ci left: 8.569281e-03	ci right 8.810130e-03	k: 19898	n:2290000
KS ci ratio: 1.012136e+00	ci left: 3.342332e-06	ci right 1.025746e-05	k: 14	n:2290000
PIK3CA   2290000 perm   2867 sec   (799 perm/sec)   p_kst 6.113537e-06   p_cons 8.689083e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.603859e-06	k: 0	n:2300000
Cons ci ratio: 2.761103e-02	ci left: 8.567429e-03	ci right 8.807723e-03	k: 19980	n:2300000
KS ci ratio: 1.012136e+00	ci left: 3.327800e-06	ci right 1.021286e-05	k: 14	n:2300000
PIK3CA   2300000 perm   2890 sec   (796 perm/sec)   p_kst 6.086957e-06   p_cons 8.686957e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.596916e-06	k: 0	n:2310000
Cons ci ratio: 2.755458e-02	ci left: 8.565594e-03	ci right 8.805337e-03	k: 20062	n:2310000
KS ci ratio: 1.012136e+00	ci left: 3.313394e-06	ci right 1.016865e-05	k: 14	n:2310000
PIK3CA   2310000 perm   2912 sec   (793 perm/sec)   p_kst 6.060606e-06   p_cons 8.684848e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.590033e-06	k: 0	n:2320000
Cons ci ratio: 2.748540e-02	ci left: 8.571908e-03	ci right 8.811217e-03	k: 20163	n:2320000
KS ci ratio: 1.012136e+00	ci left: 3.299112e-06	ci right 1.012482e-05	k: 14	n:2320000
PIK3CA   2320000 perm   2935 sec   (791 perm/sec)   p_kst 6.034483e-06   p_cons 8.690948e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.583209e-06	k: 0	n:2330000
Cons ci ratio: 2.743040e-02	ci left: 8.569644e-03	ci right 8.808403e-03	k: 20244	n:2330000
KS ci ratio: 1.012136e+00	ci left: 3.284952e-06	ci right 1.008136e-05	k: 14	n:2330000
PIK3CA   2330000 perm   2957 sec   (788 perm/sec)   p_kst 6.008584e-06   p_cons 8.688412e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.576443e-06	k: 0	n:2340000
Cons ci ratio: 2.737029e-02	ci left: 8.570796e-03	ci right 8.809055e-03	k: 20333	n:2340000
KS ci ratio: 1.012136e+00	ci left: 3.270914e-06	ci right 1.003828e-05	k: 14	n:2340000
PIK3CA   2340000 perm   2980 sec   (785 perm/sec)   p_kst 5.982906e-06   p_cons 8.689316e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.569735e-06	k: 0	n:2350000
Cons ci ratio: 2.731732e-02	ci left: 8.567711e-03	ci right 8.805417e-03	k: 20412	n:2350000
KS ci ratio: 1.012136e+00	ci left: 3.256995e-06	ci right 9.995563e-06	k: 14	n:2350000
PIK3CA   2350000 perm   3003 sec   (783 perm/sec)   p_kst 5.957447e-06   p_cons 8.685957e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.563083e-06	k: 0	n:2360000
Cons ci ratio: 2.725393e-02	ci left: 8.571387e-03	ci right 8.808634e-03	k: 20507	n:2360000
KS ci ratio: 1.012136e+00	ci left: 3.243194e-06	ci right 9.953209e-06	k: 14	n:2360000
PIK3CA   2360000 perm   3026 sec   (780 perm/sec)   p_kst 5.932203e-06   p_cons 8.689407e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.556488e-06	k: 0	n:2370000
Cons ci ratio: 2.719497e-02	ci left: 8.572518e-03	ci right 8.809276e-03	k: 20596	n:2370000
KS ci ratio: 1.012136e+00	ci left: 3.229510e-06	ci right 9.911213e-06	k: 14	n:2370000
PIK3CA   2370000 perm   3049 sec   (777 perm/sec)   p_kst 5.907173e-06   p_cons 8.690295e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.549948e-06	k: 0	n:2380000
Cons ci ratio: 2.712978e-02	ci left: 8.577814e-03	ci right 8.814141e-03	k: 20695	n:2380000
KS ci ratio: 1.012136e+00	ci left: 3.215941e-06	ci right 9.869569e-06	k: 14	n:2380000
PIK3CA   2380000 perm   3072 sec   (775 perm/sec)   p_kst 5.882353e-06   p_cons 8.695378e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.543463e-06	k: 0	n:2390000
Cons ci ratio: 2.707885e-02	ci left: 8.574338e-03	ci right 8.810119e-03	k: 20773	n:2390000
KS ci ratio: 1.012136e+00	ci left: 3.202485e-06	ci right 9.828274e-06	k: 14	n:2390000
PIK3CA   2390000 perm   3095 sec   (772 perm/sec)   p_kst 5.857741e-06   p_cons 8.691632e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.537032e-06	k: 0	n:2400000
Cons ci ratio: 2.702363e-02	ci left: 8.573788e-03	ci right 8.809066e-03	k: 20858	n:2400000
KS ci ratio: 1.012136e+00	ci left: 3.189141e-06	ci right 9.787323e-06	k: 14	n:2400000
PIK3CA   2400000 perm   3119 sec   (770 perm/sec)   p_kst 5.833333e-06   p_cons 8.690833e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.530654e-06	k: 0	n:2410000
Cons ci ratio: 2.697005e-02	ci left: 8.572420e-03	ci right 8.807186e-03	k: 20941	n:2410000
KS ci ratio: 1.012136e+00	ci left: 3.175908e-06	ci right 9.746712e-06	k: 14	n:2410000
PIK3CA   2410000 perm   3142 sec   (767 perm/sec)   p_kst 5.809129e-06   p_cons 8.689212e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.524329e-06	k: 0	n:2420000
Cons ci ratio: 2.692001e-02	ci left: 8.569011e-03	ci right 8.803242e-03	k: 21019	n:2420000
KS ci ratio: 1.012136e+00	ci left: 3.162785e-06	ci right 9.706436e-06	k: 14	n:2420000
PIK3CA   2420000 perm   3166 sec   (764 perm/sec)   p_kst 5.785124e-06   p_cons 8.685537e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.518056e-06	k: 0	n:2430000
Cons ci ratio: 2.685806e-02	ci left: 8.573397e-03	ci right 8.807200e-03	k: 21116	n:2430000
KS ci ratio: 1.012136e+00	ci left: 3.149769e-06	ci right 9.666492e-06	k: 14	n:2430000
PIK3CA   2430000 perm   3189 sec   (762 perm/sec)   p_kst 5.761317e-06   p_cons 8.689712e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.511835e-06	k: 0	n:2440000
Cons ci ratio: 2.680354e-02	ci left: 8.573269e-03	ci right 8.806587e-03	k: 21202	n:2440000
KS ci ratio: 1.012136e+00	ci left: 3.136860e-06	ci right 9.626875e-06	k: 14	n:2440000
PIK3CA   2440000 perm   3212 sec   (760 perm/sec)   p_kst 5.737705e-06   p_cons 8.689344e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.505664e-06	k: 0	n:2450000
Cons ci ratio: 2.674048e-02	ci left: 8.578820e-03	ci right 8.811731e-03	k: 21302	n:2450000
KS ci ratio: 1.012136e+00	ci left: 3.124057e-06	ci right 9.587582e-06	k: 14	n:2450000
PIK3CA   2450000 perm   3236 sec   (757 perm/sec)   p_kst 5.714286e-06   p_cons 8.694694e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.499543e-06	k: 0	n:2460000
Cons ci ratio: 2.668416e-02	ci left: 8.580288e-03	ci right 8.812741e-03	k: 21392	n:2460000
KS ci ratio: 1.012136e+00	ci left: 3.111357e-06	ci right 9.548608e-06	k: 14	n:2460000
PIK3CA   2460000 perm   3260 sec   (755 perm/sec)   p_kst 5.691057e-06   p_cons 8.695935e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.493472e-06	k: 0	n:2470000
Cons ci ratio: 2.662256e-02	ci left: 8.585364e-03	ci right 8.817410e-03	k: 21491	n:2470000
KS ci ratio: 1.012136e+00	ci left: 3.098761e-06	ci right 9.509950e-06	k: 14	n:2470000
PIK3CA   2470000 perm   3284 sec   (752 perm/sec)   p_kst 5.668016e-06   p_cons 8.700810e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.487450e-06	k: 0	n:2480000
Cons ci ratio: 2.656077e-02	ci left: 8.590800e-03	ci right 8.822446e-03	k: 21591	n:2480000
KS ci ratio: 1.012136e+00	ci left: 3.086266e-06	ci right 9.471603e-06	k: 14	n:2480000
PIK3CA   2480000 perm   3307 sec   (750 perm/sec)   p_kst 5.645161e-06   p_cons 8.706048e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.481477e-06	k: 0	n:2490000
Cons ci ratio: 2.650866e-02	ci left: 8.590209e-03	ci right 8.821377e-03	k: 21676	n:2490000
KS ci ratio: 1.012136e+00	ci left: 3.073871e-06	ci right 9.433565e-06	k: 14	n:2490000
PIK3CA   2490000 perm   3331 sec   (747 perm/sec)   p_kst 5.622490e-06   p_cons 8.705221e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.475551e-06	k: 0	n:2500000
Cons ci ratio: 2.646421e-02	ci left: 8.584855e-03	ci right 8.815485e-03	k: 21749	n:2500000
KS ci ratio: 1.012136e+00	ci left: 3.061575e-06	ci right 9.395831e-06	k: 14	n:2500000
PIK3CA   2500000 perm   3356 sec   (745 perm/sec)   p_kst 5.600000e-06   p_cons 8.699600e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.469672e-06	k: 0	n:2510000
Cons ci ratio: 2.641632e-02	ci left: 8.581918e-03	ci right 8.812046e-03	k: 21828	n:2510000
KS ci ratio: 1.012136e+00	ci left: 3.049378e-06	ci right 9.358397e-06	k: 14	n:2510000
PIK3CA   2510000 perm   3380 sec   (743 perm/sec)   p_kst 5.577689e-06   p_cons 8.696414e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.463840e-06	k: 0	n:2520000
Cons ci ratio: 2.636080e-02	ci left: 8.584130e-03	ci right 8.813827e-03	k: 21920	n:2520000
KS ci ratio: 1.012136e+00	ci left: 3.037277e-06	ci right 9.321261e-06	k: 14	n:2520000
PIK3CA   2520000 perm   3404 sec   (740 perm/sec)   p_kst 5.555556e-06   p_cons 8.698413e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.458054e-06	k: 0	n:2530000
Cons ci ratio: 2.630563e-02	ci left: 8.586325e-03	ci right 8.815592e-03	k: 22012	n:2530000
KS ci ratio: 1.012136e+00	ci left: 3.025272e-06	ci right 9.284418e-06	k: 14	n:2530000
PIK3CA   2530000 perm   3429 sec   (738 perm/sec)   p_kst 5.533597e-06   p_cons 8.700395e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.452314e-06	k: 0	n:2540000
Cons ci ratio: 2.625860e-02	ci left: 8.583418e-03	ci right 8.812192e-03	k: 22091	n:2540000
KS ci ratio: 1.012136e+00	ci left: 3.013362e-06	ci right 9.247865e-06	k: 14	n:2540000
PIK3CA   2540000 perm   3453 sec   (736 perm/sec)   p_kst 5.511811e-06   p_cons 8.697244e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.446618e-06	k: 0	n:2550000
Cons ci ratio: 2.620943e-02	ci left: 8.582093e-03	ci right 8.810397e-03	k: 22174	n:2550000
KS ci ratio: 1.012136e+00	ci left: 3.001544e-06	ci right 9.211599e-06	k: 14	n:2550000
PIK3CA   2550000 perm   3477 sec   (733 perm/sec)   p_kst 5.490196e-06   p_cons 8.695686e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.440968e-06	k: 0	n:2560000
Cons ci ratio: 2.615698e-02	ci left: 8.583108e-03	ci right 8.810975e-03	k: 22263	n:2560000
KS ci ratio: 1.012136e+00	ci left: 2.989820e-06	ci right 9.175616e-06	k: 14	n:2560000
PIK3CA   2560000 perm   3502 sec   (731 perm/sec)   p_kst 5.468750e-06   p_cons 8.696484e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.435361e-06	k: 0	n:2570000
Cons ci ratio: 2.610838e-02	ci left: 8.581795e-03	ci right 8.809197e-03	k: 22346	n:2570000
KS ci ratio: 1.012136e+00	ci left: 2.978186e-06	ci right 9.139914e-06	k: 14	n:2570000
PIK3CA   2570000 perm   3527 sec   (729 perm/sec)   p_kst 5.447471e-06   p_cons 8.694942e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.429797e-06	k: 0	n:2580000
Cons ci ratio: 2.606005e-02	ci left: 8.580493e-03	ci right 8.807434e-03	k: 22429	n:2580000
KS ci ratio: 1.012137e+00	ci left: 2.966643e-06	ci right 9.104488e-06	k: 14	n:2580000
PIK3CA   2580000 perm   3552 sec   (726 perm/sec)   p_kst 5.426357e-06   p_cons 8.693411e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.424277e-06	k: 0	n:2590000
Cons ci ratio: 2.601549e-02	ci left: 8.576900e-03	ci right 8.803352e-03	k: 22506	n:2590000
KS ci ratio: 1.012137e+00	ci left: 2.955188e-06	ci right 9.069335e-06	k: 14	n:2590000
PIK3CA   2590000 perm   3577 sec   (724 perm/sec)   p_kst 5.405405e-06   p_cons 8.689575e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.418799e-06	k: 0	n:2600000
Cons ci ratio: 2.596071e-02	ci left: 8.580213e-03	ci right 8.806268e-03	k: 22601	n:2600000
KS ci ratio: 1.012137e+00	ci left: 2.943822e-06	ci right 9.034453e-06	k: 14	n:2600000
PIK3CA   2600000 perm   3602 sec   (722 perm/sec)   p_kst 5.384615e-06   p_cons 8.692692e-03   p_joint 0

Joint ci ratio: 3.919998e+00	ci left: 0	ci right 1.413363e-06	k: 0	n:2610000
Cons ci ratio: 2.590398e-02	ci left: 8.585024e-03	ci right 8.810704e-03	k: 22700	n:2610000
KS ci ratio: 1.012137e+00	ci left: 2.932543e-06	ci right 8.999838e-06	k: 14	n:2610000
PIK3CA   2610000 perm   3627 sec   (720 perm/sec)   p_kst 5.363985e-06   p_cons 8.697318e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.407968e-06	k: 0	n:2620000
Cons ci ratio: 2.586766e-02	ci left: 8.576525e-03	ci right 8.801662e-03	k: 22764	n:2620000
KS ci ratio: 1.012137e+00	ci left: 2.921350e-06	ci right 8.965488e-06	k: 14	n:2620000
PIK3CA   2620000 perm   3655 sec   (717 perm/sec)   p_kst 5.343511e-06   p_cons 8.688550e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.402615e-06	k: 0	n:2630000
Cons ci ratio: 2.582008e-02	ci left: 8.575648e-03	ci right 8.800341e-03	k: 22848	n:2630000
KS ci ratio: 1.012137e+00	ci left: 2.910243e-06	ci right 8.931399e-06	k: 14	n:2630000
PIK3CA   2630000 perm   3680 sec   (715 perm/sec)   p_kst 5.323194e-06   p_cons 8.687452e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.397302e-06	k: 0	n:2640000
Cons ci ratio: 2.576710e-02	ci left: 8.578541e-03	ci right 8.802842e-03	k: 22942	n:2640000
KS ci ratio: 9.799968e-01	ci left: 3.180074e-06	ci right 9.371278e-06	k: 15	n:2640000
PIK3CA   2640000 perm   3705 sec   (712 perm/sec)   p_kst 5.681818e-06   p_cons 8.690152e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.392029e-06	k: 0	n:2650000
Cons ci ratio: 2.570994e-02	ci left: 8.584412e-03	ci right 8.808362e-03	k: 23044	n:2650000
KS ci ratio: 9.799969e-01	ci left: 3.168074e-06	ci right 9.335914e-06	k: 15	n:2650000
PIK3CA   2650000 perm   3731 sec   (710 perm/sec)   p_kst 5.660377e-06   p_cons 8.695849e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.386796e-06	k: 0	n:2660000
Cons ci ratio: 2.566210e-02	ci left: 8.584263e-03	ci right 8.807786e-03	k: 23130	n:2660000
KS ci ratio: 9.799969e-01	ci left: 3.156164e-06	ci right 9.300817e-06	k: 15	n:2660000
PIK3CA   2660000 perm   3756 sec   (708 perm/sec)   p_kst 5.639098e-06   p_cons 8.695489e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.381602e-06	k: 0	n:2670000
Cons ci ratio: 2.561287e-02	ci left: 8.585232e-03	ci right 8.808345e-03	k: 23219	n:2670000
KS ci ratio: 9.799969e-01	ci left: 3.144343e-06	ci right 9.265983e-06	k: 15	n:2670000
PIK3CA   2670000 perm   3782 sec   (706 perm/sec)   p_kst 5.617978e-06   p_cons 8.696255e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.376447e-06	k: 0	n:2680000
Cons ci ratio: 2.555893e-02	ci left: 8.589531e-03	ci right 8.812279e-03	k: 23317	n:2680000
KS ci ratio: 9.799969e-01	ci left: 3.132610e-06	ci right 9.231408e-06	k: 15	n:2680000
PIK3CA   2680000 perm   3807 sec   (704 perm/sec)   p_kst 5.597015e-06   p_cons 8.700373e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.371330e-06	k: 0	n:2690000
Cons ci ratio: 2.550919e-02	ci left: 8.591213e-03	ci right 8.813564e-03	k: 23408	n:2690000
KS ci ratio: 9.799969e-01	ci left: 3.120965e-06	ci right 9.197091e-06	k: 15	n:2690000
PIK3CA   2690000 perm   3833 sec   (702 perm/sec)   p_kst 5.576208e-06   p_cons 8.701859e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.366251e-06	k: 0	n:2700000
Cons ci ratio: 2.546410e-02	ci left: 8.589938e-03	ci right 8.811858e-03	k: 23491	n:2700000
KS ci ratio: 9.799969e-01	ci left: 3.109406e-06	ci right 9.163027e-06	k: 15	n:2700000
PIK3CA   2700000 perm   3859 sec   (700 perm/sec)   p_kst 5.555556e-06   p_cons 8.700370e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.361209e-06	k: 0	n:2710000
Cons ci ratio: 2.542143e-02	ci left: 8.587207e-03	ci right 8.808679e-03	k: 23570	n:2710000
KS ci ratio: 9.799969e-01	ci left: 3.097932e-06	ci right 9.129216e-06	k: 15	n:2710000
PIK3CA   2710000 perm   3885 sec   (698 perm/sec)   p_kst 5.535055e-06   p_cons 8.697417e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.356205e-06	k: 0	n:2720000
Cons ci ratio: 2.538006e-02	ci left: 8.583765e-03	ci right 8.804783e-03	k: 23647	n:2720000
KS ci ratio: 9.799969e-01	ci left: 3.086542e-06	ci right 9.095652e-06	k: 15	n:2720000
PIK3CA   2720000 perm   3911 sec   (695 perm/sec)   p_kst 5.514706e-06   p_cons 8.693750e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.351237e-06	k: 0	n:2730000
Cons ci ratio: 2.533996e-02	ci left: 8.579621e-03	ci right 8.800178e-03	k: 23722	n:2730000
KS ci ratio: 9.799969e-01	ci left: 3.075236e-06	ci right 9.062335e-06	k: 15	n:2730000
PIK3CA   2730000 perm   3938 sec   (693 perm/sec)   p_kst 5.494505e-06   p_cons 8.689377e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.346305e-06	k: 0	n:2740000
Cons ci ratio: 2.528880e-02	ci left: 8.583123e-03	ci right 8.803318e-03	k: 23818	n:2740000
KS ci ratio: 9.799970e-01	ci left: 3.064013e-06	ci right 9.029261e-06	k: 15	n:2740000
PIK3CA   2740000 perm   3964 sec   (691 perm/sec)   p_kst 5.474453e-06   p_cons 8.692701e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.341410e-06	k: 0	n:2750000
Cons ci ratio: 2.524168e-02	ci left: 8.584071e-03	ci right 8.803874e-03	k: 23907	n:2750000
KS ci ratio: 9.507365e-01	ci left: 3.325597e-06	ci right 9.448346e-06	k: 16	n:2750000
PIK3CA   2750000 perm   3991 sec   (689 perm/sec)   p_kst 5.818182e-06   p_cons 8.693455e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.336550e-06	k: 0	n:2760000
Cons ci ratio: 2.520118e-02	ci left: 8.580692e-03	ci right 8.800051e-03	k: 23984	n:2760000
KS ci ratio: 9.507365e-01	ci left: 3.313548e-06	ci right 9.414113e-06	k: 16	n:2760000
PIK3CA   2760000 perm   4017 sec   (687 perm/sec)   p_kst 5.797101e-06   p_cons 8.689855e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.331725e-06	k: 0	n:2770000
Cons ci ratio: 2.515401e-02	ci left: 8.582001e-03	ci right 8.800977e-03	k: 24074	n:2770000
KS ci ratio: 9.507366e-01	ci left: 3.301586e-06	ci right 9.380127e-06	k: 16	n:2770000
PIK3CA   2770000 perm   4044 sec   (685 perm/sec)   p_kst 5.776173e-06   p_cons 8.690975e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.326934e-06	k: 0	n:2780000
Cons ci ratio: 2.511708e-02	ci left: 8.576510e-03	ci right 8.795019e-03	k: 24145	n:2780000
KS ci ratio: 9.507366e-01	ci left: 3.289709e-06	ci right 9.346385e-06	k: 16	n:2780000
PIK3CA   2780000 perm   4070 sec   (683 perm/sec)   p_kst 5.755396e-06   p_cons 8.685252e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.322178e-06	k: 0	n:2790000
Cons ci ratio: 2.507560e-02	ci left: 8.574263e-03	ci right 8.792350e-03	k: 24225	n:2790000
KS ci ratio: 9.507366e-01	ci left: 3.277918e-06	ci right 9.312886e-06	k: 16	n:2790000
PIK3CA   2790000 perm   4097 sec   (681 perm/sec)   p_kst 5.734767e-06   p_cons 8.682796e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.317456e-06	k: 0	n:2800000
Cons ci ratio: 2.503174e-02	ci left: 8.573808e-03	ci right 8.791496e-03	k: 24310	n:2800000
KS ci ratio: 9.507366e-01	ci left: 3.266211e-06	ci right 9.279625e-06	k: 16	n:2800000
PIK3CA   2800000 perm   4124 sec   (679 perm/sec)   p_kst 5.714286e-06   p_cons 8.682143e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.312768e-06	k: 0	n:2810000
Cons ci ratio: 2.499172e-02	ci left: 8.570880e-03	ci right 8.788141e-03	k: 24388	n:2810000
KS ci ratio: 9.507366e-01	ci left: 3.254588e-06	ci right 9.246602e-06	k: 16	n:2810000
PIK3CA   2810000 perm   4151 sec   (677 perm/sec)   p_kst 5.693950e-06   p_cons 8.679004e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.308112e-06	k: 0	n:2820000
Cons ci ratio: 2.495189e-02	ci left: 8.567974e-03	ci right 8.784810e-03	k: 24466	n:2820000
KS ci ratio: 9.507366e-01	ci left: 3.243047e-06	ci right 9.213813e-06	k: 16	n:2820000
PIK3CA   2820000 perm   4178 sec   (675 perm/sec)   p_kst 5.673759e-06   p_cons 8.675887e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.303490e-06	k: 0	n:2830000
Cons ci ratio: 2.491174e-02	ci left: 8.565439e-03	ci right 8.781858e-03	k: 24545	n:2830000
KS ci ratio: 9.507366e-01	ci left: 3.231587e-06	ci right 9.181255e-06	k: 16	n:2830000
PIK3CA   2830000 perm   4208 sec   (673 perm/sec)   p_kst 5.653710e-06   p_cons 8.673145e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.298900e-06	k: 0	n:2840000
Cons ci ratio: 2.486363e-02	ci left: 8.568522e-03	ci right 8.784594e-03	k: 24640	n:2840000
KS ci ratio: 9.507366e-01	ci left: 3.220208e-06	ci right 9.148927e-06	k: 16	n:2840000
PIK3CA   2840000 perm   4235 sec   (671 perm/sec)   p_kst 5.633803e-06   p_cons 8.676056e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.294343e-06	k: 0	n:2850000
Cons ci ratio: 2.482087e-02	ci left: 8.568096e-03	ci right 8.783781e-03	k: 24725	n:2850000
KS ci ratio: 9.507366e-01	ci left: 3.208909e-06	ci right 9.116825e-06	k: 16	n:2850000
PIK3CA   2850000 perm   4262 sec   (669 perm/sec)   p_kst 5.614035e-06   p_cons 8.675439e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.289817e-06	k: 0	n:2860000
Cons ci ratio: 2.478537e-02	ci left: 8.562809e-03	ci right 8.778048e-03	k: 24796	n:2860000
KS ci ratio: 9.507367e-01	ci left: 3.197689e-06	ci right 9.084948e-06	k: 16	n:2860000
PIK3CA   2860000 perm   4290 sec   (667 perm/sec)   p_kst 5.594406e-06   p_cons 8.669930e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.285323e-06	k: 0	n:2870000
Cons ci ratio: 2.472898e-02	ci left: 8.572103e-03	ci right 8.787078e-03	k: 24909	n:2870000
KS ci ratio: 9.507367e-01	ci left: 3.186548e-06	ci right 9.053294e-06	k: 16	n:2870000
PIK3CA   2870000 perm   4317 sec   (665 perm/sec)   p_kst 5.574913e-06   p_cons 8.679094e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.280860e-06	k: 0	n:2880000
Cons ci ratio: 2.468740e-02	ci left: 8.571325e-03	ci right 8.785914e-03	k: 24993	n:2880000
KS ci ratio: 9.507367e-01	ci left: 3.175483e-06	ci right 9.021859e-06	k: 16	n:2880000
PIK3CA   2880000 perm   4344 sec   (663 perm/sec)   p_kst 5.555556e-06   p_cons 8.678125e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.276428e-06	k: 0	n:2890000
Cons ci ratio: 2.464802e-02	ci left: 8.569177e-03	ci right 8.783366e-03	k: 25073	n:2890000
KS ci ratio: 9.507367e-01	ci left: 3.164495e-06	ci right 8.990641e-06	k: 16	n:2890000
PIK3CA   2890000 perm   4371 sec   (661 perm/sec)   p_kst 5.536332e-06   p_cons 8.675779e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.272027e-06	k: 0	n:2900000
Cons ci ratio: 2.460191e-02	ci left: 8.571843e-03	ci right 8.785692e-03	k: 25167	n:2900000
KS ci ratio: 9.507367e-01	ci left: 3.153583e-06	ci right 8.959639e-06	k: 16	n:2900000
PIK3CA   2900000 perm   4399 sec   (659 perm/sec)   p_kst 5.517241e-06   p_cons 8.678276e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.267655e-06	k: 0	n:2910000
Cons ci ratio: 2.456293e-02	ci left: 8.569709e-03	ci right 8.783161e-03	k: 25247	n:2910000
KS ci ratio: 9.507367e-01	ci left: 3.142746e-06	ci right 8.928850e-06	k: 16	n:2910000
PIK3CA   2910000 perm   4427 sec   (657 perm/sec)   p_kst 5.498282e-06   p_cons 8.675945e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.263314e-06	k: 0	n:2920000
Cons ci ratio: 2.451487e-02	ci left: 8.574057e-03	ci right 8.787193e-03	k: 25346	n:2920000
KS ci ratio: 9.507367e-01	ci left: 3.131983e-06	ci right 8.898272e-06	k: 16	n:2920000
PIK3CA   2920000 perm   4455 sec   (655 perm/sec)   p_kst 5.479452e-06   p_cons 8.680137e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.259002e-06	k: 0	n:2930000
Cons ci ratio: 2.446999e-02	ci left: 8.576340e-03	ci right 8.789138e-03	k: 25439	n:2930000
KS ci ratio: 9.507367e-01	ci left: 3.121294e-06	ci right 8.867902e-06	k: 16	n:2930000
PIK3CA   2930000 perm   4483 sec   (654 perm/sec)   p_kst 5.460751e-06   p_cons 8.682253e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.254720e-06	k: 0	n:2940000
Cons ci ratio: 2.442922e-02	ci left: 8.575904e-03	ci right 8.788331e-03	k: 25524	n:2940000
KS ci ratio: 9.507367e-01	ci left: 3.110677e-06	ci right 8.837739e-06	k: 16	n:2940000
PIK3CA   2940000 perm   4515 sec   (651 perm/sec)   p_kst 5.442177e-06   p_cons 8.681633e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.250467e-06	k: 0	n:2950000
Cons ci ratio: 2.437905e-02	ci left: 8.582209e-03	ci right 8.794350e-03	k: 25629	n:2950000
KS ci ratio: 9.507367e-01	ci left: 3.100133e-06	ci right 8.807781e-06	k: 16	n:2950000
PIK3CA   2950000 perm   4543 sec   (649 perm/sec)   p_kst 5.423729e-06   p_cons 8.687797e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.246242e-06	k: 0	n:2960000
Cons ci ratio: 2.434017e-02	ci left: 8.580749e-03	ci right 8.792511e-03	k: 25711	n:2960000
KS ci ratio: 9.507368e-01	ci left: 3.089659e-06	ci right 8.778025e-06	k: 16	n:2960000
PIK3CA   2960000 perm   4572 sec   (647 perm/sec)   p_kst 5.405405e-06   p_cons 8.686149e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.242046e-06	k: 0	n:2970000
Cons ci ratio: 2.429672e-02	ci left: 8.582646e-03	ci right 8.794071e-03	k: 25803	n:2970000
KS ci ratio: 9.507368e-01	ci left: 3.079256e-06	ci right 8.748469e-06	k: 16	n:2970000
PIK3CA   2970000 perm   4600 sec   (646 perm/sec)   p_kst 5.387205e-06   p_cons 8.687879e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.237878e-06	k: 0	n:2980000
Cons ci ratio: 2.425586e-02	ci left: 8.582863e-03	ci right 8.793933e-03	k: 25890	n:2980000
KS ci ratio: 9.507368e-01	ci left: 3.068923e-06	ci right 8.719112e-06	k: 16	n:2980000
PIK3CA   2980000 perm   4629 sec   (644 perm/sec)   p_kst 5.369128e-06   p_cons 8.687919e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.233738e-06	k: 0	n:2990000
Cons ci ratio: 2.421521e-02	ci left: 8.583078e-03	ci right 8.793795e-03	k: 25977	n:2990000
KS ci ratio: 9.507368e-01	ci left: 3.058659e-06	ci right 8.689951e-06	k: 16	n:2990000
PIK3CA   2990000 perm   4657 sec   (642 perm/sec)   p_kst 5.351171e-06   p_cons 8.687960e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.229626e-06	k: 0	n:3000000
Cons ci ratio: 2.417757e-02	ci left: 8.581304e-03	ci right 8.791646e-03	k: 26058	n:3000000
KS ci ratio: 9.507368e-01	ci left: 3.048464e-06	ci right 8.660985e-06	k: 16	n:3000000
PIK3CA   3000000 perm   4686 sec   (640 perm/sec)   p_kst 5.333333e-06   p_cons 8.686000e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.225541e-06	k: 0	n:3010000
Cons ci ratio: 2.413266e-02	ci left: 8.584827e-03	ci right 8.794858e-03	k: 26155	n:3010000
KS ci ratio: 9.239499e-01	ci left: 3.290079e-06	ci right 9.042724e-06	k: 17	n:3010000
PIK3CA   3010000 perm   4714 sec   (638 perm/sec)   p_kst 5.647841e-06   p_cons 8.689369e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.221483e-06	k: 0	n:3020000
Cons ci ratio: 2.409494e-02	ci left: 8.583389e-03	ci right 8.793052e-03	k: 26237	n:3020000
KS ci ratio: 9.239500e-01	ci left: 3.279184e-06	ci right 9.012782e-06	k: 17	n:3020000
PIK3CA   3020000 perm   4743 sec   (637 perm/sec)   p_kst 5.629139e-06   p_cons 8.687748e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.217451e-06	k: 0	n:3030000
Cons ci ratio: 2.406108e-02	ci left: 8.579336e-03	ci right 8.788602e-03	k: 26311	n:3030000
KS ci ratio: 9.239500e-01	ci left: 3.268362e-06	ci right 8.983037e-06	k: 17	n:3030000
PIK3CA   3030000 perm   4772 sec   (635 perm/sec)   p_kst 5.610561e-06   p_cons 8.683498e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.213446e-06	k: 0	n:3040000
Cons ci ratio: 2.402232e-02	ci left: 8.578907e-03	ci right 8.787820e-03	k: 26396	n:3040000
KS ci ratio: 9.239500e-01	ci left: 3.257611e-06	ci right 8.953487e-06	k: 17	n:3040000
PIK3CA   3040000 perm   4801 sec   (633 perm/sec)   p_kst 5.592105e-06   p_cons 8.682895e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.209468e-06	k: 0	n:3050000
Cons ci ratio: 2.397005e-02	ci left: 8.588258e-03	ci right 8.796938e-03	k: 26511	n:3050000
KS ci ratio: 9.239500e-01	ci left: 3.246930e-06	ci right 8.924132e-06	k: 17	n:3050000
PIK3CA   3050000 perm   4830 sec   (631 perm/sec)   p_kst 5.573770e-06   p_cons 8.692131e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.205515e-06	k: 0	n:3060000
Cons ci ratio: 2.392855e-02	ci left: 8.590078e-03	ci right 8.798435e-03	k: 26603	n:3060000
KS ci ratio: 9.239500e-01	ci left: 3.236319e-06	ci right 8.894968e-06	k: 17	n:3060000
PIK3CA   3060000 perm   4859 sec   (630 perm/sec)   p_kst 5.555556e-06   p_cons 8.693791e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.201589e-06	k: 0	n:3070000
Cons ci ratio: 2.389313e-02	ci left: 8.587676e-03	ci right 8.795663e-03	k: 26682	n:3070000
KS ci ratio: 8.993067e-01	ci left: 3.474903e-06	ci right 9.266356e-06	k: 18	n:3070000
PIK3CA   3070000 perm   4889 sec   (628 perm/sec)   p_kst 5.863192e-06   p_cons 8.691205e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.197687e-06	k: 0	n:3080000
Cons ci ratio: 2.385293e-02	ci left: 8.588840e-03	ci right 8.796501e-03	k: 26772	n:3080000
KS ci ratio: 8.993068e-01	ci left: 3.463621e-06	ci right 9.236270e-06	k: 18	n:3080000
PIK3CA   3080000 perm   4919 sec   (626 perm/sec)   p_kst 5.844156e-06   p_cons 8.692208e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.193811e-06	k: 0	n:3090000
Cons ci ratio: 2.381382e-02	ci left: 8.589354e-03	ci right 8.796682e-03	k: 26860	n:3090000
KS ci ratio: 8.993068e-01	ci left: 3.452412e-06	ci right 9.206379e-06	k: 18	n:3090000
PIK3CA   3090000 perm   4948 sec   (624 perm/sec)   p_kst 5.825243e-06   p_cons 8.692557e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.189960e-06	k: 0	n:3100000
Cons ci ratio: 2.377268e-02	ci left: 8.591468e-03	ci right 8.798484e-03	k: 26953	n:3100000
KS ci ratio: 8.993068e-01	ci left: 3.441275e-06	ci right 9.176681e-06	k: 18	n:3100000
PIK3CA   3100000 perm   4978 sec   (623 perm/sec)   p_kst 5.806452e-06   p_cons 8.694516e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.186134e-06	k: 0	n:3110000
Cons ci ratio: 2.372865e-02	ci left: 8.595806e-03	ci right 8.802538e-03	k: 27053	n:3110000
KS ci ratio: 8.993068e-01	ci left: 3.430210e-06	ci right 9.147174e-06	k: 18	n:3110000
PIK3CA   3110000 perm   5008 sec   (621 perm/sec)   p_kst 5.787781e-06   p_cons 8.698714e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.182332e-06	k: 0	n:3120000
Cons ci ratio: 2.368223e-02	ci left: 8.602029e-03	ci right 8.808500e-03	k: 27159	n:3120000
KS ci ratio: 8.993068e-01	ci left: 3.419215e-06	ci right 9.117857e-06	k: 18	n:3120000
PIK3CA   3120000 perm   5037 sec   (619 perm/sec)   p_kst 5.769231e-06   p_cons 8.704808e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.178555e-06	k: 0	n:3130000
Cons ci ratio: 2.364614e-02	ci left: 8.600907e-03	ci right 8.807032e-03	k: 27242	n:3130000
KS ci ratio: 8.993068e-01	ci left: 3.408291e-06	ci right 9.088726e-06	k: 18	n:3130000
PIK3CA   3130000 perm   5067 sec   (618 perm/sec)   p_kst 5.750799e-06   p_cons 8.703514e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.174802e-06	k: 0	n:3140000
Cons ci ratio: 2.361981e-02	ci left: 8.592827e-03	ci right 8.798526e-03	k: 27303	n:3140000
KS ci ratio: 8.993068e-01	ci left: 3.397437e-06	ci right 9.059781e-06	k: 18	n:3140000
PIK3CA   3140000 perm   5097 sec   (616 perm/sec)   p_kst 5.732484e-06   p_cons 8.695223e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.171072e-06	k: 0	n:3150000
Cons ci ratio: 2.358314e-02	ci left: 8.592373e-03	ci right 8.797738e-03	k: 27388	n:3150000
KS ci ratio: 8.993068e-01	ci left: 3.386651e-06	ci right 9.031020e-06	k: 18	n:3150000
PIK3CA   3150000 perm   5127 sec   (614 perm/sec)   p_kst 5.714286e-06   p_cons 8.694603e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.167366e-06	k: 0	n:3160000
Cons ci ratio: 2.354188e-02	ci left: 8.595383e-03	ci right 8.800455e-03	k: 27484	n:3160000
KS ci ratio: 8.993068e-01	ci left: 3.375934e-06	ci right 9.002441e-06	k: 18	n:3160000
PIK3CA   3160000 perm   5158 sec   (613 perm/sec)   p_kst 5.696203e-06   p_cons 8.697468e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.163684e-06	k: 0	n:3170000
Cons ci ratio: 2.350385e-02	ci left: 8.596179e-03	ci right 8.800935e-03	k: 27573	n:3170000
KS ci ratio: 8.765357e-01	ci left: 3.608597e-06	ci right 9.359875e-06	k: 19	n:3170000
PIK3CA   3170000 perm   5188 sec   (611 perm/sec)   p_kst 5.993691e-06   p_cons 8.698107e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.160024e-06	k: 0	n:3180000
Cons ci ratio: 2.346130e-02	ci left: 8.600409e-03	ci right 8.804890e-03	k: 27673	n:3180000
KS ci ratio: 8.765358e-01	ci left: 3.597249e-06	ci right 9.330441e-06	k: 19	n:3180000
PIK3CA   3180000 perm   5219 sec   (609 perm/sec)   p_kst 5.974843e-06   p_cons 8.702201e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.156388e-06	k: 0	n:3190000
Cons ci ratio: 2.342919e-02	ci left: 8.597133e-03	ci right 8.801252e-03	k: 27749	n:3190000
KS ci ratio: 8.765358e-01	ci left: 3.585973e-06	ci right 9.301192e-06	k: 19	n:3190000
PIK3CA   3190000 perm   5250 sec   (608 perm/sec)   p_kst 5.956113e-06   p_cons 8.698746e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.152774e-06	k: 0	n:3200000
Cons ci ratio: 2.339382e-02	ci left: 8.596363e-03	ci right 8.800152e-03	k: 27833	n:3200000
KS ci ratio: 8.765358e-01	ci left: 3.574767e-06	ci right 9.272126e-06	k: 19	n:3200000
PIK3CA   3200000 perm   5280 sec   (606 perm/sec)   p_kst 5.937500e-06   p_cons 8.697813e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.149183e-06	k: 0	n:3210000
Cons ci ratio: 2.336072e-02	ci left: 8.594050e-03	ci right 8.797492e-03	k: 27912	n:3210000
KS ci ratio: 8.765358e-01	ci left: 3.563630e-06	ci right 9.243241e-06	k: 19	n:3210000
PIK3CA   3210000 perm   5311 sec   (604 perm/sec)   p_kst 5.919003e-06   p_cons 8.695327e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.145614e-06	k: 0	n:3220000
Cons ci ratio: 2.332188e-02	ci left: 8.596074e-03	ci right 8.799221e-03	k: 28005	n:3220000
KS ci ratio: 8.765358e-01	ci left: 3.552563e-06	ci right 9.214536e-06	k: 19	n:3220000
PIK3CA   3220000 perm   5342 sec   (603 perm/sec)   p_kst 5.900621e-06   p_cons 8.697205e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.142067e-06	k: 0	n:3230000
Cons ci ratio: 2.327947e-02	ci left: 8.600856e-03	ci right 8.803741e-03	k: 28107	n:3230000
KS ci ratio: 8.765358e-01	ci left: 3.541564e-06	ci right 9.186008e-06	k: 19	n:3230000
PIK3CA   3230000 perm   5372 sec   (601 perm/sec)   p_kst 5.882353e-06   p_cons 8.701858e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.138542e-06	k: 0	n:3240000
Cons ci ratio: 2.324644e-02	ci left: 8.598858e-03	ci right 8.801404e-03	k: 28187	n:3240000
KS ci ratio: 8.765358e-01	ci left: 3.530634e-06	ci right 9.157656e-06	k: 19	n:3240000
PIK3CA   3240000 perm   5403 sec   (600 perm/sec)   p_kst 5.864198e-06   p_cons 8.699691e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.135039e-06	k: 0	n:3250000
Cons ci ratio: 2.321065e-02	ci left: 8.599014e-03	ci right 8.801248e-03	k: 28274	n:3250000
KS ci ratio: 8.765358e-01	ci left: 3.519770e-06	ci right 9.129478e-06	k: 19	n:3250000
PIK3CA   3250000 perm   5434 sec   (598 perm/sec)   p_kst 5.846154e-06   p_cons 8.699692e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.131557e-06	k: 0	n:3260000
Cons ci ratio: 2.317584e-02	ci left: 8.598559e-03	ci right 8.800475e-03	k: 28359	n:3260000
KS ci ratio: 8.765358e-01	ci left: 3.508973e-06	ci right 9.101474e-06	k: 19	n:3260000
PIK3CA   3260000 perm   5466 sec   (596 perm/sec)   p_kst 5.828221e-06   p_cons 8.699080e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.128097e-06	k: 0	n:3270000
Cons ci ratio: 2.313956e-02	ci left: 8.599323e-03	ci right 8.800937e-03	k: 28448	n:3270000
KS ci ratio: 8.765358e-01	ci left: 3.498242e-06	ci right 9.073641e-06	k: 19	n:3270000
PIK3CA   3270000 perm   5497 sec   (595 perm/sec)   p_kst 5.810398e-06   p_cons 8.699694e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.124658e-06	k: 0	n:3280000
Cons ci ratio: 2.310548e-02	ci left: 8.598567e-03	ci right 8.799863e-03	k: 28532	n:3280000
KS ci ratio: 8.765358e-01	ci left: 3.487577e-06	ci right 9.045977e-06	k: 19	n:3280000
PIK3CA   3280000 perm   5528 sec   (593 perm/sec)   p_kst 5.792683e-06   p_cons 8.698780e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.121239e-06	k: 0	n:3290000
Cons ci ratio: 2.306993e-02	ci left: 8.599025e-03	ci right 8.800017e-03	k: 28620	n:3290000
KS ci ratio: 8.765358e-01	ci left: 3.476976e-06	ci right 9.018482e-06	k: 19	n:3290000
PIK3CA   3290000 perm   5559 sec   (592 perm/sec)   p_kst 5.775076e-06   p_cons 8.699088e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.117842e-06	k: 0	n:3300000
Cons ci ratio: 2.303292e-02	ci left: 8.600686e-03	ci right 8.801390e-03	k: 28712	n:3300000
KS ci ratio: 8.765359e-01	ci left: 3.466440e-06	ci right 8.991153e-06	k: 19	n:3300000
PIK3CA   3300000 perm   5590 sec   (590 perm/sec)   p_kst 5.757576e-06   p_cons 8.700606e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.114464e-06	k: 0	n:3310000
Cons ci ratio: 2.299569e-02	ci left: 8.602637e-03	ci right 8.803058e-03	k: 28805	n:3310000
KS ci ratio: 8.765359e-01	ci left: 3.455968e-06	ci right 8.963990e-06	k: 19	n:3310000
PIK3CA   3310000 perm   5622 sec   (589 perm/sec)   p_kst 5.740181e-06   p_cons 8.702417e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.111108e-06	k: 0	n:3320000
Cons ci ratio: 2.296345e-02	ci left: 8.600983e-03	ci right 8.801081e-03	k: 28886	n:3320000
KS ci ratio: 8.765359e-01	ci left: 3.445558e-06	ci right 8.936990e-06	k: 19	n:3320000
PIK3CA   3320000 perm   5653 sec   (587 perm/sec)   p_kst 5.722892e-06   p_cons 8.700602e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.107771e-06	k: 0	n:3330000
Cons ci ratio: 2.292935e-02	ci left: 8.600831e-03	ci right 8.800625e-03	k: 28972	n:3330000
KS ci ratio: 8.765359e-01	ci left: 3.435211e-06	ci right 8.910152e-06	k: 19	n:3330000
PIK3CA   3330000 perm   5685 sec   (586 perm/sec)   p_kst 5.705706e-06   p_cons 8.700300e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.104454e-06	k: 0	n:3340000
Cons ci ratio: 2.289500e-02	ci left: 8.600979e-03	ci right 8.800473e-03	k: 29059	n:3340000
KS ci ratio: 8.765359e-01	ci left: 3.424926e-06	ci right 8.883475e-06	k: 19	n:3340000
PIK3CA   3340000 perm   5717 sec   (584 perm/sec)   p_kst 5.688623e-06   p_cons 8.700299e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.101157e-06	k: 0	n:3350000
Cons ci ratio: 2.286318e-02	ci left: 8.599345e-03	ci right 8.798520e-03	k: 29140	n:3350000
KS ci ratio: 8.554113e-01	ci left: 3.646726e-06	ci right 9.220396e-06	k: 20	n:3350000
PIK3CA   3350000 perm   5749 sec   (583 perm/sec)   p_kst 5.970149e-06   p_cons 8.698507e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.097880e-06	k: 0	n:3360000
Cons ci ratio: 2.282913e-02	ci left: 8.599497e-03	ci right 8.798375e-03	k: 29227	n:3360000
KS ci ratio: 8.554113e-01	ci left: 3.635873e-06	ci right 9.192955e-06	k: 20	n:3360000
PIK3CA   3360000 perm   5781 sec   (581 perm/sec)   p_kst 5.952381e-06   p_cons 8.698512e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.094622e-06	k: 0	n:3370000
Cons ci ratio: 2.279601e-02	ci left: 8.599058e-03	ci right 8.797633e-03	k: 29312	n:3370000
KS ci ratio: 8.554113e-01	ci left: 3.625084e-06	ci right 9.165676e-06	k: 20	n:3370000
PIK3CA   3370000 perm   5813 sec   (580 perm/sec)   p_kst 5.934718e-06   p_cons 8.697923e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.091384e-06	k: 0	n:3380000
Cons ci ratio: 2.275913e-02	ci left: 8.601563e-03	ci right 8.799871e-03	k: 29407	n:3380000
KS ci ratio: 8.554113e-01	ci left: 3.614359e-06	ci right 9.138559e-06	k: 20	n:3380000
PIK3CA   3380000 perm   5845 sec   (578 perm/sec)   p_kst 5.917160e-06   p_cons 8.700296e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.088164e-06	k: 0	n:3390000
Cons ci ratio: 2.272632e-02	ci left: 8.601121e-03	ci right 8.799129e-03	k: 29492	n:3390000
KS ci ratio: 8.554114e-01	ci left: 3.603697e-06	ci right 9.111601e-06	k: 20	n:3390000
PIK3CA   3390000 perm   5877 sec   (577 perm/sec)   p_kst 5.899705e-06   p_cons 8.699705e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.084964e-06	k: 0	n:3400000
Cons ci ratio: 2.268707e-02	ci left: 8.605654e-03	ci right 8.803420e-03	k: 29594	n:3400000
KS ci ratio: 8.554114e-01	ci left: 3.593098e-06	ci right 9.084802e-06	k: 20	n:3400000
PIK3CA   3400000 perm   5909 sec   (575 perm/sec)   p_kst 5.882353e-06   p_cons 8.704118e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.081782e-06	k: 0	n:3410000
Cons ci ratio: 2.265842e-02	ci left: 8.602287e-03	ci right 8.799722e-03	k: 29669	n:3410000
KS ci ratio: 8.357440e-01	ci left: 3.812124e-06	ci right 9.413689e-06	k: 21	n:3410000
PIK3CA   3410000 perm   5942 sec   (574 perm/sec)   p_kst 6.158358e-06   p_cons 8.700587e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.078619e-06	k: 0	n:3420000
Cons ci ratio: 2.262067e-02	ci left: 8.605917e-03	ci right 8.803103e-03	k: 29768	n:3420000
KS ci ratio: 8.357440e-01	ci left: 3.800978e-06	ci right 9.386163e-06	k: 21	n:3420000
PIK3CA   3420000 perm   5974 sec   (572 perm/sec)   p_kst 6.140351e-06   p_cons 8.704094e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.075474e-06	k: 0	n:3430000
Cons ci ratio: 2.259571e-02	ci left: 8.599960e-03	ci right 8.796789e-03	k: 29834	n:3430000
KS ci ratio: 8.357440e-01	ci left: 3.789896e-06	ci right 9.358798e-06	k: 21	n:3430000
PIK3CA   3430000 perm   6007 sec   (571 perm/sec)   p_kst 6.122449e-06   p_cons 8.697959e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.072348e-06	k: 0	n:3440000
Cons ci ratio: 2.256055e-02	ci left: 8.601843e-03	ci right 8.798404e-03	k: 29927	n:3440000
KS ci ratio: 8.993071e-01	ci left: 3.101148e-06	ci right 8.269685e-06	k: 18	n:3440000
PIK3CA   3440000 perm   6040 sec   (570 perm/sec)   p_kst 5.232558e-06   p_cons 8.699709e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.069240e-06	k: 0	n:3450000
Cons ci ratio: 2.252632e-02	ci left: 8.603138e-03	ci right 8.799427e-03	k: 30018	n:3450000
KS ci ratio: 8.993071e-01	ci left: 3.092160e-06	ci right 8.245715e-06	k: 18	n:3450000
PIK3CA   3450000 perm   6073 sec   (568 perm/sec)   p_kst 5.217391e-06   p_cons 8.700870e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.066150e-06	k: 0	n:3460000
Cons ci ratio: 2.249638e-02	ci left: 8.601265e-03	ci right 8.797247e-03	k: 30098	n:3460000
KS ci ratio: 8.993071e-01	ci left: 3.083223e-06	ci right 8.221884e-06	k: 18	n:3460000
PIK3CA   3460000 perm   6106 sec   (567 perm/sec)   p_kst 5.202312e-06   p_cons 8.698844e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.063077e-06	k: 0	n:3470000
Cons ci ratio: 2.246282e-02	ci left: 8.602268e-03	ci right 8.797977e-03	k: 30188	n:3470000
KS ci ratio: 8.993071e-01	ci left: 3.074337e-06	ci right 8.198189e-06	k: 18	n:3470000
PIK3CA   3470000 perm   6139 sec   (565 perm/sec)   p_kst 5.187320e-06   p_cons 8.699712e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.060022e-06	k: 0	n:3480000
Cons ci ratio: 2.243052e-02	ci left: 8.602409e-03	ci right 8.797836e-03	k: 30275	n:3480000
KS ci ratio: 8.993071e-01	ci left: 3.065503e-06	ci right 8.174631e-06	k: 18	n:3480000
PIK3CA   3480000 perm   6172 sec   (564 perm/sec)   p_kst 5.172414e-06   p_cons 8.699713e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.056985e-06	k: 0	n:3490000
Cons ci ratio: 2.239687e-02	ci left: 8.603688e-03	ci right 8.798847e-03	k: 30366	n:3490000
KS ci ratio: 8.993071e-01	ci left: 3.056719e-06	ci right 8.151209e-06	k: 18	n:3490000
PIK3CA   3490000 perm   6205 sec   (562 perm/sec)   p_kst 5.157593e-06   p_cons 8.700860e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.053965e-06	k: 0	n:3500000
Cons ci ratio: 2.237116e-02	ci left: 8.598994e-03	ci right 8.793820e-03	k: 30436	n:3500000
KS ci ratio: 8.993071e-01	ci left: 3.047986e-06	ci right 8.127919e-06	k: 18	n:3500000
PIK3CA   3500000 perm   6238 sec   (561 perm/sec)   p_kst 5.142857e-06   p_cons 8.696000e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.050962e-06	k: 0	n:3510000
Cons ci ratio: 2.233778e-02	ci left: 8.600277e-03	ci right 8.794837e-03	k: 30527	n:3510000
KS ci ratio: 8.993071e-01	ci left: 3.039302e-06	ci right 8.104763e-06	k: 18	n:3510000
PIK3CA   3510000 perm   6271 sec   (560 perm/sec)   p_kst 5.128205e-06   p_cons 8.697151e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.047977e-06	k: 0	n:3520000
Cons ci ratio: 2.230565e-02	ci left: 8.600705e-03	ci right 8.794991e-03	k: 30615	n:3520000
KS ci ratio: 8.993071e-01	ci left: 3.030668e-06	ci right 8.081738e-06	k: 18	n:3520000
PIK3CA   3520000 perm   6304 sec   (558 perm/sec)   p_kst 5.113636e-06   p_cons 8.697443e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.045008e-06	k: 0	n:3530000
Cons ci ratio: 2.228244e-02	ci left: 8.594369e-03	ci right 8.788308e-03	k: 30679	n:3530000
KS ci ratio: 8.993071e-01	ci left: 3.022082e-06	ci right 8.058844e-06	k: 18	n:3530000
PIK3CA   3530000 perm   6337 sec   (557 perm/sec)   p_kst 5.099150e-06   p_cons 8.690935e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.042056e-06	k: 0	n:3540000
Cons ci ratio: 2.225274e-02	ci left: 8.593126e-03	ci right 8.786775e-03	k: 30761	n:3540000
KS ci ratio: 8.993071e-01	ci left: 3.013545e-06	ci right 8.036079e-06	k: 18	n:3540000
PIK3CA   3540000 perm   6372 sec   (556 perm/sec)   p_kst 5.084746e-06   p_cons 8.689548e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.039120e-06	k: 0	n:3550000
Cons ci ratio: 2.222316e-02	ci left: 8.591890e-03	ci right 8.785251e-03	k: 30843	n:3550000
KS ci ratio: 8.993071e-01	ci left: 3.005056e-06	ci right 8.013442e-06	k: 18	n:3550000
PIK3CA   3550000 perm   6405 sec   (554 perm/sec)   p_kst 5.070423e-06   p_cons 8.688169e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.036202e-06	k: 0	n:3560000
Cons ci ratio: 2.219622e-02	ci left: 8.588706e-03	ci right 8.781758e-03	k: 30918	n:3560000
KS ci ratio: 8.993072e-01	ci left: 2.996615e-06	ci right 7.990932e-06	k: 18	n:3560000
PIK3CA   3560000 perm   6439 sec   (553 perm/sec)   p_kst 5.056180e-06   p_cons 8.684831e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.033299e-06	k: 0	n:3570000
Cons ci ratio: 2.216831e-02	ci left: 8.586375e-03	ci right 8.779129e-03	k: 30996	n:3570000
KS ci ratio: 8.993072e-01	ci left: 2.988221e-06	ci right 7.968549e-06	k: 18	n:3570000
PIK3CA   3570000 perm   6473 sec   (551 perm/sec)   p_kst 5.042017e-06   p_cons 8.682353e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.030413e-06	k: 0	n:3580000
Cons ci ratio: 2.214481e-02	ci left: 8.580724e-03	ci right 8.773144e-03	k: 31062	n:3580000
KS ci ratio: 8.993072e-01	ci left: 2.979874e-06	ci right 7.946290e-06	k: 18	n:3580000
PIK3CA   3580000 perm   6507 sec   (550 perm/sec)   p_kst 5.027933e-06   p_cons 8.676536e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.027542e-06	k: 0	n:3590000
Cons ci ratio: 2.211279e-02	ci left: 8.581753e-03	ci right 8.773915e-03	k: 31152	n:3590000
KS ci ratio: 8.993072e-01	ci left: 2.971574e-06	ci right 7.924156e-06	k: 18	n:3590000
PIK3CA   3590000 perm   6541 sec   (549 perm/sec)   p_kst 5.013928e-06   p_cons 8.677437e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.024688e-06	k: 0	n:3600000
Cons ci ratio: 2.208269e-02	ci left: 8.581396e-03	ci right 8.773284e-03	k: 31237	n:3600000
KS ci ratio: 8.993072e-01	ci left: 2.963319e-06	ci right 7.902144e-06	k: 18	n:3600000
PIK3CA   3600000 perm   6575 sec   (548 perm/sec)   p_kst 5.000000e-06   p_cons 8.676944e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.021850e-06	k: 0	n:3610000
Cons ci ratio: 2.205662e-02	ci left: 8.578010e-03	ci right 8.769594e-03	k: 31311	n:3610000
KS ci ratio: 8.993072e-01	ci left: 2.955111e-06	ci right 7.880255e-06	k: 18	n:3610000
PIK3CA   3610000 perm   6609 sec   (546 perm/sec)   p_kst 4.986150e-06   p_cons 8.673407e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.019027e-06	k: 0	n:3620000
Cons ci ratio: 2.202286e-02	ci left: 8.580687e-03	ci right 8.772034e-03	k: 31407	n:3620000
KS ci ratio: 8.993072e-01	ci left: 2.946948e-06	ci right 7.858486e-06	k: 18	n:3620000
PIK3CA   3620000 perm   6643 sec   (545 perm/sec)   p_kst 4.972376e-06   p_cons 8.675967e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.016220e-06	k: 0	n:3630000
Cons ci ratio: 2.199523e-02	ci left: 8.578692e-03	ci right 8.769751e-03	k: 31486	n:3630000
KS ci ratio: 8.993072e-01	ci left: 2.938829e-06	ci right 7.836837e-06	k: 18	n:3630000
PIK3CA   3630000 perm   6676 sec   (544 perm/sec)   p_kst 4.958678e-06   p_cons 8.673829e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.013428e-06	k: 0	n:3640000
Cons ci ratio: 2.197334e-02	ci left: 8.572337e-03	ci right 8.763062e-03	k: 31549	n:3640000
KS ci ratio: 8.993072e-01	ci left: 2.930756e-06	ci right 7.815308e-06	k: 18	n:3640000
PIK3CA   3640000 perm   6710 sec   (542 perm/sec)   p_kst 4.945055e-06   p_cons 8.667308e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.010651e-06	k: 0	n:3650000
Cons ci ratio: 2.194415e-02	ci left: 8.571738e-03	ci right 8.762193e-03	k: 31633	n:3650000
KS ci ratio: 8.993072e-01	ci left: 2.922726e-06	ci right 7.793896e-06	k: 18	n:3650000
PIK3CA   3650000 perm   6745 sec   (541 perm/sec)   p_kst 4.931507e-06   p_cons 8.666575e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.007890e-06	k: 0	n:3660000
Cons ci ratio: 2.191996e-02	ci left: 8.567339e-03	ci right 8.757484e-03	k: 31703	n:3660000
KS ci ratio: 8.993072e-01	ci left: 2.914740e-06	ci right 7.772601e-06	k: 18	n:3660000
PIK3CA   3660000 perm   6780 sec   (540 perm/sec)   p_kst 4.918033e-06   p_cons 8.662022e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.005144e-06	k: 0	n:3670000
Cons ci ratio: 2.188474e-02	ci left: 8.571635e-03	ci right 8.761566e-03	k: 31805	n:3670000
KS ci ratio: 8.993072e-01	ci left: 2.906798e-06	ci right 7.751422e-06	k: 18	n:3670000
PIK3CA   3670000 perm   6815 sec   (538 perm/sec)   p_kst 4.904632e-06   p_cons 8.666213e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 1.002412e-06	k: 0	n:3680000
Cons ci ratio: 2.185210e-02	ci left: 8.574017e-03	ci right 8.763714e-03	k: 31900	n:3680000
KS ci ratio: 8.993072e-01	ci left: 2.898899e-06	ci right 7.730359e-06	k: 18	n:3680000
PIK3CA   3680000 perm   6850 sec   (537 perm/sec)   p_kst 4.891304e-06   p_cons 8.668478e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.996958e-07	k: 0	n:3690000
Cons ci ratio: 2.181858e-02	ci left: 8.577195e-03	ci right 8.766667e-03	k: 31998	n:3690000
KS ci ratio: 8.993072e-01	ci left: 2.891043e-06	ci right 7.709409e-06	k: 18	n:3690000
PIK3CA   3690000 perm   6885 sec   (536 perm/sec)   p_kst 4.878049e-06   p_cons 8.671545e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.969940e-07	k: 0	n:3700000
Cons ci ratio: 2.179344e-02	ci left: 8.573904e-03	ci right 8.763082e-03	k: 32072	n:3700000
KS ci ratio: 8.993072e-01	ci left: 2.883230e-06	ci right 7.688573e-06	k: 18	n:3700000
PIK3CA   3700000 perm   6919 sec   (535 perm/sec)   p_kst 4.864865e-06   p_cons 8.668108e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.943066e-07	k: 0	n:3710000
Cons ci ratio: 2.176018e-02	ci left: 8.577065e-03	ci right 8.766021e-03	k: 32170	n:3710000
KS ci ratio: 8.993073e-01	ci left: 2.875458e-06	ci right 7.667849e-06	k: 18	n:3710000
PIK3CA   3710000 perm   6954 sec   (534 perm/sec)   p_kst 4.851752e-06   p_cons 8.671159e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.916338e-07	k: 0	n:3720000
Cons ci ratio: 2.172980e-02	ci left: 8.578071e-03	ci right 8.766781e-03	k: 32260	n:3720000
KS ci ratio: 8.993073e-01	ci left: 2.867728e-06	ci right 7.647237e-06	k: 18	n:3720000
PIK3CA   3720000 perm   6989 sec   (532 perm/sec)   p_kst 4.838710e-06   p_cons 8.672043e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.889752e-07	k: 0	n:3730000
Cons ci ratio: 2.170360e-02	ci left: 8.575871e-03	ci right 8.764303e-03	k: 32338	n:3730000
KS ci ratio: 8.993073e-01	ci left: 2.860040e-06	ci right 7.626735e-06	k: 18	n:3730000
PIK3CA   3730000 perm   7024 sec   (531 perm/sec)   p_kst 4.825737e-06   p_cons 8.669705e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.863309e-07	k: 0	n:3740000
Cons ci ratio: 2.167986e-02	ci left: 8.571822e-03	ci right 8.759956e-03	k: 32409	n:3740000
KS ci ratio: 8.993073e-01	ci left: 2.852393e-06	ci right 7.606342e-06	k: 18	n:3740000
PIK3CA   3740000 perm   7059 sec   (530 perm/sec)   p_kst 4.812834e-06   p_cons 8.665508e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.837007e-07	k: 0	n:3750000
Cons ci ratio: 2.165385e-02	ci left: 8.569651e-03	ci right 8.757509e-03	k: 32487	n:3750000
KS ci ratio: 8.993073e-01	ci left: 2.844787e-06	ci right 7.586059e-06	k: 18	n:3750000
PIK3CA   3750000 perm   7095 sec   (529 perm/sec)   p_kst 4.800000e-06   p_cons 8.663200e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.810845e-07	k: 0	n:3760000
Cons ci ratio: 2.162994e-02	ci left: 8.565904e-03	ci right 8.753471e-03	k: 32559	n:3760000
KS ci ratio: 8.993073e-01	ci left: 2.837221e-06	ci right 7.565883e-06	k: 18	n:3760000
PIK3CA   3760000 perm   7130 sec   (527 perm/sec)   p_kst 4.787234e-06   p_cons 8.659309e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.784821e-07	k: 0	n:3770000
Cons ci ratio: 2.160276e-02	ci left: 8.564816e-03	ci right 8.752120e-03	k: 32641	n:3770000
KS ci ratio: 8.765362e-01	ci left: 3.034284e-06	ci right 7.870242e-06	k: 19	n:3770000
PIK3CA   3770000 perm   7165 sec   (526 perm/sec)   p_kst 5.039788e-06   p_cons 8.658090e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.758936e-07	k: 0	n:3780000
Cons ci ratio: 2.157470e-02	ci left: 8.564523e-03	ci right 8.751575e-03	k: 32726	n:3780000
KS ci ratio: 8.765362e-01	ci left: 3.026257e-06	ci right 7.849421e-06	k: 19	n:3780000
PIK3CA   3780000 perm   7201 sec   (525 perm/sec)   p_kst 5.026455e-06   p_cons 8.657672e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.733186e-07	k: 0	n:3790000
Cons ci ratio: 2.154177e-02	ci left: 8.568169e-03	ci right 8.755011e-03	k: 32826	n:3790000
KS ci ratio: 8.765362e-01	ci left: 3.018272e-06	ci right 7.828710e-06	k: 19	n:3790000
PIK3CA   3790000 perm   7237 sec   (524 perm/sec)   p_kst 5.013193e-06   p_cons 8.661214e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.707573e-07	k: 0	n:3800000
Cons ci ratio: 2.150933e-02	ci left: 8.571533e-03	ci right 8.758164e-03	k: 32925	n:3800000
KS ci ratio: 8.765362e-01	ci left: 3.010329e-06	ci right 7.808108e-06	k: 19	n:3800000
PIK3CA   3800000 perm   7272 sec   (523 perm/sec)   p_kst 5.000000e-06   p_cons 8.664474e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.682094e-07	k: 0	n:3810000
Cons ci ratio: 2.148556e-02	ci left: 8.568093e-03	ci right 8.754440e-03	k: 32998	n:3810000
KS ci ratio: 8.765362e-01	ci left: 3.002428e-06	ci right 7.787615e-06	k: 19	n:3810000
PIK3CA   3810000 perm   7307 sec   (521 perm/sec)   p_kst 4.986877e-06   p_cons 8.660892e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.656748e-07	k: 0	n:3820000
Cons ci ratio: 2.145958e-02	ci left: 8.566493e-03	ci right 8.752577e-03	k: 33078	n:3820000
KS ci ratio: 8.765362e-01	ci left: 2.994568e-06	ci right 7.767228e-06	k: 19	n:3820000
PIK3CA   3820000 perm   7343 sec   (520 perm/sec)   p_kst 4.973822e-06   p_cons 8.659162e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.631534e-07	k: 0	n:3830000
Cons ci ratio: 2.142653e-02	ci left: 8.570616e-03	ci right 8.756499e-03	k: 33180	n:3830000
KS ci ratio: 8.765362e-01	ci left: 2.986750e-06	ci right 7.746948e-06	k: 19	n:3830000
PIK3CA   3830000 perm   7379 sec   (519 perm/sec)   p_kst 4.960836e-06   p_cons 8.663185e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.606452e-07	k: 0	n:3840000
Cons ci ratio: 2.139525e-02	ci left: 8.573422e-03	ci right 8.759091e-03	k: 33277	n:3840000
KS ci ratio: 8.765363e-01	ci left: 2.978972e-06	ci right 7.726774e-06	k: 19	n:3840000
PIK3CA   3840000 perm   7415 sec   (518 perm/sec)   p_kst 4.947917e-06   p_cons 8.665885e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.581500e-07	k: 0	n:3850000
Cons ci ratio: 2.136572e-02	ci left: 8.574922e-03	ci right 8.760364e-03	k: 33369	n:3850000
KS ci ratio: 8.765363e-01	ci left: 2.971234e-06	ci right 7.706705e-06	k: 19	n:3850000
PIK3CA   3850000 perm   7451 sec   (517 perm/sec)   p_kst 4.935065e-06   p_cons 8.667273e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.556678e-07	k: 0	n:3860000
Cons ci ratio: 2.133696e-02	ci left: 8.575898e-03	ci right 8.761109e-03	k: 33459	n:3860000
KS ci ratio: 8.765363e-01	ci left: 2.963536e-06	ci right 7.686739e-06	k: 19	n:3860000
PIK3CA   3860000 perm   7487 sec   (516 perm/sec)   p_kst 4.922280e-06   p_cons 8.668135e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.531984e-07	k: 0	n:3870000
Cons ci ratio: 2.130767e-02	ci left: 8.577384e-03	ci right 8.762370e-03	k: 33551	n:3870000
KS ci ratio: 8.765363e-01	ci left: 2.955879e-06	ci right 7.666877e-06	k: 19	n:3870000
PIK3CA   3870000 perm   7523 sec   (514 perm/sec)   p_kst 4.909561e-06   p_cons 8.669509e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.507417e-07	k: 0	n:3880000
Cons ci ratio: 2.128457e-02	ci left: 8.573992e-03	ci right 8.758701e-03	k: 33624	n:3880000
KS ci ratio: 8.765363e-01	ci left: 2.948261e-06	ci right 7.647117e-06	k: 19	n:3880000
PIK3CA   3880000 perm   7560 sec   (513 perm/sec)   p_kst 4.896907e-06   p_cons 8.665979e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.482976e-07	k: 0	n:3890000
Cons ci ratio: 2.126026e-02	ci left: 8.571640e-03	ci right 8.756085e-03	k: 33701	n:3890000
KS ci ratio: 8.765363e-01	ci left: 2.940681e-06	ci right 7.627458e-06	k: 19	n:3890000
PIK3CA   3890000 perm   7596 sec   (512 perm/sec)   p_kst 4.884319e-06   p_cons 8.663496e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.458661e-07	k: 0	n:3900000
Cons ci ratio: 2.123509e-02	ci left: 8.570065e-03	ci right 8.754256e-03	k: 33781	n:3900000
KS ci ratio: 8.765363e-01	ci left: 2.933141e-06	ci right 7.607901e-06	k: 19	n:3900000
PIK3CA   3900000 perm   7633 sec   (511 perm/sec)   p_kst 4.871795e-06   p_cons 8.661795e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.434470e-07	k: 0	n:3910000
Cons ci ratio: 2.121001e-02	ci left: 8.568498e-03	ci right 8.752435e-03	k: 33861	n:3910000
KS ci ratio: 8.765363e-01	ci left: 2.925640e-06	ci right 7.588443e-06	k: 19	n:3910000
PIK3CA   3910000 perm   7669 sec   (510 perm/sec)   p_kst 4.859335e-06   p_cons 8.660102e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.410402e-07	k: 0	n:3920000
Cons ci ratio: 2.117841e-02	ci left: 8.572269e-03	ci right 8.756009e-03	k: 33962	n:3920000
KS ci ratio: 8.765363e-01	ci left: 2.918176e-06	ci right 7.569085e-06	k: 19	n:3920000
PIK3CA   3920000 perm   7706 sec   (509 perm/sec)   p_kst 4.846939e-06   p_cons 8.663776e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.386457e-07	k: 0	n:3930000
Cons ci ratio: 2.115447e-02	ci left: 8.569946e-03	ci right 8.753426e-03	k: 34039	n:3930000
KS ci ratio: 8.765363e-01	ci left: 2.910751e-06	ci right 7.549825e-06	k: 19	n:3930000
PIK3CA   3930000 perm   7742 sec   (508 perm/sec)   p_kst 4.834606e-06   p_cons 8.661323e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.362634e-07	k: 0	n:3940000
Cons ci ratio: 2.112718e-02	ci left: 8.570411e-03	ci right 8.753662e-03	k: 34127	n:3940000
KS ci ratio: 8.554117e-01	ci left: 3.100642e-06	ci right 7.839679e-06	k: 20	n:3940000
PIK3CA   3940000 perm   7779 sec   (507 perm/sec)   p_kst 5.076142e-06   p_cons 8.661675e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.338931e-07	k: 0	n:3950000
Cons ci ratio: 2.109564e-02	ci left: 8.574401e-03	ci right 8.757460e-03	k: 34229	n:3950000
KS ci ratio: 8.554117e-01	ci left: 3.092792e-06	ci right 7.819832e-06	k: 20	n:3950000
PIK3CA   3950000 perm   7815 sec   (505 perm/sec)   p_kst 5.063291e-06   p_cons 8.665570e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.315348e-07	k: 0	n:3960000
Cons ci ratio: 2.106609e-02	ci left: 8.576863e-03	ci right 8.759715e-03	k: 34325	n:3960000
KS ci ratio: 8.554118e-01	ci left: 3.084982e-06	ci right 7.800085e-06	k: 20	n:3960000
PIK3CA   3960000 perm   7852 sec   (504 perm/sec)   p_kst 5.050505e-06   p_cons 8.667929e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.291883e-07	k: 0	n:3970000
Cons ci ratio: 2.104006e-02	ci left: 8.576557e-03	ci right 8.759174e-03	k: 34410	n:3970000
KS ci ratio: 8.554118e-01	ci left: 3.077212e-06	ci right 7.780437e-06	k: 20	n:3970000
PIK3CA   3970000 perm   7890 sec   (503 perm/sec)   p_kst 5.037783e-06   p_cons 8.667506e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.268537e-07	k: 0	n:3980000
Cons ci ratio: 2.101167e-02	ci left: 8.578252e-03	ci right 8.760655e-03	k: 34503	n:3980000
KS ci ratio: 8.554118e-01	ci left: 3.069480e-06	ci right 7.760888e-06	k: 20	n:3980000
PIK3CA   3980000 perm   7928 sec   (502 perm/sec)   p_kst 5.025126e-06   p_cons 8.669095e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.245308e-07	k: 0	n:3990000
Cons ci ratio: 2.098309e-02	ci left: 8.580188e-03	ci right 8.762381e-03	k: 34597	n:3990000
KS ci ratio: 8.554118e-01	ci left: 3.061787e-06	ci right 7.741438e-06	k: 20	n:3990000
PIK3CA   3990000 perm   7965 sec   (501 perm/sec)   p_kst 5.012531e-06   p_cons 8.670927e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.222194e-07	k: 0	n:4000000
Cons ci ratio: 2.095950e-02	ci left: 8.578135e-03	ci right 8.760078e-03	k: 34675	n:4000000
KS ci ratio: 8.554118e-01	ci left: 3.054132e-06	ci right 7.722084e-06	k: 20	n:4000000
PIK3CA   4000000 perm   8003 sec   (500 perm/sec)   p_kst 5.000000e-06   p_cons 8.668750e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.199196e-07	k: 0	n:4010000
Cons ci ratio: 2.093629e-02	ci left: 8.575844e-03	ci right 8.757535e-03	k: 34752	n:4010000
KS ci ratio: 8.554118e-01	ci left: 3.046516e-06	ci right 7.702827e-06	k: 20	n:4010000
PIK3CA   4010000 perm   8041 sec   (499 perm/sec)   p_kst 4.987531e-06   p_cons 8.666334e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.176313e-07	k: 0	n:4020000
Cons ci ratio: 2.090590e-02	ci left: 8.579504e-03	ci right 8.761005e-03	k: 34853	n:4020000
KS ci ratio: 8.554118e-01	ci left: 3.038938e-06	ci right 7.683666e-06	k: 20	n:4020000
PIK3CA   4020000 perm   8079 sec   (498 perm/sec)   p_kst 4.975124e-06   p_cons 8.669900e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.153543e-07	k: 0	n:4030000
Cons ci ratio: 2.087744e-02	ci left: 8.581666e-03	ci right 8.762962e-03	k: 34948	n:4030000
KS ci ratio: 8.554118e-01	ci left: 3.031397e-06	ci right 7.664600e-06	k: 20	n:4030000
PIK3CA   4030000 perm   8116 sec   (497 perm/sec)   p_kst 4.962779e-06   p_cons 8.671960e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.130886e-07	k: 0	n:4040000
Cons ci ratio: 2.084610e-02	ci left: 8.586279e-03	ci right 8.767397e-03	k: 35053	n:4040000
KS ci ratio: 8.554118e-01	ci left: 3.023894e-06	ci right 7.645628e-06	k: 20	n:4040000
PIK3CA   4040000 perm   8154 sec   (495 perm/sec)   p_kst 4.950495e-06   p_cons 8.676485e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.108340e-07	k: 0	n:4050000
Cons ci ratio: 2.082297e-02	ci left: 8.584237e-03	ci right 8.765109e-03	k: 35131	n:4050000
KS ci ratio: 8.554118e-01	ci left: 3.016427e-06	ci right 7.626750e-06	k: 20	n:4050000
PIK3CA   4050000 perm   8192 sec   (494 perm/sec)   p_kst 4.938272e-06   p_cons 8.674321e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.085906e-07	k: 0	n:4060000
Cons ci ratio: 2.079664e-02	ci left: 8.584900e-03	ci right 8.765555e-03	k: 35220	n:4060000
KS ci ratio: 8.554118e-01	ci left: 3.008997e-06	ci right 7.607965e-06	k: 20	n:4060000
PIK3CA   4060000 perm   8230 sec   (493 perm/sec)   p_kst 4.926108e-06   p_cons 8.674877e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.063582e-07	k: 0	n:4070000
Cons ci ratio: 2.077071e-02	ci left: 8.585317e-03	ci right 8.765752e-03	k: 35308	n:4070000
KS ci ratio: 8.554118e-01	ci left: 3.001604e-06	ci right 7.589272e-06	k: 20	n:4070000
PIK3CA   4070000 perm   8267 sec   (492 perm/sec)   p_kst 4.914005e-06   p_cons 8.675184e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.041367e-07	k: 0	n:4080000
Cons ci ratio: 2.074132e-02	ci left: 8.588657e-03	ci right 8.768904e-03	k: 35408	n:4080000
KS ci ratio: 8.554118e-01	ci left: 2.994247e-06	ci right 7.570671e-06	k: 20	n:4080000
PIK3CA   4080000 perm   8307 sec   (491 perm/sec)   p_kst 4.901961e-06   p_cons 8.678431e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 9.019261e-07	k: 0	n:4090000
Cons ci ratio: 2.071147e-02	ci left: 8.592468e-03	ci right 8.772532e-03	k: 35510	n:4090000
KS ci ratio: 8.554118e-01	ci left: 2.986927e-06	ci right 7.552161e-06	k: 20	n:4090000
PIK3CA   4090000 perm   8346 sec   (490 perm/sec)   p_kst 4.889976e-06   p_cons 8.682152e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.997263e-07	k: 0	n:4100000
Cons ci ratio: 2.068673e-02	ci left: 8.592135e-03	ci right 8.771975e-03	k: 35595	n:4100000
KS ci ratio: 8.554118e-01	ci left: 2.979641e-06	ci right 7.533741e-06	k: 20	n:4100000
PIK3CA   4100000 perm   8385 sec   (489 perm/sec)   p_kst 4.878049e-06   p_cons 8.681707e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.975372e-07	k: 0	n:4110000
Cons ci ratio: 2.066150e-02	ci left: 8.592288e-03	ci right 8.771909e-03	k: 35682	n:4110000
KS ci ratio: 8.554118e-01	ci left: 2.972392e-06	ci right 7.515410e-06	k: 20	n:4110000
PIK3CA   4110000 perm   8424 sec   (488 perm/sec)   p_kst 4.866180e-06   p_cons 8.681752e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.953587e-07	k: 0	n:4120000
Cons ci ratio: 2.063723e-02	ci left: 8.591716e-03	ci right 8.771112e-03	k: 35766	n:4120000
KS ci ratio: 8.554118e-01	ci left: 2.965177e-06	ci right 7.497169e-06	k: 20	n:4120000
PIK3CA   4120000 perm   8463 sec   (487 perm/sec)   p_kst 4.854369e-06   p_cons 8.681068e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.931908e-07	k: 0	n:4130000
Cons ci ratio: 2.060957e-02	ci left: 8.594037e-03	ci right 8.773238e-03	k: 35862	n:4130000
KS ci ratio: 8.554119e-01	ci left: 2.957997e-06	ci right 7.479016e-06	k: 20	n:4130000
PIK3CA   4130000 perm   8502 sec   (486 perm/sec)   p_kst 4.842615e-06   p_cons 8.683293e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.910333e-07	k: 0	n:4140000
Cons ci ratio: 2.058692e-02	ci left: 8.592263e-03	ci right 8.771228e-03	k: 35941	n:4140000
KS ci ratio: 8.554119e-01	ci left: 2.950853e-06	ci right 7.460951e-06	k: 20	n:4140000
PIK3CA   4140000 perm   8541 sec   (485 perm/sec)   p_kst 4.830918e-06   p_cons 8.681401e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.888862e-07	k: 0	n:4150000
Cons ci ratio: 2.056378e-02	ci left: 8.590976e-03	ci right 8.769711e-03	k: 36022	n:4150000
KS ci ratio: 8.357445e-01	ci left: 3.132372e-06	ci right 7.735105e-06	k: 21	n:4150000
PIK3CA   4150000 perm   8580 sec   (484 perm/sec)   p_kst 5.060241e-06   p_cons 8.680000e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.867495e-07	k: 0	n:4160000
Cons ci ratio: 2.053756e-02	ci left: 8.592326e-03	ci right 8.770858e-03	k: 36114	n:4160000
KS ci ratio: 8.357445e-01	ci left: 3.124842e-06	ci right 7.716512e-06	k: 21	n:4160000
PIK3CA   4160000 perm   8619 sec   (483 perm/sec)   p_kst 5.048077e-06   p_cons 8.681250e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.846230e-07	k: 0	n:4170000
Cons ci ratio: 2.050801e-02	ci left: 8.596534e-03	ci right 8.774893e-03	k: 36218	n:4170000
KS ci ratio: 8.357445e-01	ci left: 3.117348e-06	ci right 7.698007e-06	k: 21	n:4170000
PIK3CA   4170000 perm   8657 sec   (482 perm/sec)   p_kst 5.035971e-06   p_cons 8.685372e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.825067e-07	k: 0	n:4180000
Cons ci ratio: 2.048655e-02	ci left: 8.594056e-03	ci right 8.772176e-03	k: 36294	n:4180000
KS ci ratio: 8.357445e-01	ci left: 3.109890e-06	ci right 7.679590e-06	k: 21	n:4180000
PIK3CA   4180000 perm   8697 sec   (481 perm/sec)   p_kst 5.023923e-06   p_cons 8.682775e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.804004e-07	k: 0	n:4190000
Cons ci ratio: 2.046658e-02	ci left: 8.590404e-03	ci right 8.768272e-03	k: 36365	n:4190000
KS ci ratio: 8.357445e-01	ci left: 3.102468e-06	ci right 7.661262e-06	k: 21	n:4190000
PIK3CA   4190000 perm   8737 sec   (480 perm/sec)   p_kst 5.011933e-06   p_cons 8.678998e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.783042e-07	k: 0	n:4200000
Cons ci ratio: 2.044328e-02	ci left: 8.589611e-03	ci right 8.767258e-03	k: 36448	n:4200000
KS ci ratio: 8.357445e-01	ci left: 3.095081e-06	ci right 7.643021e-06	k: 21	n:4200000
PIK3CA   4200000 perm   8777 sec   (479 perm/sec)   p_kst 5.000000e-06   p_cons 8.678095e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.762180e-07	k: 0	n:4210000
Cons ci ratio: 2.042090e-02	ci left: 8.588113e-03	ci right 8.765532e-03	k: 36528	n:4210000
KS ci ratio: 8.357445e-01	ci left: 3.087730e-06	ci right 7.624867e-06	k: 21	n:4210000
PIK3CA   4210000 perm   8816 sec   (478 perm/sec)   p_kst 4.988124e-06   p_cons 8.676485e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.741417e-07	k: 0	n:4220000
Cons ci ratio: 2.039522e-02	ci left: 8.589452e-03	ci right 8.766673e-03	k: 36620	n:4220000
KS ci ratio: 8.357445e-01	ci left: 3.080413e-06	ci right 7.606798e-06	k: 21	n:4220000
PIK3CA   4220000 perm   8855 sec   (477 perm/sec)   p_kst 4.976303e-06   p_cons 8.677725e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.720751e-07	k: 0	n:4230000
Cons ci ratio: 2.037383e-02	ci left: 8.587257e-03	ci right 8.764244e-03	k: 36697	n:4230000
KS ci ratio: 8.357445e-01	ci left: 3.073130e-06	ci right 7.588815e-06	k: 21	n:4230000
PIK3CA   4230000 perm   8895 sec   (476 perm/sec)   p_kst 4.964539e-06   p_cons 8.675414e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.700184e-07	k: 0	n:4240000
Cons ci ratio: 2.035670e-02	ci left: 8.581552e-03	ci right 8.758271e-03	k: 36759	n:4240000
KS ci ratio: 8.357445e-01	ci left: 3.065882e-06	ci right 7.570917e-06	k: 21	n:4240000
PIK3CA   4240000 perm   8935 sec   (475 perm/sec)   p_kst 4.952830e-06   p_cons 8.669575e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.679713e-07	k: 0	n:4250000
Cons ci ratio: 2.033126e-02	ci left: 8.582897e-03	ci right 8.759421e-03	k: 36851	n:4250000
KS ci ratio: 8.357445e-01	ci left: 3.058669e-06	ci right 7.553103e-06	k: 21	n:4250000
PIK3CA   4250000 perm   8975 sec   (474 perm/sec)   p_kst 4.941176e-06   p_cons 8.670824e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.659338e-07	k: 0	n:4260000
Cons ci ratio: 2.030953e-02	ci left: 8.581199e-03	ci right 8.757498e-03	k: 36930	n:4260000
KS ci ratio: 8.357446e-01	ci left: 3.051489e-06	ci right 7.535373e-06	k: 21	n:4260000
PIK3CA   4260000 perm   9014 sec   (473 perm/sec)   p_kst 4.929577e-06   p_cons 8.669014e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.639058e-07	k: 0	n:4270000
Cons ci ratio: 2.028896e-02	ci left: 8.578578e-03	ci right 8.754642e-03	k: 37005	n:4270000
KS ci ratio: 8.357446e-01	ci left: 3.044342e-06	ci right 7.517726e-06	k: 21	n:4270000
PIK3CA   4270000 perm   9054 sec   (472 perm/sec)   p_kst 4.918033e-06   p_cons 8.666276e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.618874e-07	k: 0	n:4280000
Cons ci ratio: 2.026956e-02	ci left: 8.575039e-03	ci right 8.750860e-03	k: 37076	n:4280000
KS ci ratio: 8.357446e-01	ci left: 3.037229e-06	ci right 7.500161e-06	k: 21	n:4280000
PIK3CA   4280000 perm   9096 sec   (471 perm/sec)   p_kst 4.906542e-06   p_cons 8.662617e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.598783e-07	k: 0	n:4290000
Cons ci ratio: 2.024308e-02	ci left: 8.577547e-03	ci right 8.753187e-03	k: 37173	n:4290000
KS ci ratio: 8.357446e-01	ci left: 3.030150e-06	ci right 7.482678e-06	k: 21	n:4290000
PIK3CA   4290000 perm   9135 sec   (470 perm/sec)   p_kst 4.895105e-06   p_cons 8.665035e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.578786e-07	k: 0	n:4300000
Cons ci ratio: 2.022135e-02	ci left: 8.576110e-03	ci right 8.751530e-03	k: 37253	n:4300000
KS ci ratio: 8.357446e-01	ci left: 3.023103e-06	ci right 7.465277e-06	k: 21	n:4300000
PIK3CA   4300000 perm   9175 sec   (469 perm/sec)   p_kst 4.883721e-06   p_cons 8.663488e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.558881e-07	k: 0	n:4310000
Cons ci ratio: 2.019505e-02	ci left: 8.578604e-03	ci right 8.753844e-03	k: 37350	n:4310000
KS ci ratio: 8.357446e-01	ci left: 3.016089e-06	ci right 7.447956e-06	k: 21	n:4310000
PIK3CA   4310000 perm   9215 sec   (468 perm/sec)   p_kst 4.872390e-06   p_cons 8.665893e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.539069e-07	k: 0	n:4320000
Cons ci ratio: 2.017401e-02	ci left: 8.576710e-03	ci right 8.751727e-03	k: 37428	n:4320000
KS ci ratio: 8.357446e-01	ci left: 3.009107e-06	ci right 7.430715e-06	k: 21	n:4320000
PIK3CA   4320000 perm   9255 sec   (467 perm/sec)   p_kst 4.861111e-06   p_cons 8.663889e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.519348e-07	k: 0	n:4330000
Cons ci ratio: 2.014465e-02	ci left: 8.581949e-03	ci right 8.756815e-03	k: 37537	n:4330000
KS ci ratio: 8.357446e-01	ci left: 3.002157e-06	ci right 7.413554e-06	k: 21	n:4330000
PIK3CA   4330000 perm   9295 sec   (466 perm/sec)   p_kst 4.849885e-06   p_cons 8.669053e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.499719e-07	k: 0	n:4340000
Cons ci ratio: 2.012108e-02	ci left: 8.582350e-03	ci right 8.757017e-03	k: 37625	n:4340000
KS ci ratio: 8.357446e-01	ci left: 2.995240e-06	ci right 7.396472e-06	k: 21	n:4340000
PIK3CA   4340000 perm   9335 sec   (465 perm/sec)   p_kst 4.838710e-06   p_cons 8.669355e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.480179e-07	k: 0	n:4350000
Cons ci ratio: 2.009490e-02	ci left: 8.585036e-03	ci right 8.759527e-03	k: 37723	n:4350000
KS ci ratio: 8.173742e-01	ci left: 3.169493e-06	ci right 7.657062e-06	k: 22	n:4350000
PIK3CA   4350000 perm   9376 sec   (464 perm/sec)   p_kst 5.057471e-06   p_cons 8.671954e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.460729e-07	k: 0	n:4360000
Cons ci ratio: 2.007096e-02	ci left: 8.585884e-03	ci right 8.760183e-03	k: 37813	n:4360000
KS ci ratio: 8.173743e-01	ci left: 3.162223e-06	ci right 7.639500e-06	k: 22	n:4360000
PIK3CA   4360000 perm   9416 sec   (463 perm/sec)   p_kst 5.045872e-06   p_cons 8.672706e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.441368e-07	k: 0	n:4370000
Cons ci ratio: 2.004231e-02	ci left: 8.590827e-03	ci right 8.764974e-03	k: 37921	n:4370000
KS ci ratio: 8.173743e-01	ci left: 3.154987e-06	ci right 7.622019e-06	k: 22	n:4370000
PIK3CA   4370000 perm   9457 sec   (462 perm/sec)   p_kst 5.034325e-06   p_cons 8.677574e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.422096e-07	k: 0	n:4380000
Cons ci ratio: 2.001750e-02	ci left: 8.592567e-03	ci right 8.766531e-03	k: 38015	n:4380000
KS ci ratio: 8.173743e-01	ci left: 3.147784e-06	ci right 7.604617e-06	k: 22	n:4380000
PIK3CA   4380000 perm   9498 sec   (461 perm/sec)   p_kst 5.022831e-06   p_cons 8.679224e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.402911e-07	k: 0	n:4390000
Cons ci ratio: 1.999331e-02	ci left: 8.593846e-03	ci right 8.767623e-03	k: 38107	n:4390000
KS ci ratio: 8.173743e-01	ci left: 3.140614e-06	ci right 7.587294e-06	k: 22	n:4390000
PIK3CA   4390000 perm   9540 sec   (460 perm/sec)   p_kst 5.011390e-06   p_cons 8.680410e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.383813e-07	k: 0	n:4400000
Cons ci ratio: 1.997343e-02	ci left: 8.591501e-03	ci right 8.765056e-03	k: 38183	n:4400000
KS ci ratio: 8.173743e-01	ci left: 3.133476e-06	ci right 7.570050e-06	k: 22	n:4400000
PIK3CA   4400000 perm   9581 sec   (459 perm/sec)   p_kst 5.000000e-06   p_cons 8.677955e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.364803e-07	k: 0	n:4410000
Cons ci ratio: 1.994861e-02	ci left: 8.593453e-03	ci right 8.766830e-03	k: 38278	n:4410000
KS ci ratio: 8.173743e-01	ci left: 3.126371e-06	ci right 7.552885e-06	k: 22	n:4410000
PIK3CA   4410000 perm   9622 sec   (458 perm/sec)   p_kst 4.988662e-06   p_cons 8.679819e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.345878e-07	k: 0	n:4420000
Cons ci ratio: 1.992572e-02	ci left: 8.593821e-03	ci right 8.767004e-03	k: 38366	n:4420000
KS ci ratio: 8.173743e-01	ci left: 3.119297e-06	ci right 7.535797e-06	k: 22	n:4420000
PIK3CA   4420000 perm   9663 sec   (457 perm/sec)   p_kst 4.977376e-06   p_cons 8.680090e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.327038e-07	k: 0	n:4430000
Cons ci ratio: 1.990369e-02	ci left: 8.593514e-03	ci right 8.766497e-03	k: 38451	n:4430000
KS ci ratio: 8.173743e-01	ci left: 3.112256e-06	ci right 7.518786e-06	k: 22	n:4430000
PIK3CA   4430000 perm   9705 sec   (456 perm/sec)   p_kst 4.966140e-06   p_cons 8.679684e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.308284e-07	k: 0	n:4440000
Cons ci ratio: 1.988667e-02	ci left: 8.588950e-03	ci right 8.761692e-03	k: 38517	n:4440000
KS ci ratio: 8.173743e-01	ci left: 3.105246e-06	ci right 7.501852e-06	k: 22	n:4440000
PIK3CA   4440000 perm   9747 sec   (456 perm/sec)   p_kst 4.954955e-06   p_cons 8.675000e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.289613e-07	k: 0	n:4450000
Cons ci ratio: 1.986295e-02	ci left: 8.590220e-03	ci right 8.762779e-03	k: 38609	n:4450000
KS ci ratio: 8.173743e-01	ci left: 3.098268e-06	ci right 7.484994e-06	k: 22	n:4450000
PIK3CA   4450000 perm   9788 sec   (455 perm/sec)   p_kst 4.943820e-06   p_cons 8.676180e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.271027e-07	k: 0	n:4460000
Cons ci ratio: 1.984268e-02	ci left: 8.588585e-03	ci right 8.760933e-03	k: 38688	n:4460000
KS ci ratio: 8.173743e-01	ci left: 3.091322e-06	ci right 7.468211e-06	k: 22	n:4460000
PIK3CA   4460000 perm   9830 sec   (454 perm/sec)   p_kst 4.932735e-06   p_cons 8.674439e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.252523e-07	k: 0	n:4470000
Cons ci ratio: 1.982247e-02	ci left: 8.586957e-03	ci right 8.759095e-03	k: 38767	n:4470000
KS ci ratio: 8.173743e-01	ci left: 3.084406e-06	ci right 7.451504e-06	k: 22	n:4470000
PIK3CA   4470000 perm   9871 sec   (453 perm/sec)   p_kst 4.921700e-06   p_cons 8.672707e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.234103e-07	k: 0	n:4480000
Cons ci ratio: 1.979975e-02	ci left: 8.587557e-03	ci right 8.759507e-03	k: 38856	n:4480000
KS ci ratio: 8.173743e-01	ci left: 3.077521e-06	ci right 7.434871e-06	k: 22	n:4480000
PIK3CA   4480000 perm   9913 sec   (452 perm/sec)   p_kst 4.910714e-06   p_cons 8.673214e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.215764e-07	k: 0	n:4490000
Cons ci ratio: 1.977071e-02	ci left: 8.593695e-03	ci right 8.765514e-03	k: 38970	n:4490000
KS ci ratio: 8.173743e-01	ci left: 3.070667e-06	ci right 7.418312e-06	k: 22	n:4490000
PIK3CA   4490000 perm   9954 sec   (451 perm/sec)   p_kst 4.899777e-06   p_cons 8.679287e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.197507e-07	k: 0	n:4500000
Cons ci ratio: 1.974587e-02	ci left: 8.596269e-03	ci right 8.767920e-03	k: 39068	n:4500000
KS ci ratio: 8.173743e-01	ci left: 3.063843e-06	ci right 7.401827e-06	k: 22	n:4500000
PIK3CA   4500000 perm   9996 sec   (450 perm/sec)   p_kst 4.888889e-06   p_cons 8.681778e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.179330e-07	k: 0	n:4510000
Cons ci ratio: 1.972113e-02	ci left: 8.598831e-03	ci right 8.770315e-03	k: 39166	n:4510000
KS ci ratio: 8.173743e-01	ci left: 3.057050e-06	ci right 7.385415e-06	k: 22	n:4510000
PIK3CA   4510000 perm   10038 sec   (449 perm/sec)   p_kst 4.878049e-06   p_cons 8.684257e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.161234e-07	k: 0	n:4520000
Cons ci ratio: 1.969926e-02	ci left: 8.598960e-03	ci right 8.770255e-03	k: 39253	n:4520000
KS ci ratio: 8.173743e-01	ci left: 3.050286e-06	ci right 7.369076e-06	k: 22	n:4520000
PIK3CA   4520000 perm   10080 sec   (448 perm/sec)   p_kst 4.867257e-06   p_cons 8.684292e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.143218e-07	k: 0	n:4530000
Cons ci ratio: 1.967545e-02	ci left: 8.600846e-03	ci right 8.771969e-03	k: 39348	n:4530000
KS ci ratio: 8.173743e-01	ci left: 3.043553e-06	ci right 7.352809e-06	k: 22	n:4530000
PIK3CA   4530000 perm   10122 sec   (448 perm/sec)   p_kst 4.856512e-06   p_cons 8.686093e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.125282e-07	k: 0	n:4540000
Cons ci ratio: 1.965298e-02	ci left: 8.601627e-03	ci right 8.772568e-03	k: 39438	n:4540000
KS ci ratio: 8.173743e-01	ci left: 3.036849e-06	ci right 7.336613e-06	k: 22	n:4540000
PIK3CA   4540000 perm   10165 sec   (447 perm/sec)   p_kst 4.845815e-06   p_cons 8.686784e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.107424e-07	k: 0	n:4550000
Cons ci ratio: 1.962884e-02	ci left: 8.603937e-03	ci right 8.774711e-03	k: 39535	n:4550000
KS ci ratio: 8.173743e-01	ci left: 3.030174e-06	ci right 7.320489e-06	k: 22	n:4550000
PIK3CA   4550000 perm   10207 sec   (446 perm/sec)   p_kst 4.835165e-06   p_cons 8.689011e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.089645e-07	k: 0	n:4560000
Cons ci ratio: 1.961002e-02	ci left: 8.601653e-03	ci right 8.772217e-03	k: 39611	n:4560000
KS ci ratio: 8.173744e-01	ci left: 3.023529e-06	ci right 7.304435e-06	k: 22	n:4560000
PIK3CA   4560000 perm   10249 sec   (445 perm/sec)   p_kst 4.824561e-06   p_cons 8.686623e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.071943e-07	k: 0	n:4570000
Cons ci ratio: 1.959126e-02	ci left: 8.599380e-03	ci right 8.769734e-03	k: 39687	n:4570000
KS ci ratio: 8.173744e-01	ci left: 3.016913e-06	ci right 7.288451e-06	k: 22	n:4570000
PIK3CA   4570000 perm   10292 sec   (444 perm/sec)   p_kst 4.814004e-06   p_cons 8.684245e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.054319e-07	k: 0	n:4580000
Cons ci ratio: 1.956833e-02	ci left: 8.600810e-03	ci right 8.770991e-03	k: 39780	n:4580000
KS ci ratio: 8.001645e-01	ci left: 3.183415e-06	ci right 7.535207e-06	k: 23	n:4580000
PIK3CA   4580000 perm   10335 sec   (443 perm/sec)   p_kst 5.021834e-06   p_cons 8.685590e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.036771e-07	k: 0	n:4590000
Cons ci ratio: 1.954450e-02	ci left: 8.603102e-03	ci right 8.773118e-03	k: 39877	n:4590000
KS ci ratio: 8.001645e-01	ci left: 3.176479e-06	ci right 7.518791e-06	k: 23	n:4590000
PIK3CA   4590000 perm   10378 sec   (442 perm/sec)   p_kst 5.010893e-06   p_cons 8.687800e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.019300e-07	k: 0	n:4600000
Cons ci ratio: 1.952395e-02	ci left: 8.602571e-03	ci right 8.772396e-03	k: 39961	n:4600000
KS ci ratio: 8.001645e-01	ci left: 3.169574e-06	ci right 7.502446e-06	k: 23	n:4600000
PIK3CA   4600000 perm   10420 sec   (441 perm/sec)   p_kst 5.000000e-06   p_cons 8.687174e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 8.001904e-07	k: 0	n:4610000
Cons ci ratio: 1.950126e-02	ci left: 8.603986e-03	ci right 8.773639e-03	k: 40054	n:4610000
KS ci ratio: 8.001645e-01	ci left: 3.162698e-06	ci right 7.486171e-06	k: 23	n:4610000
PIK3CA   4610000 perm   10463 sec   (441 perm/sec)   p_kst 4.989154e-06   p_cons 8.688503e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.984584e-07	k: 0	n:4620000
Cons ci ratio: 1.947914e-02	ci left: 8.604963e-03	ci right 8.774441e-03	k: 40145	n:4620000
KS ci ratio: 8.001645e-01	ci left: 3.155853e-06	ci right 7.469968e-06	k: 23	n:4620000
PIK3CA   4620000 perm   10506 sec   (440 perm/sec)   p_kst 4.978355e-06   p_cons 8.689394e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.967339e-07	k: 0	n:4630000
Cons ci ratio: 1.945514e-02	ci left: 8.607656e-03	ci right 8.776976e-03	k: 40244	n:4630000
KS ci ratio: 7.839978e-01	ci left: 3.321224e-06	ci right 7.712754e-06	k: 24	n:4630000
PIK3CA   4630000 perm   10549 sec   (439 perm/sec)   p_kst 5.183585e-06   p_cons 8.692009e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.950168e-07	k: 0	n:4640000
Cons ci ratio: 1.943026e-02	ci left: 8.611196e-03	ci right 8.780366e-03	k: 40347	n:4640000
KS ci ratio: 7.839978e-01	ci left: 3.314066e-06	ci right 7.696132e-06	k: 24	n:4640000
PIK3CA   4640000 perm   10592 sec   (438 perm/sec)   p_kst 5.172414e-06   p_cons 8.695474e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.933071e-07	k: 0	n:4650000
Cons ci ratio: 1.941055e-02	ci left: 8.610226e-03	ci right 8.779204e-03	k: 40429	n:4650000
KS ci ratio: 7.839978e-01	ci left: 3.306939e-06	ci right 7.679581e-06	k: 24	n:4650000
PIK3CA   4650000 perm   10635 sec   (437 perm/sec)   p_kst 5.161290e-06   p_cons 8.694409e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.916047e-07	k: 0	n:4660000
Cons ci ratio: 1.938874e-02	ci left: 8.611182e-03	ci right 8.779987e-03	k: 40520	n:4660000
KS ci ratio: 7.839978e-01	ci left: 3.299842e-06	ci right 7.663101e-06	k: 24	n:4660000
PIK3CA   4660000 perm   10678 sec   (436 perm/sec)   p_kst 5.150215e-06   p_cons 8.695279e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.899096e-07	k: 0	n:4670000
Cons ci ratio: 1.936820e-02	ci left: 8.611069e-03	ci right 8.779691e-03	k: 40606	n:4670000
KS ci ratio: 7.839978e-01	ci left: 3.292776e-06	ci right 7.646692e-06	k: 24	n:4670000
PIK3CA   4670000 perm   10722 sec   (436 perm/sec)   p_kst 5.139186e-06   p_cons 8.695075e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.882218e-07	k: 0	n:4680000
Cons ci ratio: 1.934652e-02	ci left: 8.612020e-03	ci right 8.780469e-03	k: 40697	n:4680000
KS ci ratio: 7.839978e-01	ci left: 3.285740e-06	ci right 7.630353e-06	k: 24	n:4680000
PIK3CA   4680000 perm   10765 sec   (435 perm/sec)   p_kst 5.128205e-06   p_cons 8.695940e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.865412e-07	k: 0	n:4690000
Cons ci ratio: 1.932635e-02	ci left: 8.611693e-03	ci right 8.779959e-03	k: 40782	n:4690000
KS ci ratio: 7.839978e-01	ci left: 3.278735e-06	ci right 7.614084e-06	k: 24	n:4690000
PIK3CA   4690000 perm   10809 sec   (434 perm/sec)   p_kst 5.117271e-06   p_cons 8.695522e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.848677e-07	k: 0	n:4700000
Cons ci ratio: 1.930387e-02	ci left: 8.613486e-03	ci right 8.781588e-03	k: 40877	n:4700000
KS ci ratio: 7.839978e-01	ci left: 3.271759e-06	ci right 7.597884e-06	k: 24	n:4700000
PIK3CA   4700000 perm   10853 sec   (433 perm/sec)   p_kst 5.106383e-06   p_cons 8.697234e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.832013e-07	k: 0	n:4710000
Cons ci ratio: 1.928526e-02	ci left: 8.611890e-03	ci right 8.779798e-03	k: 40956	n:4710000
KS ci ratio: 7.839978e-01	ci left: 3.264812e-06	ci right 7.581752e-06	k: 24	n:4710000
PIK3CA   4710000 perm   10897 sec   (432 perm/sec)   p_kst 5.095541e-06   p_cons 8.695541e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.815419e-07	k: 0	n:4720000
Cons ci ratio: 1.926789e-02	ci left: 8.609247e-03	ci right 8.776950e-03	k: 41030	n:4720000
KS ci ratio: 7.839978e-01	ci left: 3.257895e-06	ci right 7.565689e-06	k: 24	n:4720000
PIK3CA   4720000 perm   10941 sec   (431 perm/sec)   p_kst 5.084746e-06   p_cons 8.692797e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.798896e-07	k: 0	n:4730000
Cons ci ratio: 1.924796e-02	ci left: 8.608929e-03	ci right 8.776451e-03	k: 41115	n:4730000
KS ci ratio: 7.839978e-01	ci left: 3.251007e-06	ci right 7.549694e-06	k: 24	n:4730000
PIK3CA   4730000 perm   10985 sec   (431 perm/sec)   p_kst 5.073996e-06   p_cons 8.692389e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.782443e-07	k: 0	n:4740000
Cons ci ratio: 1.922669e-02	ci left: 8.609873e-03	ci right 8.777226e-03	k: 41206	n:4740000
KS ci ratio: 7.687731e-01	ci left: 3.413227e-06	ci right 7.785841e-06	k: 25	n:4740000
PIK3CA   4740000 perm   11029 sec   (430 perm/sec)   p_kst 5.274262e-06   p_cons 8.693249e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.766059e-07	k: 0	n:4750000
Cons ci ratio: 1.920361e-02	ci left: 8.612489e-03	ci right 8.779690e-03	k: 41305	n:4750000
KS ci ratio: 7.687731e-01	ci left: 3.406041e-06	ci right 7.769450e-06	k: 25	n:4750000
PIK3CA   4750000 perm   11074 sec   (429 perm/sec)   p_kst 5.263158e-06   p_cons 8.695789e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.749744e-07	k: 0	n:4760000
Cons ci ratio: 1.918038e-02	ci left: 8.615303e-03	ci right 8.782354e-03	k: 41405	n:4760000
KS ci ratio: 7.687731e-01	ci left: 3.398886e-06	ci right 7.753127e-06	k: 25	n:4760000
PIK3CA   4760000 perm   11118 sec   (428 perm/sec)   p_kst 5.252101e-06   p_cons 8.698529e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.733497e-07	k: 0	n:4770000
Cons ci ratio: 1.915607e-02	ci left: 8.619149e-03	ci right 8.786060e-03	k: 41510	n:4770000
KS ci ratio: 7.687731e-01	ci left: 3.391760e-06	ci right 7.736873e-06	k: 25	n:4770000
PIK3CA   4770000 perm   11162 sec   (427 perm/sec)   p_kst 5.241090e-06   p_cons 8.702306e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.717318e-07	k: 0	n:4780000
Cons ci ratio: 1.913696e-02	ci left: 8.618398e-03	ci right 8.785127e-03	k: 41593	n:4780000
KS ci ratio: 7.687731e-01	ci left: 3.384664e-06	ci right 7.720687e-06	k: 25	n:4780000
PIK3CA   4780000 perm   11207 sec   (427 perm/sec)   p_kst 5.230126e-06   p_cons 8.701464e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.701207e-07	k: 0	n:4790000
Cons ci ratio: 1.911674e-02	ci left: 8.618690e-03	ci right 8.785245e-03	k: 41681	n:4790000
KS ci ratio: 7.687731e-01	ci left: 3.377598e-06	ci right 7.704569e-06	k: 25	n:4790000
PIK3CA   4790000 perm   11252 sec   (426 perm/sec)   p_kst 5.219207e-06   p_cons 8.701670e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.685163e-07	k: 0	n:4800000
Cons ci ratio: 1.909751e-02	ci left: 8.618150e-03	ci right 8.784526e-03	k: 41765	n:4800000
KS ci ratio: 7.687731e-01	ci left: 3.370561e-06	ci right 7.688518e-06	k: 25	n:4800000
PIK3CA   4800000 perm   11297 sec   (425 perm/sec)   p_kst 5.208333e-06   p_cons 8.701042e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.669185e-07	k: 0	n:4810000
Cons ci ratio: 1.907743e-02	ci left: 8.618441e-03	ci right 8.784646e-03	k: 41853	n:4810000
KS ci ratio: 7.687731e-01	ci left: 3.363554e-06	ci right 7.672533e-06	k: 25	n:4810000
PIK3CA   4810000 perm   11341 sec   (424 perm/sec)   p_kst 5.197505e-06   p_cons 8.701247e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.653274e-07	k: 0	n:4820000
Cons ci ratio: 1.905740e-02	ci left: 8.618731e-03	ci right 8.784765e-03	k: 41941	n:4820000
KS ci ratio: 7.687731e-01	ci left: 3.356576e-06	ci right 7.656615e-06	k: 25	n:4820000
PIK3CA   4820000 perm   11386 sec   (423 perm/sec)   p_kst 5.186722e-06   p_cons 8.701452e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.637429e-07	k: 0	n:4830000
Cons ci ratio: 1.903675e-02	ci left: 8.619637e-03	ci right 8.785507e-03	k: 42032	n:4830000
KS ci ratio: 7.687731e-01	ci left: 3.349626e-06	ci right 7.640763e-06	k: 25	n:4830000
PIK3CA   4830000 perm   11432 sec   (422 perm/sec)   p_kst 5.175983e-06   p_cons 8.702277e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.621649e-07	k: 0	n:4840000
Cons ci ratio: 1.901480e-02	ci left: 8.621774e-03	ci right 8.787492e-03	k: 42129	n:4840000
KS ci ratio: 7.687731e-01	ci left: 3.342706e-06	ci right 7.624977e-06	k: 25	n:4840000
PIK3CA   4840000 perm   11478 sec   (422 perm/sec)   p_kst 5.165289e-06   p_cons 8.704339e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.605934e-07	k: 0	n:4850000
Cons ci ratio: 1.899475e-02	ci left: 8.622261e-03	ci right 8.787811e-03	k: 42218	n:4850000
KS ci ratio: 7.687731e-01	ci left: 3.335813e-06	ci right 7.609255e-06	k: 25	n:4850000
PIK3CA   4850000 perm   11522 sec   (421 perm/sec)   p_kst 5.154639e-06   p_cons 8.704742e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.590284e-07	k: 0	n:4860000
Cons ci ratio: 1.897770e-02	ci left: 8.620083e-03	ci right 8.785441e-03	k: 42294	n:4860000
KS ci ratio: 7.687731e-01	ci left: 3.328950e-06	ci right 7.593598e-06	k: 25	n:4860000
PIK3CA   4860000 perm   11566 sec   (420 perm/sec)   p_kst 5.144033e-06   p_cons 8.702469e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.574698e-07	k: 0	n:4870000
Cons ci ratio: 1.895595e-02	ci left: 8.622206e-03	ci right 8.787414e-03	k: 42391	n:4870000
KS ci ratio: 7.687731e-01	ci left: 3.322114e-06	ci right 7.578005e-06	k: 25	n:4870000
PIK3CA   4870000 perm   11613 sec   (419 perm/sec)   p_kst 5.133470e-06   p_cons 8.704517e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.559176e-07	k: 0	n:4880000
Cons ci ratio: 1.893968e-02	ci left: 8.619426e-03	ci right 8.784437e-03	k: 42464	n:4880000
KS ci ratio: 7.687731e-01	ci left: 3.315306e-06	ci right 7.562477e-06	k: 25	n:4880000
PIK3CA   4880000 perm   11657 sec   (419 perm/sec)   p_kst 5.122951e-06   p_cons 8.701639e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.543718e-07	k: 0	n:4890000
Cons ci ratio: 1.892188e-02	ci left: 8.618082e-03	ci right 8.782910e-03	k: 42544	n:4890000
KS ci ratio: 7.687731e-01	ci left: 3.308527e-06	ci right 7.547012e-06	k: 25	n:4890000
PIK3CA   4890000 perm   11703 sec   (418 perm/sec)   p_kst 5.112474e-06   p_cons 8.700204e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.528323e-07	k: 0	n:4900000
Cons ci ratio: 1.890726e-02	ci left: 8.613899e-03	ci right 8.778519e-03	k: 42610	n:4900000
KS ci ratio: 7.687731e-01	ci left: 3.301774e-06	ci right 7.531610e-06	k: 25	n:4900000
PIK3CA   4900000 perm   11748 sec   (417 perm/sec)   p_kst 5.102041e-06   p_cons 8.695918e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.512990e-07	k: 0	n:4910000
Cons ci ratio: 1.888955e-02	ci left: 8.612572e-03	ci right 8.777010e-03	k: 42690	n:4910000
KS ci ratio: 7.687731e-01	ci left: 3.295050e-06	ci right 7.516270e-06	k: 25	n:4910000
PIK3CA   4910000 perm   11794 sec   (416 perm/sec)   p_kst 5.091650e-06   p_cons 8.694501e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.497720e-07	k: 0	n:4920000
Cons ci ratio: 1.886699e-02	ci left: 8.615701e-03	ci right 8.780000e-03	k: 42792	n:4920000
KS ci ratio: 7.544022e-01	ci left: 3.452048e-06	ci right 7.743085e-06	k: 26	n:4920000
PIK3CA   4920000 perm   11840 sec   (416 perm/sec)   p_kst 5.284553e-06   p_cons 8.697561e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.482511e-07	k: 0	n:4930000
Cons ci ratio: 1.884651e-02	ci left: 8.617000e-03	ci right 8.781144e-03	k: 42885	n:4930000
KS ci ratio: 7.544022e-01	ci left: 3.445046e-06	ci right 7.727379e-06	k: 26	n:4930000
PIK3CA   4930000 perm   11886 sec   (415 perm/sec)   p_kst 5.273834e-06   p_cons 8.698783e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.467365e-07	k: 0	n:4940000
Cons ci ratio: 1.882853e-02	ci left: 8.616077e-03	ci right 8.780046e-03	k: 42967	n:4940000
KS ci ratio: 7.544022e-01	ci left: 3.438072e-06	ci right 7.711736e-06	k: 26	n:4940000
PIK3CA   4940000 perm   11932 sec   (414 perm/sec)   p_kst 5.263158e-06   p_cons 8.697773e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.452279e-07	k: 0	n:4950000
Cons ci ratio: 1.880752e-02	ci left: 8.617974e-03	ci right 8.781793e-03	k: 43063	n:4950000
KS ci ratio: 7.544022e-01	ci left: 3.431127e-06	ci right 7.696157e-06	k: 26	n:4950000
PIK3CA   4950000 perm   11978 sec   (413 perm/sec)   p_kst 5.252525e-06   p_cons 8.699596e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.437254e-07	k: 0	n:4960000
Cons ci ratio: 1.879162e-02	ci left: 8.615248e-03	ci right 8.778875e-03	k: 43136	n:4960000
KS ci ratio: 7.544022e-01	ci left: 3.424209e-06	ci right 7.680641e-06	k: 26	n:4960000
PIK3CA   4960000 perm   12024 sec   (412 perm/sec)   p_kst 5.241935e-06   p_cons 8.696774e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.422290e-07	k: 0	n:4970000
Cons ci ratio: 1.877029e-02	ci left: 8.617539e-03	ci right 8.781022e-03	k: 43234	n:4970000
KS ci ratio: 7.544022e-01	ci left: 3.417319e-06	ci right 7.665187e-06	k: 26	n:4970000
PIK3CA   4970000 perm   12069 sec   (412 perm/sec)   p_kst 5.231388e-06   p_cons 8.698994e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.407386e-07	k: 0	n:4980000
Cons ci ratio: 1.875034e-02	ci left: 8.618622e-03	ci right 8.781950e-03	k: 43326	n:4980000
KS ci ratio: 7.544022e-01	ci left: 3.410457e-06	ci right 7.649795e-06	k: 26	n:4980000
PIK3CA   4980000 perm   12115 sec   (411 perm/sec)   p_kst 5.220884e-06   p_cons 8.700000e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.392541e-07	k: 0	n:4990000
Cons ci ratio: 1.873263e-02	ci left: 8.617706e-03	ci right 8.780861e-03	k: 43408	n:4990000
KS ci ratio: 7.544022e-01	ci left: 3.403623e-06	ci right 7.634465e-06	k: 26	n:4990000
PIK3CA   4990000 perm   12160 sec   (410 perm/sec)   p_kst 5.210421e-06   p_cons 8.698998e-03   p_joint 0

Joint ci ratio: 3.919999e+00	ci left: 0	ci right 7.377756e-07	k: 0	n:5000000
Cons ci ratio: 1.871476e-02	ci left: 8.616993e-03	ci right 8.779977e-03	k: 43491	n:5000000
KS ci ratio: 7.544022e-01	ci left: 3.396815e-06	ci right 7.619196e-06	k: 26	n:5000000
PIK3CA   5000000 perm   12206 sec   (410 perm/sec)   p_kst 5.200000e-06   p_cons 8.698200e-03   p_joint 0

Outputting figure to mutsig2_images.part000000000131/PIK3CA.11_3287_5000000_5.2e-06_0.0086982_0.png
                gene_name: PIK3CA
               theta_stop: 3.9 
                    nperm: 5000000 
                     p_ks: 5.20e-06 
        ci_ks_bounds_left: 3.40e-06 
       ci_ks_bounds_right: 7.62e-06 
                   p_cons: 0.0087 
      ci_cons_bounds_left: 0.0086 
     ci_cons_bounds_right: 0.0088 
                  p_joint: 0 
     ci_joint_bounds_left: 0 
    ci_joint_bounds_right: 7.38e-07 

Current progress: 17 percent done.
PIK3C3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.372405e-03	ci left: 9.413886e-01	ci right 9.503494e-01	k: 9460	n:10000
Cons ci ratio: 1.750921e-02	ci left: 8.262552e-01	ci right 8.409500e-01	k: 8337	n:10000
KS ci ratio: 4.363748e-02	ci left: 4.367232e-01	ci right 4.563080e-01	k: 4465	n:10000
PIK3C3   10000 perm   2 sec   (5556 perm/sec)   p_kst 4.465000e-01   p_cons 8.337000e-01   p_joint 9.460000e-01

Outputting figure to mutsig2_images.part000000000131/PIK3C3.2_2764_10000_0.4465_0.8337_0.946.png
                gene_name: PIK3C3
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 33 percent done.
PIWIL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.928043e-02	ci left: 4.890517e-01	ci right 5.087489e-01	k: 4989	n:10000
Cons ci ratio: 6.913041e-02	ci left: 2.348172e-01	ci right 2.517326e-01	k: 2432	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
PIWIL1   10000 perm   2 sec   (5570 perm/sec)   p_kst 1   p_cons 2.432000e-01   p_joint 4.989000e-01

Outputting figure to mutsig2_images.part000000000131/PIWIL1.2_2666_10000_1_0.2432_0.4989.png
                gene_name: PIWIL1
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 50 percent done.
PIWIL4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.618316e-02	ci left: 2.510282e-01	ci right 2.683120e-01	k: 2596	n:10000
Cons ci ratio: 9.703224e-02	ci left: 1.334506e-01	ci right 1.471597e-01	k: 1402	n:10000
KS ci ratio: 5.560388e-02	ci left: 3.226707e-01	ci right 3.412273e-01	k: 3319	n:10000
PIWIL4   10000 perm   2 sec   (5638 perm/sec)   p_kst 3.319000e-01   p_cons 1.402000e-01   p_joint 2.596000e-01

Outputting figure to mutsig2_images.part000000000131/PIWIL4.2_2639_10000_0.3319_0.1402_0.2596.png
                gene_name: PIWIL4
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.25 
    ci_joint_bounds_right: 0.27 

Current progress: 67 percent done.
PKD1
Processing conservation and coverage...
76% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.444450e-02	ci left: 7.110866e-01	ci right 7.287851e-01	k: 7200	n:10000
Cons ci ratio: 3.686500e-02	ci left: 5.207608e-01	ci right 5.404213e-01	k: 5306	n:10000
KS ci ratio: 3.762664e-02	ci left: 5.105536e-01	ci right 5.302345e-01	k: 5204	n:10000
PKD1   10000 perm   4 sec   (2564 perm/sec)   p_kst 5.204000e-01   p_cons 5.306000e-01   p_joint 7.200000e-01

Outputting figure to mutsig2_images.part000000000131/PKD1.2_13096_10000_0.5204_0.5306_0.72.png
                gene_name: PKD1
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.71 
    ci_joint_bounds_right: 0.73 

Current progress: 83 percent done.
PKD1L1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.337237e-03	ci left: 9.856678e-01	ci right 9.900411e-01	k: 9880	n:10000
Cons ci ratio: 1.167382e-02	ci left: 9.130677e-01	ci right 9.238870e-01	k: 9186	n:10000
KS ci ratio: 3.169744e-02	ci left: 5.949377e-01	ci right 6.142014e-01	k: 6046	n:10000
PKD1L1   10000 perm   3 sec   (3345 perm/sec)   p_kst 6.046000e-01   p_cons 9.186000e-01   p_joint 9.880000e-01

Outputting figure to mutsig2_images.part000000000131/PKD1L1.2_8778_10000_0.6046_0.9186_0.988.png
                gene_name: PKD1L1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000131
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 131 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1553>
Subject: Job 4398233: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1553>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000132> was used as the working directory.
Started at Wed Oct 24 16:15:30 2012
Results reported at Wed Oct 24 16:20:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000132.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000132.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 132  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000132.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    414.23 sec.
    Max Memory :      1610 MB
    Max Swap   :      4022 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
132
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 132
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 132: processing genes 11753 - 11842
Calculating significance of each gene.
Using projection method.
11753	PKD2	1
11754	PKD2L1	1
11755	PKD2L2	1.802799e-01
11756	PKDCC	1
11757	PKDREJ	6.692988e-01
11758	PKHD1	3.031262e-01
11759	PKHD1L1	7.527207e-01
11760	PKIA	1
11761	PKIB	1
11762	PKIG	1
11763	PKLR	1
11764	PKM2	1
11765	PKMYT1	1
11766	PKN1	1
11767	PKN2	1
11768	PKN3	3.201278e-02
11769	PKNOX1	2.188176e-01
11770	PKNOX2	1
11771	PKP1	3.159543e-01
11772	PKP2	1.554547e-01
11773	PKP3	1.152569e-02
11774	PKP4	1
11775	PLA1A	1.239144e-01
11776	PLA2G10	1
11777	PLA2G12A	1
11778	PLA2G12B	1
11779	PLA2G15	1
11780	PLA2G16	1
11781	PLA2G1B	1
11782	PLA2G2A	1
11783	PLA2G2C	1
11784	PLA2G2D	1
11785	PLA2G2E	1
11786	PLA2G2F	1
11787	PLA2G3	1
11788	PLA2G4A	1.480862e-01
11789	PLA2G4B	1
11790	PLA2G4C	1
11791	PLA2G4D	1.700840e-01
11792	PLA2G4E	1
11793	PLA2G4F	1
11794	PLA2G5	1
11795	PLA2G6	1
11796	PLA2G7	1
11797	PLA2R1	1
11798	PLAA	1
11799	PLAC1	1
11800	PLAC1L	1
11801	PLAC4	1
11802	PLAC8	1
11803	PLAC8L1	1
11804	PLAC9	1
11805	PLAG1	1
11806	PLAGL1	1
11807	PLAGL2	1.390804e-01
11808	PLAT	3.687192e-02
11809	PLAU	2.612672e-02
11810	PLAUR	1
11811	PLB1	1
11812	PLBD1	1.189571e-02
11813	PLBD2	1
11814	PLCB1	1
11815	PLCB2	1.361264e-01
11816	PLCB3	1
11817	PLCB4	3.561454e-01
11818	PLCD1	1
11819	PLCD3	1
11820	PLCD4	1
11821	PLCE1	1
11822	PLCG1	1
11823	PLCG2	8.183434e-02
11824	PLCH1	1
11825	PLCH2	1
11826	PLCL1	7.294753e-02
11827	PLCL2	3.187276e-01
11828	PLCXD1	1
11829	PLCXD2	1
11830	PLCXD3	1
11831	PLCZ1	1
11832	PLD1	1
11833	PLD2	1
11834	PLD3	1
11835	PLD4	1
11836	PLD5	8.708472e-02
11837	PLD6	1
11838	PLDN	1
11839	PLEC	2.040827e-01
11840	PLEK	1
11841	PLEK2	1
11842	PLEKHA1	7.123980e-03
Done

Running MutSig 2:
Scatter job 132: processing genes 11753 - 11842
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PLEC
Processing conservation and coverage...
67% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.908968e-02	ci left: 2.964797e-01	ci right 3.146337e-01	k: 3055	n:10000
Cons ci ratio: 7.306490e-02	ci left: 2.152677e-01	ci right 2.316936e-01	k: 2234	n:10000
KS ci ratio: 5.833270e-02	ci left: 3.019334e-01	ci right 3.201768e-01	k: 3110	n:10000
PLEC   10000 perm   4 sec   (2292 perm/sec)   p_kst 3.110000e-01   p_cons 2.234000e-01   p_joint 3.055000e-01

Outputting figure to mutsig2_images.part000000000132/PLEC.7_14884_10000_0.311_0.2234_0.3055.png
                gene_name: PLEC
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.31 

Current progress: 9 percent done.
PKNOX1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.809000e-01	ci left: 5.020040e-03	ci right 8.277383e-03	k: 65	n:10000
Cons ci ratio: 6.494961e-02	ci left: 2.582492e-01	ci right 2.756868e-01	k: 2669	n:10000
KS ci ratio: 6.109146e-01	ci left: 2.859150e-03	ci right 5.442922e-03	k: 40	n:10000
PKNOX1   10000 perm   2 sec   (6395 perm/sec)   p_kst 4.000000e-03   p_cons 2.669000e-01   p_joint 6.500000e-03

Joint ci ratio: 4.193426e-01	ci left: 3.440841e-03	ci right 5.307780e-03	k: 86	n:20000
Cons ci ratio: 4.615060e-02	ci left: 2.589427e-01	ci right 2.712257e-01	k: 5301	n:20000
KS ci ratio: 4.193426e-01	ci left: 3.440841e-03	ci right 5.307780e-03	k: 86	n:20000
PKNOX1   20000 perm   4 sec   (5568 perm/sec)   p_kst 4.300000e-03   p_cons 2.650500e-01   p_joint 4.300000e-03

Joint ci ratio: 3.417378e-01	ci left: 3.621720e-03	ci right 5.143390e-03	k: 130	n:30000
Cons ci ratio: 3.786325e-02	ci left: 2.582233e-01	ci right 2.682226e-01	k: 7896	n:30000
KS ci ratio: 3.417378e-01	ci left: 3.621720e-03	ci right 5.143390e-03	k: 130	n:30000
PKNOX1   30000 perm   6 sec   (5391 perm/sec)   p_kst 4.333333e-03   p_cons 2.632000e-01   p_joint 4.333333e-03

Joint ci ratio: 3.000070e-01	ci left: 3.613074e-03	ci right 4.910520e-03	k: 169	n:40000
Cons ci ratio: 3.453753e-02	ci left: 2.393748e-01	ci right 2.478125e-01	k: 9743	n:40000
KS ci ratio: 3.000070e-01	ci left: 3.613074e-03	ci right 4.910520e-03	k: 169	n:40000
PKNOX1   40000 perm   8 sec   (5243 perm/sec)   p_kst 4.225000e-03   p_cons 2.435750e-01   p_joint 4.225000e-03

Joint ci ratio: 2.637017e-01	ci left: 3.820107e-03	ci right 4.998573e-03	k: 219	n:50000
Cons ci ratio: 3.097033e-02	ci left: 2.388876e-01	ci right 2.464223e-01	k: 12132	n:50000
KS ci ratio: 2.637017e-01	ci left: 3.820107e-03	ci right 4.998573e-03	k: 219	n:50000
PKNOX1   50000 perm   10 sec   (5112 perm/sec)   p_kst 4.380000e-03   p_cons 2.426400e-01   p_joint 4.380000e-03

Joint ci ratio: 2.439966e-01	ci left: 3.760892e-03	ci right 4.821271e-03	k: 256	n:60000
Cons ci ratio: 2.818070e-02	ci left: 2.404017e-01	ci right 2.472898e-01	k: 14630	n:60000
KS ci ratio: 2.439966e-01	ci left: 3.760892e-03	ci right 4.821271e-03	k: 256	n:60000
PKNOX1   60000 perm   12 sec   (4991 perm/sec)   p_kst 4.266667e-03   p_cons 2.438333e-01   p_joint 4.266667e-03

Joint ci ratio: 2.269768e-01	ci left: 3.761374e-03	ci right 4.737567e-03	k: 296	n:70000
Cons ci ratio: 2.610291e-02	ci left: 2.404805e-01	ci right 2.468550e-01	k: 17056	n:70000
KS ci ratio: 2.269768e-01	ci left: 3.761374e-03	ci right 4.737567e-03	k: 296	n:70000
PKNOX1   70000 perm   14 sec   (4883 perm/sec)   p_kst 4.228571e-03   p_cons 2.436571e-01   p_joint 4.228571e-03

Joint ci ratio: 2.090727e-01	ci left: 3.917612e-03	ci right 4.843897e-03	k: 349	n:80000
Cons ci ratio: 2.437630e-02	ci left: 2.413008e-01	ci right 2.472678e-01	k: 19542	n:80000
KS ci ratio: 2.090727e-01	ci left: 3.917612e-03	ci right 4.843897e-03	k: 349	n:80000
PKNOX1   80000 perm   17 sec   (4778 perm/sec)   p_kst 4.362500e-03   p_cons 2.442750e-01   p_joint 4.362500e-03

Joint ci ratio: 1.993528e-01	ci left: 3.851319e-03	ci right 4.714446e-03	k: 384	n:90000
Cons ci ratio: 2.297451e-02	ci left: 2.415952e-01	ci right 2.472213e-01	k: 21996	n:90000
KS ci ratio: 1.993528e-01	ci left: 3.851319e-03	ci right 4.714446e-03	k: 384	n:90000
PKNOX1   90000 perm   19 sec   (4681 perm/sec)   p_kst 4.266667e-03   p_cons 2.444000e-01   p_joint 4.266667e-03

Joint ci ratio: 1.873233e-01	ci left: 3.951539e-03	ci right 4.777615e-03	k: 435	n:100000
Cons ci ratio: 2.180269e-02	ci left: 2.416194e-01	ci right 2.469554e-01	k: 24428	n:100000
KS ci ratio: 1.873233e-01	ci left: 3.951539e-03	ci right 4.777615e-03	k: 435	n:100000
PKNOX1   100000 perm   22 sec   (4587 perm/sec)   p_kst 4.350000e-03   p_cons 2.442800e-01   p_joint 4.350000e-03

Joint ci ratio: 1.792829e-01	ci left: 3.939262e-03	ci right 4.723589e-03	k: 475	n:110000
Cons ci ratio: 2.075427e-02	ci left: 2.423428e-01	ci right 2.474343e-01	k: 26937	n:110000
KS ci ratio: 1.792829e-01	ci left: 3.939262e-03	ci right 4.723589e-03	k: 475	n:110000
PKNOX1   110000 perm   24 sec   (4495 perm/sec)   p_kst 4.318182e-03   p_cons 2.448818e-01   p_joint 4.318182e-03

Joint ci ratio: 1.711995e-01	ci left: 3.977523e-03	ci right 4.730073e-03	k: 521	n:120000
Cons ci ratio: 1.991419e-02	ci left: 2.416467e-01	ci right 2.465156e-01	k: 29289	n:120000
KS ci ratio: 1.711995e-01	ci left: 3.977523e-03	ci right 4.730073e-03	k: 521	n:120000
PKNOX1   120000 perm   27 sec   (4404 perm/sec)   p_kst 4.341667e-03   p_cons 2.440750e-01   p_joint 4.341667e-03

Joint ci ratio: 1.628286e-01	ci left: 4.076977e-03	ci right 4.806937e-03	k: 576	n:130000
Cons ci ratio: 1.912729e-02	ci left: 2.418512e-01	ci right 2.465295e-01	k: 31744	n:130000
KS ci ratio: 1.628286e-01	ci left: 4.076977e-03	ci right 4.806937e-03	k: 576	n:130000
PKNOX1   130000 perm   30 sec   (4317 perm/sec)   p_kst 4.430769e-03   p_cons 2.441846e-01   p_joint 4.430769e-03

Joint ci ratio: 1.550841e-01	ci left: 4.190456e-03	ci right 4.901733e-03	k: 635	n:140000
Cons ci ratio: 1.842080e-02	ci left: 2.421507e-01	ci right 2.466599e-01	k: 34216	n:140000
KS ci ratio: 1.550841e-01	ci left: 4.190456e-03	ci right 4.901733e-03	k: 635	n:140000
PKNOX1   140000 perm   33 sec   (4238 perm/sec)   p_kst 4.535714e-03   p_cons 2.444000e-01   p_joint 4.535714e-03

Joint ci ratio: 1.500944e-01	ci left: 4.186814e-03	ci right 4.872554e-03	k: 678	n:150000
Cons ci ratio: 1.778273e-02	ci left: 2.425061e-01	ci right 2.468638e-01	k: 36702	n:150000
KS ci ratio: 1.500944e-01	ci left: 4.186814e-03	ci right 4.872554e-03	k: 678	n:150000
PKNOX1   150000 perm   36 sec   (4159 perm/sec)   p_kst 4.520000e-03   p_cons 2.446800e-01   p_joint 4.520000e-03

Joint ci ratio: 1.457603e-01	ci left: 4.171902e-03	ci right 4.833750e-03	k: 719	n:160000
Cons ci ratio: 1.721248e-02	ci left: 2.426947e-01	ci right 2.469145e-01	k: 39168	n:160000
KS ci ratio: 1.457603e-01	ci left: 4.171902e-03	ci right 4.833750e-03	k: 719	n:160000
PKNOX1   160000 perm   39 sec   (4087 perm/sec)   p_kst 4.493750e-03   p_cons 2.448000e-01   p_joint 4.493750e-03

Joint ci ratio: 1.404888e-01	ci left: 4.238452e-03	ci right 4.884505e-03	k: 774	n:170000
Cons ci ratio: 1.671746e-02	ci left: 2.423411e-01	ci right 2.464324e-01	k: 41545	n:170000
KS ci ratio: 1.404888e-01	ci left: 4.238452e-03	ci right 4.884505e-03	k: 774	n:170000
PKNOX1   170000 perm   42 sec   (4018 perm/sec)   p_kst 4.552941e-03   p_cons 2.443824e-01   p_joint 4.552941e-03

Joint ci ratio: 1.361634e-01	ci left: 4.271153e-03	ci right 4.900522e-03	k: 824	n:180000
Cons ci ratio: 1.624276e-02	ci left: 2.424826e-01	ci right 2.464590e-01	k: 44004	n:180000
KS ci ratio: 1.361634e-01	ci left: 4.271153e-03	ci right 4.900522e-03	k: 824	n:180000
PKNOX1   180000 perm   46 sec   (3949 perm/sec)   p_kst 4.577778e-03   p_cons 2.444667e-01   p_joint 4.577778e-03

Joint ci ratio: 1.327489e-01	ci left: 4.265058e-03	ci right 4.876525e-03	k: 867	n:190000
Cons ci ratio: 1.581692e-02	ci left: 2.423640e-01	ci right 2.462332e-01	k: 46416	n:190000
KS ci ratio: 1.327489e-01	ci left: 4.265058e-03	ci right 4.876525e-03	k: 867	n:190000
PKNOX1   190000 perm   49 sec   (3879 perm/sec)   p_kst 4.563158e-03   p_cons 2.442947e-01   p_joint 4.563158e-03

Joint ci ratio: 1.285203e-01	ci left: 4.332339e-03	ci right 4.932158e-03	k: 925	n:200000
Cons ci ratio: 1.542582e-02	ci left: 2.421887e-01	ci right 2.459587e-01	k: 48814	n:200000
KS ci ratio: 1.285203e-01	ci left: 4.332339e-03	ci right 4.932158e-03	k: 925	n:200000
PKNOX1   200000 perm   52 sec   (3814 perm/sec)   p_kst 4.625000e-03   p_cons 2.440700e-01   p_joint 4.625000e-03

Joint ci ratio: 1.252484e-01	ci left: 4.351967e-03	ci right 4.938025e-03	k: 974	n:210000
Cons ci ratio: 1.504508e-02	ci left: 2.424540e-01	ci right 2.461341e-01	k: 51301	n:210000
KS ci ratio: 1.252484e-01	ci left: 4.351967e-03	ci right 4.938025e-03	k: 974	n:210000
PKNOX1   210000 perm   56 sec   (3739 perm/sec)   p_kst 4.638095e-03   p_cons 2.442905e-01   p_joint 4.638095e-03

Joint ci ratio: 1.225152e-01	ci left: 4.347952e-03	ci right 4.919765e-03	k: 1018	n:220000
Cons ci ratio: 1.471329e-02	ci left: 2.421429e-01	ci right 2.457365e-01	k: 53666	n:220000
KS ci ratio: 1.225152e-01	ci left: 4.347952e-03	ci right 4.919765e-03	k: 1018	n:220000
PKNOX1   220000 perm   60 sec   (3674 perm/sec)   p_kst 4.627273e-03   p_cons 2.439364e-01   p_joint 4.627273e-03

Joint ci ratio: 1.191120e-01	ci left: 4.407689e-03	ci right 4.970123e-03	k: 1077	n:230000
Cons ci ratio: 1.439352e-02	ci left: 2.420897e-01	ci right 2.456037e-01	k: 56084	n:230000
KS ci ratio: 1.191120e-01	ci left: 4.407689e-03	ci right 4.970123e-03	k: 1077	n:230000
PKNOX1   230000 perm   64 sec   (3611 perm/sec)   p_kst 4.682609e-03   p_cons 2.438435e-01   p_joint 4.682609e-03

Joint ci ratio: 1.160288e-01	ci left: 4.458602e-03	ci right 5.011797e-03	k: 1135	n:240000
Cons ci ratio: 1.409022e-02	ci left: 2.421331e-01	ci right 2.455731e-01	k: 58524	n:240000
KS ci ratio: 1.160288e-01	ci left: 4.458602e-03	ci right 5.011797e-03	k: 1135	n:240000
PKNOX1   240000 perm   68 sec   (3540 perm/sec)   p_kst 4.729167e-03   p_cons 2.438500e-01   p_joint 4.729167e-03

Joint ci ratio: 1.134600e-01	ci left: 4.482291e-03	ci right 5.025288e-03	k: 1187	n:250000
Cons ci ratio: 1.379874e-02	ci left: 2.423493e-01	ci right 2.457206e-01	k: 61008	n:250000
KS ci ratio: 1.134600e-01	ci left: 4.482291e-03	ci right 5.025288e-03	k: 1187	n:250000
PKNOX1   250000 perm   72 sec   (3491 perm/sec)   p_kst 4.748000e-03   p_cons 2.440320e-01   p_joint 4.748000e-03

Joint ci ratio: 1.111898e-01	ci left: 4.493064e-03	ci right 5.025761e-03	k: 1236	n:260000
Cons ci ratio: 1.352617e-02	ci left: 2.425074e-01	ci right 2.458137e-01	k: 63481	n:260000
KS ci ratio: 1.111898e-01	ci left: 4.493064e-03	ci right 5.025761e-03	k: 1236	n:260000
PKNOX1   260000 perm   76 sec   (3442 perm/sec)   p_kst 4.753846e-03   p_cons 2.441577e-01   p_joint 4.753846e-03

Joint ci ratio: 1.087959e-01	ci left: 4.524757e-03	ci right 5.048922e-03	k: 1291	n:270000
Cons ci ratio: 1.327367e-02	ci left: 2.425287e-01	ci right 2.457731e-01	k: 65920	n:270000
KS ci ratio: 1.087959e-01	ci left: 4.524757e-03	ci right 5.048922e-03	k: 1291	n:270000
PKNOX1   270000 perm   80 sec   (3391 perm/sec)   p_kst 4.781481e-03   p_cons 2.441481e-01   p_joint 4.781481e-03

Joint ci ratio: 1.069901e-01	ci left: 4.516060e-03	ci right 5.029987e-03	k: 1335	n:280000
Cons ci ratio: 1.304705e-02	ci left: 2.422034e-01	ci right 2.453877e-01	k: 68262	n:280000
KS ci ratio: 1.069901e-01	ci left: 4.516060e-03	ci right 5.029987e-03	k: 1335	n:280000
PKNOX1   280000 perm   84 sec   (3344 perm/sec)   p_kst 4.767857e-03   p_cons 2.437929e-01   p_joint 4.767857e-03

Joint ci ratio: 1.055020e-01	ci left: 4.487883e-03	ci right 4.991059e-03	k: 1373	n:290000
Cons ci ratio: 1.282757e-02	ci left: 2.420179e-01	ci right 2.451458e-01	k: 70638	n:290000
KS ci ratio: 1.055020e-01	ci left: 4.487883e-03	ci right 4.991059e-03	k: 1373	n:290000
PKNOX1   290000 perm   88 sec   (3298 perm/sec)   p_kst 4.734483e-03   p_cons 2.435793e-01   p_joint 4.734483e-03

Joint ci ratio: 1.037426e-01	ci left: 4.490854e-03	ci right 4.985455e-03	k: 1420	n:300000
Cons ci ratio: 1.261594e-02	ci left: 2.419284e-01	ci right 2.450032e-01	k: 73039	n:300000
KS ci ratio: 1.037426e-01	ci left: 4.490854e-03	ci right 4.985455e-03	k: 1420	n:300000
PKNOX1   300000 perm   92 sec   (3253 perm/sec)   p_kst 4.733333e-03   p_cons 2.434633e-01   p_joint 4.733333e-03

Joint ci ratio: 1.021034e-01	ci left: 4.490555e-03	ci right 4.976839e-03	k: 1466	n:310000
Cons ci ratio: 1.241379e-02	ci left: 2.418644e-01	ci right 2.448888e-01	k: 75446	n:310000
KS ci ratio: 1.021034e-01	ci left: 4.490555e-03	ci right 4.976839e-03	k: 1466	n:310000
PKNOX1   310000 perm   97 sec   (3209 perm/sec)   p_kst 4.729032e-03   p_cons 2.433742e-01   p_joint 4.729032e-03

Joint ci ratio: 1.003398e-01	ci left: 4.508613e-03	ci right 4.987923e-03	k: 1518	n:320000
Cons ci ratio: 1.222221e-02	ci left: 2.417705e-01	ci right 2.447467e-01	k: 77842	n:320000
KS ci ratio: 1.003398e-01	ci left: 4.508613e-03	ci right 4.987923e-03	k: 1518	n:320000
PKNOX1   320000 perm   101 sec   (3169 perm/sec)   p_kst 4.743750e-03   p_cons 2.432563e-01   p_joint 4.743750e-03

Joint ci ratio: 9.844441e-02	ci left: 4.546337e-03	ci right 5.020000e-03	k: 1577	n:330000
Cons ci ratio: 1.204200e-02	ci left: 2.415979e-01	ci right 2.445278e-01	k: 80210	n:330000
KS ci ratio: 9.844441e-02	ci left: 4.546337e-03	ci right 5.020000e-03	k: 1577	n:330000
PKNOX1   330000 perm   106 sec   (3128 perm/sec)   p_kst 4.778788e-03   p_cons 2.430606e-01   p_joint 4.778788e-03

Outputting figure to mutsig2_images.part000000000132/PKNOX1.3_1351_330000_0.0047788_0.24306_0.0047788.png
                gene_name: PKNOX1
               theta_stop: 0.098 
                    nperm: 330000 
                     p_ks: 0.0048 
        ci_ks_bounds_left: 0.0045 
       ci_ks_bounds_right: 0.0050 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.0048 
     ci_joint_bounds_left: 0.0045 
    ci_joint_bounds_right: 0.0050 

Current progress: 18 percent done.
PKDREJ
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.403001e-03	ci left: 9.707953e-01	ci right 9.771245e-01	k: 9741	n:10000
Cons ci ratio: 5.107307e-03	ci left: 9.807002e-01	ci right 9.858126e-01	k: 9834	n:10000
KS ci ratio: 2.757116e-02	ci left: 6.596787e-01	ci right 6.782228e-01	k: 6690	n:10000
PKDREJ   10000 perm   2 sec   (4098 perm/sec)   p_kst 6.690000e-01   p_cons 9.834000e-01   p_joint 9.741000e-01

Outputting figure to mutsig2_images.part000000000132/PKDREJ.2_6766_10000_0.669_0.9834_0.9741.png
                gene_name: PKDREJ
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 27 percent done.
PKHD1
Processing conservation and coverage...
79% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.728838e-02	ci left: 3.975486e-01	ci right 4.169054e-01	k: 4072	n:10000
Cons ci ratio: 6.730302e-02	ci left: 2.447000e-01	ci right 2.618439e-01	k: 2532	n:10000
KS ci ratio: 3.553197e-02	ci left: 5.390841e-01	ci right 5.586874e-01	k: 5489	n:10000
PKHD1   10000 perm   4 sec   (2745 perm/sec)   p_kst 5.489000e-01   p_cons 2.532000e-01   p_joint 4.072000e-01

Outputting figure to mutsig2_images.part000000000132/PKHD1.2_12528_10000_0.5489_0.2532_0.4072.png
                gene_name: PKHD1
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 36 percent done.
PKN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.351896e-02	ci left: 7.265354e-01	ci right 7.439273e-01	k: 7353	n:10000
Cons ci ratio: 3.406768e-03	ci left: 9.907188e-01	ci right 9.941851e-01	k: 9926	n:10000
KS ci ratio: 9.379027e-02	ci left: 1.416816e-01	ci right 1.557237e-01	k: 1486	n:10000
PKN3   10000 perm   2 sec   (5469 perm/sec)   p_kst 1.486000e-01   p_cons 9.926000e-01   p_joint 7.353000e-01

Outputting figure to mutsig2_images.part000000000132/PKN3.2_2758_10000_0.1486_0.9926_0.7353.png
                gene_name: PKN3
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.73 
    ci_joint_bounds_right: 0.74 

Current progress: 45 percent done.
PKP3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.002699e-02	ci left: 1.856990e-01	ci right 2.012800e-01	k: 1934	n:10000
Cons ci ratio: 8.863152e-02	ci left: 1.563004e-01	ci right 1.708961e-01	k: 1635	n:10000
KS ci ratio: 6.684359e-02	ci left: 2.472706e-01	ci right 2.644719e-01	k: 2558	n:10000
PKP3   10000 perm   2 sec   (5688 perm/sec)   p_kst 2.558000e-01   p_cons 1.635000e-01   p_joint 1.934000e-01

Outputting figure to mutsig2_images.part000000000132/PKP3.2_2446_10000_0.2558_0.1635_0.1934.png
                gene_name: PKP3
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 55 percent done.
PLBD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.027820e-02	ci left: 7.807680e-01	ci right 7.968634e-01	k: 7889	n:10000
Cons ci ratio: 2.229388e-02	ci left: 7.470537e-01	ci right 7.639972e-01	k: 7556	n:10000
KS ci ratio: 4.910833e-02	ci left: 3.795277e-01	ci right 3.987369e-01	k: 3891	n:10000
PLBD1   10000 perm   2 sec   (6191 perm/sec)   p_kst 3.891000e-01   p_cons 7.556000e-01   p_joint 7.889000e-01

Outputting figure to mutsig2_images.part000000000132/PLBD1.2_1706_10000_0.3891_0.7556_0.7889.png
                gene_name: PLBD1
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 64 percent done.
PLCG2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.788665e-02	ci left: 3.052063e-01	ci right 3.235020e-01	k: 3143	n:10000
Cons ci ratio: 1.325683e-01	ci left: 7.504646e-02	ci right 8.579947e-02	k: 803	n:10000
KS ci ratio: 6.241010e-02	ci left: 2.739874e-01	ci right 2.917393e-01	k: 2828	n:10000
PLCG2   10000 perm   2 sec   (5009 perm/sec)   p_kst 2.828000e-01   p_cons 8.030000e-02   p_joint 3.143000e-01

Joint ci ratio: 6.180551e-02	ci left: 1.622496e-01	ci right 1.726473e-01	k: 3348	n:20000
Cons ci ratio: 8.917600e-02	ci left: 8.415788e-02	ci right 9.206234e-02	k: 1761	n:20000
KS ci ratio: 4.360382e-02	ci left: 2.814820e-01	ci right 2.940797e-01	k: 5755	n:20000
PLCG2   20000 perm   4 sec   (4507 perm/sec)   p_kst 2.877500e-01   p_cons 8.805000e-02   p_joint 1.674000e-01

Outputting figure to mutsig2_images.part000000000132/PLCG2.2_3926_20000_0.28775_0.08805_0.1674.png
                gene_name: PLCG2
               theta_stop: 0.089 
                    nperm: 20000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.088 
      ci_cons_bounds_left: 0.084 
     ci_cons_bounds_right: 0.092 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.16 
    ci_joint_bounds_right: 0.17 

Current progress: 73 percent done.
PLCL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.910361e-02	ci left: 2.963806e-01	ci right 3.145329e-01	k: 3054	n:10000
KS ci ratio: 4.114718e-02	ci left: 4.658700e-01	ci right 4.855441e-01	k: 4757	n:10000
PLCL1   10000 perm   2 sec   (5358 perm/sec)   p_kst 4.757000e-01   p_cons 3.054000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000132/PLCL1.2_3312_10000_0.4757_0.3054_1.png
                gene_name: PLCL1
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 82 percent done.
PLD5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.293953e-02	ci left: 8.957999e-01	ci right 9.075649e-01	k: 9018	n:10000
Cons ci ratio: 1.208994e-02	ci left: 9.075108e-01	ci right 9.186472e-01	k: 9132	n:10000
KS ci ratio: 3.165106e-02	ci left: 5.956404e-01	ci right 6.148982e-01	k: 6053	n:10000
PLD5   10000 perm   2 sec   (6410 perm/sec)   p_kst 6.053000e-01   p_cons 9.132000e-01   p_joint 9.018000e-01

Outputting figure to mutsig2_images.part000000000132/PLD5.2_1371_10000_0.6053_0.9132_0.9018.png
                gene_name: PLD5
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.91 

Current progress: 91 percent done.
PLEKHA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.856056e-02	ci left: 6.437780e-01	ci right 6.625327e-01	k: 6532	n:10000
Cons ci ratio: 3.105821e-02	ci left: 6.046775e-01	ci right 6.238559e-01	k: 6143	n:10000
KS ci ratio: 3.723660e-02	ci left: 5.157568e-01	ci right 5.354283e-01	k: 5256	n:10000
PLEKHA1   10000 perm   2 sec   (6051 perm/sec)   p_kst 5.256000e-01   p_cons 6.143000e-01   p_joint 6.532000e-01

Outputting figure to mutsig2_images.part000000000132/PLEKHA1.2_1259_10000_0.5256_0.6143_0.6532.png
                gene_name: PLEKHA1
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000132
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 132 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1418>
Subject: Job 4398237: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1418>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000133> was used as the working directory.
Started at Wed Oct 24 16:15:30 2012
Results reported at Wed Oct 24 16:18:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000133.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000133.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 133  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000133.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    252.30 sec.
    Max Memory :      1703 MB
    Max Swap   :      4044 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
133
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 133
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 133: processing genes 11843 - 11931
Calculating significance of each gene.
Using projection method.
11843	PLEKHA2	1
11844	PLEKHA3	1
11845	PLEKHA4	1
11846	PLEKHA5	1
11847	PLEKHA6	1
11848	PLEKHA7	1
11849	PLEKHA8	1
11850	PLEKHA9	1
11851	PLEKHB1	1
11852	PLEKHB2	1
11853	PLEKHF1	1
11854	PLEKHF2	1
11855	PLEKHG1	1
11856	PLEKHG2	1
11857	PLEKHG3	3.877957e-01
11858	PLEKHG4	1
11859	PLEKHG4B	4.470457e-01
11860	PLEKHG5	1
11861	PLEKHG6	1
11862	PLEKHG7	1
11863	PLEKHH1	1
11864	PLEKHH2	4.136068e-01
11865	PLEKHH3	1
11866	PLEKHJ1	1
11867	PLEKHM1	1
11868	PLEKHM2	7.909600e-02
11869	PLEKHM3	1.174045e-01
11870	PLEKHN1	1
11871	PLEKHO1	1
11872	PLEKHO2	2.056902e-02
11873	PLG	1.906740e-01
11874	PLIN1	1
11875	PLIN2	1
11876	PLIN3	2.029708e-01
11877	PLIN4	1.558003e-01
11878	PLIN5	1
11879	PLK1	1
11880	PLK1S1	1
11881	PLK2	1
11882	PLK3	1
11883	PLK4	1
11884	PLLP	1
11885	PLN	1
11886	PLOD1	1
11887	PLOD2	1
11888	PLOD3	1
11889	PLP1	1
11890	PLP2	1
11891	PLRG1	1
11892	PLS1	2.913828e-01
11893	PLS3	1
11894	PLSCR1	1
11895	PLSCR2	1
11896	PLSCR3	1
11897	PLSCR4	1
11898	PLSCR5	1
11899	PLTP	1
11900	PLUNC	1
11901	PLVAP	2.287632e-01
11902	PLXDC1	1
11903	PLXDC2	1
11904	PLXNA1	4.547289e-02
11905	PLXNA2	1
11906	PLXNA3	5.724443e-02
11907	PLXNA4	4.743729e-01
11908	PLXNB1	1
11909	PLXNB2	2.187878e-01
11910	PLXNB3	1
11911	PLXNC1	1.005262e-01
11912	PLXND1	1
11913	PM20D1	1
11914	PM20D2	1.481124e-01
11915	PMAIP1	1
11916	PMCH	1
11917	PMEPA1	1
11918	PMF1	1
11919	PMFBP1	1
11920	PML	1.040526e-01
11921	PMM1	1
11922	PMM2	5.138826e-02
11923	PMP2	1
11924	PMP22	1
11925	PMPCA	1
11926	PMPCB	1
11927	PMS1	9.380413e-02
11928	PMS2	1
11929	PMVK	1
11930	PNCK	1
11931	PNKD	1
Done

Running MutSig 2:
Scatter job 133: processing genes 11843 - 11931
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PLXNA3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.545513e-02	ci left: 1.373691e-01	ci right 1.512388e-01	k: 1442	n:10000
Cons ci ratio: 1.696151e-01	ci left: 4.638557e-02	ci right 5.507852e-02	k: 506	n:10000
KS ci ratio: 3.983416e-02	ci left: 4.820550e-01	ci right 5.017497e-01	k: 4919	n:10000
PLXNA3   10000 perm   3 sec   (3898 perm/sec)   p_kst 4.919000e-01   p_cons 5.060000e-02   p_joint 1.442000e-01

Joint ci ratio: 3.788648e-02	ci left: 3.419932e-01	ci right 3.552508e-01	k: 6972	n:20000
Cons ci ratio: 1.157310e-01	ci left: 5.110214e-02	ci right 5.742824e-02	k: 1084	n:20000
KS ci ratio: 2.844383e-02	ci left: 4.801001e-01	ci right 4.940037e-01	k: 9741	n:20000
PLXNA3   20000 perm   8 sec   (2368 perm/sec)   p_kst 4.870500e-01   p_cons 5.420000e-02   p_joint 3.486000e-01

Joint ci ratio: 2.572009e-02	ci left: 4.307445e-01	ci right 4.420012e-01	k: 13091	n:30000
Cons ci ratio: 9.494270e-02	ci left: 5.120836e-02	ci right 5.634516e-02	k: 1612	n:30000
KS ci ratio: 2.322102e-02	ci left: 4.814621e-01	ci right 4.928071e-01	k: 14614	n:30000
PLXNA3   30000 perm   11 sec   (2610 perm/sec)   p_kst 4.871333e-01   p_cons 5.373333e-02   p_joint 4.363667e-01

Outputting figure to mutsig2_images.part000000000133/PLXNA3.3_5744_30000_0.48713_0.053733_0.43637.png
                gene_name: PLXNA3
               theta_stop: 0.095 
                    nperm: 30000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.054 
      ci_cons_bounds_left: 0.051 
     ci_cons_bounds_right: 0.056 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.44 

Current progress: 14 percent done.
PLEKHG3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.607332e-02	ci left: 5.315730e-01	ci right 5.512029e-01	k: 5414	n:10000
Cons ci ratio: 1.684207e-02	ci left: 8.369418e-01	ci right 8.512571e-01	k: 8442	n:10000
KS ci ratio: 8.101469e-02	ci left: 1.819585e-01	ci right 1.974227e-01	k: 1896	n:10000
PLEKHG3   10000 perm   2 sec   (5493 perm/sec)   p_kst 1.896000e-01   p_cons 8.442000e-01   p_joint 5.414000e-01

Outputting figure to mutsig2_images.part000000000133/PLEKHG3.2_3548_10000_0.1896_0.8442_0.5414.png
                gene_name: PLEKHG3
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 29 percent done.
PLEKHO2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.830757e-03	ci left: 9.360983e-01	ci right 9.454429e-01	k: 9409	n:10000
Cons ci ratio: 3.969896e-02	ci left: 4.837540e-01	ci right 5.034497e-01	k: 4936	n:10000
KS ci ratio: 2.067928e-02	ci left: 7.740800e-01	ci right 7.903553e-01	k: 7823	n:10000
PLEKHO2   10000 perm   1 sec   (6694 perm/sec)   p_kst 7.823000e-01   p_cons 4.936000e-01   p_joint 9.409000e-01

Outputting figure to mutsig2_images.part000000000133/PLEKHO2.2_1497_10000_0.7823_0.4936_0.9409.png
                gene_name: PLEKHO2
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 43 percent done.
PLXNA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.635299e-02	ci left: 8.446839e-01	ci right 8.587105e-01	k: 8518	n:10000
Cons ci ratio: 1.520918e-02	ci left: 8.624338e-01	ci right 8.757504e-01	k: 8692	n:10000
KS ci ratio: 1.813050e-02	ci left: 8.161888e-01	ci right 8.312222e-01	k: 8238	n:10000
PLXNA1   10000 perm   2 sec   (4209 perm/sec)   p_kst 8.238000e-01   p_cons 8.692000e-01   p_joint 8.518000e-01

Outputting figure to mutsig2_images.part000000000133/PLXNA1.2_5815_10000_0.8238_0.8692_0.8518.png
                gene_name: PLXNA1
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.88 
                  p_joint: 0.85 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.86 

Current progress: 57 percent done.
PLXNB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.165368e-02	ci left: 4.597784e-01	ci right 4.794394e-01	k: 4696	n:10000
Cons ci ratio: 1.738085e-01	ci left: 4.417993e-02	ci right 5.268561e-02	k: 483	n:10000
KS ci ratio: 1.595611e-02	ci left: 8.509025e-01	ci right 8.646883e-01	k: 8579	n:10000
PLXNB2   10000 perm   2 sec   (4599 perm/sec)   p_kst 8.579000e-01   p_cons 4.830000e-02   p_joint 4.696000e-01

Joint ci ratio: 2.122081e-02	ci left: 6.237169e-01	ci right 6.371452e-01	k: 12609	n:20000
Cons ci ratio: 1.246736e-01	ci left: 4.415643e-02	ci right 5.007613e-02	k: 941	n:20000
KS ci ratio: 1.136269e-02	ci left: 8.512096e-01	ci right 8.609866e-01	k: 17123	n:20000
PLXNB2   20000 perm   5 sec   (4010 perm/sec)   p_kst 8.561500e-01   p_cons 4.705000e-02   p_joint 6.304500e-01

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 1.052010e-01	ci left: 4.190172e-02	ci right 4.658706e-02	k: 1326	n:30000
KS ci ratio: 9.329416e-03	ci left: 8.507287e-01	ci right 8.587358e-01	k: 25643	n:30000
PLXNB2   30000 perm   8 sec   (3867 perm/sec)   p_kst 8.547667e-01   p_cons 4.420000e-02   p_joint 1

Joint ci ratio: 6.037570e-03	ci left: 9.105505e-01	ci right 9.160893e-01	k: 36534	n:40000
Cons ci ratio: 9.144106e-02	ci left: 4.191296e-02	ci right 4.595359e-02	k: 1756	n:40000
KS ci ratio: 8.154651e-03	ci left: 8.489364e-01	ci right 8.559124e-01	k: 34098	n:40000
PLXNB2   40000 perm   11 sec   (3758 perm/sec)   p_kst 8.524500e-01   p_cons 4.390000e-02   p_joint 9.133500e-01

Outputting figure to mutsig2_images.part000000000133/PLXNB2.2_5657_40000_0.85245_0.0439_0.91335.png
                gene_name: PLXNB2
               theta_stop: 0.091 
                    nperm: 40000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.044 
      ci_cons_bounds_left: 0.042 
     ci_cons_bounds_right: 0.046 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 71 percent done.
PLXNC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.071196e-02	ci left: 6.100009e-01	ci right 6.291294e-01	k: 6196	n:10000
Cons ci ratio: 2.886371e-02	ci left: 6.389496e-01	ci right 6.577639e-01	k: 6484	n:10000
KS ci ratio: 3.206990e-02	ci left: 5.893165e-01	ci right 6.086258e-01	k: 5990	n:10000
PLXNC1   10000 perm   2 sec   (4691 perm/sec)   p_kst 5.990000e-01   p_cons 6.484000e-01   p_joint 6.196000e-01

Outputting figure to mutsig2_images.part000000000133/PLXNC1.2_4831_10000_0.599_0.6484_0.6196.png
                gene_name: PLXNC1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.63 

Current progress: 86 percent done.
PML
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.516126e-02	ci left: 4.198695e-01	ci right 4.393715e-01	k: 4296	n:10000
Cons ci ratio: 4.193059e-02	ci left: 4.564835e-01	ci right 4.761362e-01	k: 4663	n:10000
KS ci ratio: 1.956251e-01	ci left: 3.481398e-02	ci right 4.245779e-02	k: 385	n:10000
PML   10000 perm   2 sec   (4884 perm/sec)   p_kst 3.850000e-02   p_cons 4.663000e-01   p_joint 4.296000e-01

Joint ci ratio: 6.899993e-02	ci left: 1.341347e-01	ci right 1.437705e-01	k: 2778	n:20000
Cons ci ratio: 3.141121e-02	ci left: 4.308589e-01	ci right 4.446592e-01	k: 8755	n:20000
KS ci ratio: 1.370436e-01	ci left: 3.660089e-02	ci right 4.203409e-02	k: 785	n:20000
PML   20000 perm   4 sec   (4526 perm/sec)   p_kst 3.925000e-02   p_cons 4.377500e-01   p_joint 1.389000e-01

Joint ci ratio: 3.848478e-02	ci left: 2.519960e-01	ci right 2.619178e-01	k: 7708	n:30000
Cons ci ratio: 2.553964e-02	ci left: 4.342059e-01	ci right 4.454724e-01	k: 13195	n:30000
KS ci ratio: 1.112595e-01	ci left: 3.751855e-02	ci right 4.197115e-02	k: 1191	n:30000
PML   30000 perm   7 sec   (4337 perm/sec)   p_kst 3.970000e-02   p_cons 4.398333e-01   p_joint 2.569333e-01

Joint ci ratio: 3.680085e-02	ci left: 2.168921e-01	ci right 2.250485e-01	k: 8838	n:40000
Cons ci ratio: 2.210297e-02	ci left: 4.353023e-01	ci right 4.450564e-01	k: 17607	n:40000
KS ci ratio: 9.598766e-02	ci left: 3.810059e-02	ci right 4.196655e-02	k: 1600	n:40000
PML   40000 perm   9 sec   (4224 perm/sec)   p_kst 4.000000e-02   p_cons 4.401750e-01   p_joint 2.209500e-01

Outputting figure to mutsig2_images.part000000000133/PML.2_3702_40000_0.04_0.44017_0.22095.png
                gene_name: PML
               theta_stop: 0.096 
                    nperm: 40000 
                     p_ks: 0.040 
        ci_ks_bounds_left: 0.038 
       ci_ks_bounds_right: 0.042 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000133
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 133 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4398240: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000134> was used as the working directory.
Started at Wed Oct 24 16:15:33 2012
Results reported at Wed Oct 24 16:17:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000134.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000134.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 134  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000134.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    140.59 sec.
    Max Memory :      1070 MB
    Max Swap   :      3871 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
134
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 134
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 134: processing genes 11932 - 12021
Calculating significance of each gene.
Using projection method.
11932	PNKP	2.087336e-01
11933	PNLDC1	1
11934	PNLIP	1
11935	PNLIPRP1	1
11936	PNLIPRP2	1
11937	PNLIPRP3	2.117621e-01
11938	PNMA1	1
11939	PNMA2	1
11940	PNMA3	1
11941	PNMA5	1
11942	PNMAL1	9.484993e-02
11943	PNMAL2	1
11944	PNMT	1
11945	PNN	1
11946	PNO1	1
11947	PNOC	1
11948	PNP	9.841106e-02
11949	PNPLA1	1
11950	PNPLA2	1
11951	PNPLA3	1
11952	PNPLA4	1
11953	PNPLA5	1
11954	PNPLA6	1.424367e-01
11955	PNPLA7	1
11956	PNPLA8	1
11957	PNPO	1
11958	PNPT1	1
11959	PNRC1	1
11960	POC1A	1
11961	POC1B	1
11962	POC5	1
11963	PODN	1
11964	PODNL1	1
11965	PODXL	1
11966	PODXL2	1.459324e-01
11967	POF1B	1
11968	POFUT1	1
11969	POFUT2	1
11970	POGK	1
11971	POGZ	1
11972	POLA1	3.705292e-01
11973	POLA2	1
11974	POLB	1
11975	POLD1	1
11976	POLD2	1
11977	POLD3	1
11978	POLD4	1
11979	POLDIP2	2.589131e-02
11980	POLDIP3	1
11981	POLE	1
11982	POLE2	1
11983	POLE3	1
11984	POLE4	1
11985	POLG	7.270295e-02
11986	POLG2	1
11987	POLH	1
11988	POLI	1
11989	POLK	1
11990	POLL	1
11991	POLM	1
11992	POLN	1
11993	POLQ	4.009956e-01
11994	POLR1A	1.817901e-01
11995	POLR1B	1
11996	POLR1C	1
11997	POLR1D	1
11998	POLR1E	1
11999	POLR2A	1
12000/17942 12000	POLR2B	1
12001	POLR2C	1
12002	POLR2D	1
12003	POLR2E	1
12004	POLR2F	1
12005	POLR2G	1
12006	POLR2H	1
12007	POLR2I	1
12008	POLR2J	1
12009	POLR2K	1
12010	POLR2L	1
12011	POLR3A	1
12012	POLR3B	2.368832e-01
12013	POLR3C	1
12014	POLR3D	1
12015	POLR3E	1.550912e-02
12016	POLR3F	3.594472e-02
12017	POLR3G	5.453757e-02
12018	POLR3GL	1
12019	POLR3H	1
12020	POLR3K	1
12021	POLRMT	3.675567e-01
Done

Running MutSig 2:
Scatter job 134: processing genes 11932 - 12021
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
POLG
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.360699e-03	ci left: 9.909413e-01	ci right 9.943623e-01	k: 9928	n:10000
KS ci ratio: 6.808752e-03	ci left: 9.673099e-01	ci right 9.740122e-01	k: 9708	n:10000
POLG   10000 perm   2 sec   (5187 perm/sec)   p_kst 9.708000e-01   p_cons 9.928000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000134/POLG.2_3808_10000_0.9708_0.9928_1.png
                gene_name: POLG
               theta_stop: 0.0068 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 20 percent done.
POLR1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.047280e-02	ci left: 7.775249e-01	ci right 7.937083e-01	k: 7857	n:10000
Cons ci ratio: 2.424458e-02	ci left: 7.144176e-01	ci right 7.320522e-01	k: 7233	n:10000
KS ci ratio: 5.546629e-02	ci left: 3.237627e-01	ci right 3.423347e-01	k: 3330	n:10000
POLR1A   10000 perm   2 sec   (5079 perm/sec)   p_kst 3.330000e-01   p_cons 7.233000e-01   p_joint 7.857000e-01

Outputting figure to mutsig2_images.part000000000134/POLR1A.2_5299_10000_0.333_0.7233_0.7857.png
                gene_name: POLR1A
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.79 

Current progress: 40 percent done.
POLR3B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.933629e-02	ci left: 3.773383e-01	ci right 3.965276e-01	k: 3869	n:10000
KS ci ratio: 3.382151e-02	ci left: 5.634356e-01	ci right 5.829217e-01	k: 5732	n:10000
POLR3B   10000 perm   2 sec   (5738 perm/sec)   p_kst 5.732000e-01   p_cons 3.869000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000134/POLR3B.2_3514_10000_0.5732_0.3869_1.png
                gene_name: POLR3B
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
POLR3E
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.330595e-02	ci left: 5.709563e-01	ci right 5.903967e-01	k: 5807	n:10000
Cons ci ratio: 3.236439e-02	ci left: 5.849008e-01	ci right 6.042441e-01	k: 5946	n:10000
KS ci ratio: 5.918727e-02	ci left: 2.957857e-01	ci right 3.139281e-01	k: 3048	n:10000
POLR3E   10000 perm   2 sec   (5995 perm/sec)   p_kst 3.048000e-01   p_cons 5.946000e-01   p_joint 5.807000e-01

Outputting figure to mutsig2_images.part000000000134/POLR3E.2_2207_10000_0.3048_0.5946_0.5807.png
                gene_name: POLR3E
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 80 percent done.
POLRMT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.504163e-02	ci left: 8.649871e-01	ci right 8.781956e-01	k: 8717	n:10000
Cons ci ratio: 4.689887e-02	ci left: 4.015330e-01	ci right 4.209187e-01	k: 4112	n:10000
KS ci ratio: 1.923880e-02	ci left: 7.980096e-01	ci right 8.136118e-01	k: 8059	n:10000
POLRMT   10000 perm   2 sec   (5674 perm/sec)   p_kst 8.059000e-01   p_cons 4.112000e-01   p_joint 8.717000e-01

Outputting figure to mutsig2_images.part000000000134/POLRMT.2_3777_10000_0.8059_0.4112_0.8717.png
                gene_name: POLRMT
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.88 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000134
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 134 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4398242: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000135> was used as the working directory.
Started at Wed Oct 24 16:15:33 2012
Results reported at Wed Oct 24 16:16:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000135.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000135.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 135  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000135.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     76.89 sec.
    Max Memory :      1284 MB
    Max Swap   :      3950 MB

    Max Processes  :         7
    Max Threads    :        72

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
135
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 135
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 135: processing genes 12022 - 12111
Calculating significance of each gene.
Using projection method.
12022	POM121	6.648991e-02
12023	POM121C	2.273016e-01
12024	POM121L12	1
12025	POMC	1
12026	POMGNT1	1
12027	POMP	1
12028	POMT1	1
12029	POMT2	1
12030	POMZP3	1
12031	PON1	1
12032	PON2	1
12033	PON3	9.344304e-02
12034	POP1	1
12035	POP4	1
12036	POP5	1
12037	POP7	6.185917e-02
12038	POPDC2	1
12039	POPDC3	1
12040	POR	1
12041	PORCN	1.810837e-02
12042	POSTN	3.621578e-01
12043	POT1	1
12044	POTEA	2.278044e-01
12045	POTEE	1.279622e-01
12046	POTEF	1.197046e-01
12047	POTEG	1.401133e-01
12048	POTEH	1
12049	POU1F1	1
12050	POU2AF1	1
12051	POU2F1	2.940491e-02
12052	POU2F2	1
12053	POU2F3	1
12054	POU3F1	5.779448e-02
12055	POU3F2	2.340391e-02
12056	POU3F3	1
12057	POU3F4	1
12058	POU4F1	3.916263e-05
12059	POU4F2	1
12060	POU4F3	1
12061	POU5F1	6.691668e-02
12062	POU5F2	1
12063	POU6F1	1
12064	POU6F2	1
12065	PPA1	1
12066	PPA2	1
12067	PPAN	1
12068	PPAN-P2RY11	1
12069	PPAP2A	1
12070	PPAP2B	3.829635e-03
12071	PPAP2C	1
12072	PPAPDC1A	1
12073	PPAPDC1B	2.137724e-02
12074	PPAPDC2	1
12075	PPAPDC3	1
12076	PPARA	1
12077	PPARD	1
12078	PPARG	1
12079	PPARGC1A	1
12080	PPARGC1B	1
12081	PPAT	1.444809e-01
12082	PPBP	1
12083	PPCDC	7.798600e-02
12084	PPCS	1
12085	PPDPF	1
12086	PPEF1	1.872754e-01
12087	PPEF2	1
12088	PPFIA1	1
12089	PPFIA2	1
12090	PPFIA3	1
12091	PPFIA4	1
12092	PPFIBP1	1
12093	PPFIBP2	1
12094	PPHLN1	1
12095	PPIA	1
12096	PPIAL4G	1
12097	PPIB	1
12098	PPIC	1
12099	PPID	1
12100	PPIE	1
12101	PPIF	1
12102	PPIG	3.764204e-01
12103	PPIH	1
12104	PPIL1	1
12105	PPIL2	1
12106	PPIL3	1
12107	PPIL4	1
12108	PPIL5	1
12109	PPIL6	1
12110	PPIP5K1	1.324899e-01
12111	PPIP5K2	1
Done

Running MutSig 2:
Scatter job 135: processing genes 12022 - 12111
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
POU4F1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.186327e-02	ci left: 4.572822e-01	ci right 4.769370e-01	k: 4671	n:10000
Cons ci ratio: 3.618968e-02	ci left: 5.299709e-01	ci right 5.496059e-01	k: 5398	n:10000
KS ci ratio: 5.230103e-02	ci left: 3.501865e-01	ci right 3.690954e-01	k: 3596	n:10000
POU4F1   10000 perm   1 sec   (7009 perm/sec)   p_kst 3.596000e-01   p_cons 5.398000e-01   p_joint 4.671000e-01

Outputting figure to mutsig2_images.part000000000135/POU4F1.3_1268_10000_0.3596_0.5398_0.4671.png
                gene_name: POU4F1
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 25 percent done.
PORCN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.280774e-02	ci left: 8.976473e-01	ci right 9.093165e-01	k: 9036	n:10000
Cons ci ratio: 2.010768e-02	ci left: 7.836063e-01	ci right 7.996234e-01	k: 7917	n:10000
KS ci ratio: 3.060783e-02	ci left: 6.116083e-01	ci right 6.307211e-01	k: 6212	n:10000
PORCN   10000 perm   1 sec   (7580 perm/sec)   p_kst 6.212000e-01   p_cons 7.917000e-01   p_joint 9.036000e-01

Outputting figure to mutsig2_images.part000000000135/PORCN.2_1442_10000_0.6212_0.7917_0.9036.png
                gene_name: PORCN
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.91 

Current progress: 50 percent done.
POU2F1
Processing conservation and coverage...
Processing mutations... 
Skipping 1 mutations outside transcript range of this gene.
Fewer than 2 mutations to analyze: skipping this gene...
Current progress: 75 percent done.
PPAP2B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.051746e-02	ci left: 1.838286e-01	ci right 1.993515e-01	k: 1915	n:10000
Cons ci ratio: 3.981027e-02	ci left: 4.823548e-01	ci right 5.020497e-01	k: 4922	n:10000
KS ci ratio: 1.761150e-01	ci left: 4.303019e-02	ci right 5.143610e-02	k: 471	n:10000
PPAP2B   10000 perm   1 sec   (7440 perm/sec)   p_kst 4.710000e-02   p_cons 4.922000e-01   p_joint 1.915000e-01

Joint ci ratio: 4.245690e-02	ci left: 2.924609e-01	ci right 3.051976e-01	k: 5976	n:20000
Cons ci ratio: 2.722752e-02	ci left: 5.019457e-01	ci right 5.158517e-01	k: 10178	n:20000
KS ci ratio: 1.223076e-01	ci left: 4.585485e-02	ci right 5.187718e-02	k: 976	n:20000
PPAP2B   20000 perm   3 sec   (6585 perm/sec)   p_kst 4.880000e-02   p_cons 5.089000e-01   p_joint 2.988000e-01

Joint ci ratio: 2.704506e-02	ci left: 4.062562e-01	ci right 4.174276e-01	k: 12355	n:30000
Cons ci ratio: 2.225396e-02	ci left: 5.027256e-01	ci right 5.140728e-01	k: 15252	n:30000
KS ci ratio: 9.917276e-02	ci left: 4.703999e-02	ci right 5.198105e-02	k: 1484	n:30000
PPAP2B   30000 perm   5 sec   (6286 perm/sec)   p_kst 4.946667e-02   p_cons 5.084000e-01   p_joint 4.118333e-01

Outputting figure to mutsig2_images.part000000000135/PPAP2B.2_960_30000_0.049467_0.5084_0.41183.png
                gene_name: PPAP2B
               theta_stop: 0.099 
                    nperm: 30000 
                     p_ks: 0.049 
        ci_ks_bounds_left: 0.047 
       ci_ks_bounds_right: 0.052 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.42 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000135
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 135 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1652>
Subject: Job 4398249: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1652>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000136> was used as the working directory.
Started at Wed Oct 24 16:15:33 2012
Results reported at Wed Oct 24 16:17:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000136.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000136.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 136  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000136.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    132.86 sec.
    Max Memory :      1518 MB
    Max Swap   :      4010 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
136
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 136
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 136: processing genes 12112 - 12201
Calculating significance of each gene.
Using projection method.
12112	PPL	3.927556e-01
12113	PPM1A	1.038059e-01
12114	PPM1B	1
12115	PPM1D	1
12116	PPM1E	1
12117	PPM1F	1
12118	PPM1G	1
12119	PPM1H	1
12120	PPM1J	1.965418e-01
12121	PPM1K	1
12122	PPM1L	1
12123	PPM1M	1
12124	PPM1N	1
12125	PPME1	1
12126	PPOX	5.260169e-02
12127	PPP1CA	1
12128	PPP1CB	1.698590e-01
12129	PPP1CC	1
12130	PPP1R10	1.768960e-01
12131	PPP1R11	1
12132	PPP1R12A	1.392884e-02
12133	PPP1R12B	3.522611e-01
12134	PPP1R12C	1
12135	PPP1R13B	1
12136	PPP1R13L	1
12137	PPP1R14A	1
12138	PPP1R14B	1
12139	PPP1R14C	1
12140	PPP1R14D	2.089951e-02
12141	PPP1R15A	1
12142	PPP1R15B	9.560850e-02
12143	PPP1R16A	1
12144	PPP1R16B	1
12145	PPP1R1A	1
12146	PPP1R1B	1
12147	PPP1R1C	1
12148	PPP1R2	1
12149	PPP1R3A	2.255838e-01
12150	PPP1R3B	1
12151	PPP1R3C	1
12152	PPP1R3D	1
12153	PPP1R3F	1.570122e-01
12154	PPP1R7	1
12155	PPP1R8	1.764054e-01
12156	PPP1R9A	5.301966e-01
12157	PPP1R9B	1
12158	PPP2CA	1
12159	PPP2CB	1
12160	PPP2R1A	1.148085e-02
12161	PPP2R1B	1
12162	PPP2R2A	1
12163	PPP2R2B	1
12164	PPP2R2C	1
12165	PPP2R2D	7.492031e-02
12166	PPP2R3A	4.191934e-01
12167	PPP2R3B	1
12168	PPP2R3C	1
12169	PPP2R4	1
12170	PPP2R5A	1.711150e-01
12171	PPP2R5B	7.322766e-02
12172	PPP2R5C	1
12173	PPP2R5D	1
12174	PPP2R5E	1
12175	PPP3CA	1
12176	PPP3CB	1
12177	PPP3CC	1
12178	PPP3R1	1
12179	PPP3R2	1
12180	PPP4C	1
12181	PPP4R1	1
12182	PPP4R2	1
12183	PPP4R4	1.127998e-01
12184	PPP5C	1
12185	PPP6C	1
12186	PPPDE1	1
12187	PPPDE2	1
12188	PPRC1	3.091605e-01
12189	PPT1	1
12190	PPT2	1
12191	PPTC7	2.722826e-03
12192	PPWD1	1.052902e-01
12193	PPY	1
12194	PPYR1	1
12195	PQBP1	1
12196	PQLC1	1
12197	PQLC2	1
12198	PQLC3	1
12199	PRAC	1
12200	PRAF2	1
12201	PRAM1	1
Done

Running MutSig 2:
Scatter job 136: processing genes 12112 - 12201
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PPP1R12A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.486767e-02	ci left: 4.230598e-01	ci right 4.425793e-01	k: 4328	n:10000
Cons ci ratio: 2.335591e-02	ci left: 7.292631e-01	ci right 7.465981e-01	k: 7380	n:10000
KS ci ratio: 6.186093e-02	ci left: 2.775527e-01	ci right 2.953719e-01	k: 2864	n:10000
PPP1R12A   10000 perm   2 sec   (4451 perm/sec)   p_kst 2.864000e-01   p_cons 7.380000e-01   p_joint 4.328000e-01

Outputting figure to mutsig2_images.part000000000136/PPP1R12A.3_3193_10000_0.2864_0.738_0.4328.png
                gene_name: PPP1R12A
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 25 percent done.
PPP2R1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.251899e-02	ci left: 5.825929e-01	ci right 6.019533e-01	k: 5923	n:10000
KS ci ratio: 2.424458e-02	ci left: 7.144176e-01	ci right 7.320522e-01	k: 7233	n:10000
PPP2R1A   10000 perm   2 sec   (5285 perm/sec)   p_kst 7.233000e-01   p_cons 5.923000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000136/PPP2R1A.2_1830_10000_0.7233_0.5923_1.png
                gene_name: PPP2R1A
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
PPTC7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.196322e-02	ci left: 5.909224e-01	ci right 6.102190e-01	k: 6006	n:10000
Cons ci ratio: 4.966014e-02	ci left: 3.742535e-01	ci right 3.934142e-01	k: 3838	n:10000
KS ci ratio: 3.417529e-02	ci left: 5.583228e-01	ci right 5.778375e-01	k: 5681	n:10000
PPTC7   10000 perm   1 sec   (6889 perm/sec)   p_kst 5.681000e-01   p_cons 3.838000e-01   p_joint 6.006000e-01

Outputting figure to mutsig2_images.part000000000136/PPTC7.2_939_10000_0.5681_0.3838_0.6006.png
                gene_name: PPTC7
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 75 percent done.
PPWD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.759258e-02	ci left: 3.073885e-01	ci right 3.257185e-01	k: 3165	n:10000
Cons ci ratio: 4.468541e-02	ci left: 4.250540e-01	ci right 4.445840e-01	k: 4348	n:10000
KS ci ratio: 8.392110e-02	ci left: 1.715307e-01	ci right 1.866567e-01	k: 1790	n:10000
PPWD1   10000 perm   2 sec   (6358 perm/sec)   p_kst 1.790000e-01   p_cons 4.348000e-01   p_joint 3.165000e-01

Outputting figure to mutsig2_images.part000000000136/PPWD1.2_1985_10000_0.179_0.4348_0.3165.png
                gene_name: PPWD1
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000136
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 136 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1654>
Subject: Job 4398254: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1654>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000137> was used as the working directory.
Started at Wed Oct 24 16:15:35 2012
Results reported at Wed Oct 24 16:17:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000137.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000137.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 137  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000137.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    129.36 sec.
    Max Memory :      1266 MB
    Max Swap   :      4125 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
137
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 137
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 137: processing genes 12202 - 12290
Calculating significance of each gene.
Using projection method.
12202	PRAME	1
12203	PRAMEF1	2.727356e-02
12204	PRAMEF10	1
12205	PRAMEF12	1
12206	PRAMEF14	1
12207	PRAMEF17	1
12208	PRAMEF18	1
12209	PRAMEF19	1
12210	PRAMEF2	1
12211	PRAMEF4	1.086123e-02
12212	PRAP1	4.192722e-02
12213	PRB1	1
12214	PRB2	2.127141e-02
12215	PRB3	1
12216	PRB4	1
12217	PRC1	1
12218	PRCC	1
12219	PRCD	1
12220	PRCP	1
12221	PRDM1	1
12222	PRDM10	1
12223	PRDM11	1
12224	PRDM12	1.894350e-02
12225	PRDM13	1
12226	PRDM14	1
12227	PRDM15	1
12228	PRDM16	2.863432e-01
12229	PRDM2	1
12230	PRDM4	1
12231	PRDM5	6.712048e-02
12232	PRDM7	1
12233	PRDM8	1
12234	PRDM9	1
12235	PRDX1	1
12236	PRDX2	1
12237	PRDX3	1
12238	PRDX4	1
12239	PRDX5	1
12240	PRDX6	1
12241	PREB	1.125885e-01
12242	PRELID1	1
12243	PRELID2	1
12244	PRELP	2.187231e-02
12245	PREP	1
12246	PREPL	1
12247	PREX1	5.171740e-01
12248	PREX2	1
12249	PRF1	1
12250	PRG2	1
12251	PRG3	1
12252	PRG4	1.273217e-02
12253	PRH1	7.939428e-02
12254	PRH2	1
12255	PRHOXNB	1
12256	PRIC285	1
12257	PRICKLE1	1
12258	PRICKLE2	1
12259	PRICKLE3	1.549540e-01
12260	PRICKLE4	1
12261	PRIM1	1.222358e-01
12262	PRIM2	1
12263	PRIMA1	1
12264	PRKAA1	1
12265	PRKAA2	1
12266	PRKAB1	1
12267	PRKAB2	1
12268	PRKACA	1
12269	PRKACB	1
12270	PRKACG	1
12271	PRKAG1	1
12272	PRKAG2	3.576427e-02
12273	PRKAG3	1
12274	PRKAR1A	1
12275	PRKAR1B	1
12276	PRKAR2A	1
12277	PRKAR2B	1.200689e-01
12278	PRKCA	3.237651e-01
12279	PRKCB	1
12280	PRKCD	1
12281	PRKCDBP	1
12282	PRKCE	1
12283	PRKCG	1
12284	PRKCH	1
12285	PRKCI	1
12286	PRKCQ	1
12287	PRKCSH	1
12288	PRKCZ	1
12289	PRKD1	1.536623e-01
12290	PRKD2	1
Done

Running MutSig 2:
Scatter job 137: processing genes 12202 - 12290
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PRG4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.986017e-02	ci left: 3.723630e-01	ci right 3.915058e-01	k: 3819	n:10000
Cons ci ratio: 5.918727e-02	ci left: 2.957857e-01	ci right 3.139281e-01	k: 3048	n:10000
KS ci ratio: 4.154516e-02	ci left: 4.610765e-01	ci right 4.807405e-01	k: 4709	n:10000
PRG4   10000 perm   2 sec   (4984 perm/sec)   p_kst 4.709000e-01   p_cons 3.048000e-01   p_joint 3.819000e-01

Outputting figure to mutsig2_images.part000000000137/PRG4.4_4263_10000_0.4709_0.3048_0.3819.png
                gene_name: PRG4
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.30 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 33 percent done.
PRAMEF4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.150350e-02	ci left: 4.615758e-01	ci right 4.812409e-01	k: 4714	n:10000
Cons ci ratio: 5.769921e-02	ci left: 3.065949e-01	ci right 3.249125e-01	k: 3157	n:10000
KS ci ratio: 3.857208e-02	ci left: 4.981503e-01	ci right 5.178450e-01	k: 5080	n:10000
PRAMEF4   10000 perm   2 sec   (6559 perm/sec)   p_kst 5.080000e-01   p_cons 3.157000e-01   p_joint 4.714000e-01

Outputting figure to mutsig2_images.part000000000137/PRAMEF4.2_1449_10000_0.508_0.3157_0.4714.png
                gene_name: PRAMEF4
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 67 percent done.
PRKAG2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.659038e-02	ci left: 4.047210e-01	ci right 4.241289e-01	k: 4144	n:10000
Cons ci ratio: 7.747908e-02	ci left: 1.958434e-01	ci right 2.117295e-01	k: 2037	n:10000
KS ci ratio: 4.074522e-02	ci left: 4.707644e-01	ci right 4.904469e-01	k: 4806	n:10000
PRKAG2   10000 perm   2 sec   (6489 perm/sec)   p_kst 4.806000e-01   p_cons 2.037000e-01   p_joint 4.144000e-01

Outputting figure to mutsig2_images.part000000000137/PRKAG2.2_1774_10000_0.4806_0.2037_0.4144.png
                gene_name: PRKAG2
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000137
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 137 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4398258: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000138> was used as the working directory.
Started at Wed Oct 24 16:15:37 2012
Results reported at Wed Oct 24 16:17:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000138.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000138.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 138  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000138.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    136.01 sec.
    Max Memory :      1367 MB
    Max Swap   :      4012 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
138
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 138
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 138: processing genes 12291 - 12380
Calculating significance of each gene.
Using projection method.
12291	PRKD3	1
12292	PRKDC	9.960513e-02
12293	PRKG1	1
12294	PRKG2	1
12295	PRKRA	1
12296	PRKRIP1	1
12297	PRKRIR	3.260092e-01
12298	PRKX	1
12299	PRL	1
12300	PRLH	1
12301	PRLHR	1
12302	PRLR	1
12303	PRM1	1
12304	PRM2	1
12305	PRM3	1
12306	PRMT1	1.334845e-01
12307	PRMT10	7.866426e-02
12308	PRMT2	1
12309	PRMT3	1
12310	PRMT5	1
12311	PRMT6	1
12312	PRMT7	1
12313	PRMT8	1
12314	PRND	1
12315	PRNP	1
12316	PROC	1
12317	PROCA1	1
12318	PROCR	1
12319	PRODH	1
12320	PRODH2	1
12321	PROK1	1
12322	PROK2	1
12323	PROKR1	1
12324	PROKR2	1
12325	PROL1	1
12326	PROM1	1
12327	PROM2	3.383446e-01
12328	PROP1	1
12329	PROS1	1
12330	PROSC	8.853061e-02
12331	PROX1	3.769173e-02
12332	PROX2	1
12333	PROZ	1
12334	PRPF18	1
12335	PRPF19	1
12336	PRPF3	1
12337	PRPF31	1
12338	PRPF38A	8.399140e-02
12339	PRPF38B	1
12340	PRPF39	1.411333e-01
12341	PRPF4	1
12342	PRPF40A	2.250903e-01
12343	PRPF40B	1.144956e-01
12344	PRPF4B	1
12345	PRPF6	1
12346	PRPF8	1
12347	PRPH	1
12348	PRPH2	1
12349	PRPS1	1
12350	PRPS1L1	1
12351	PRPS2	3.372244e-02
12352	PRPSAP1	1
12353	PRPSAP2	1
12354	PRR11	1
12355	PRR12	3.444551e-01
12356	PRR13	1
12357	PRR14	1
12358	PRR15	1
12359	PRR15L	1
12360	PRR16	1
12361	PRR19	1
12362	PRR21	9.975163e-02
12363	PRR22	1
12364	PRR23B	1
12365	PRR25	1
12366	PRR3	1
12367	PRR4	1
12368	PRR5	1
12369	PRR5-ARHGAP8	1
12370	PRR5L	1.917345e-01
12371	PRR7	4.322468e-02
12372	PRRC1	1
12373	PRRG1	2.372992e-03
12374	PRRG2	2.718312e-02
12375	PRRG3	1
12376	PRRG4	1
12377	PRRT1	1
12378	PRRT2	1
12379	PRRT3	1
12380	PRRX1	1
Done

Running MutSig 2:
Scatter job 138: processing genes 12291 - 12380
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PRKDC
Processing conservation and coverage...
78% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.856056e-02	ci left: 6.437780e-01	ci right 6.625327e-01	k: 6532	n:10000
Cons ci ratio: 1.076007e-02	ci left: 9.248228e-01	ci right 9.349250e-01	k: 9300	n:10000
KS ci ratio: 4.393885e-02	ci left: 4.333316e-01	ci right 4.529016e-01	k: 4431	n:10000
PRKDC   10000 perm   3 sec   (3362 perm/sec)   p_kst 4.431000e-01   p_cons 9.300000e-01   p_joint 6.532000e-01

Outputting figure to mutsig2_images.part000000000138/PRKDC.5_12730_10000_0.4431_0.93_0.6532.png
                gene_name: PRKDC
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 33 percent done.
PROX1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.029588e-02	ci left: 3.682841e-01	ci right 3.873871e-01	k: 3778	n:10000
Cons ci ratio: 1.115922e-02	ci left: 9.197660e-01	ci right 9.301849e-01	k: 9251	n:10000
KS ci ratio: 7.132045e-02	ci left: 2.236571e-01	ci right 2.402993e-01	k: 2319	n:10000
PROX1   10000 perm   2 sec   (6005 perm/sec)   p_kst 2.319000e-01   p_cons 9.251000e-01   p_joint 3.778000e-01

Outputting figure to mutsig2_images.part000000000138/PROX1.4_2230_10000_0.2319_0.9251_0.3778.png
                gene_name: PROX1
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 67 percent done.
PRRG1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.429861e-01	ci left: 6.488166e-02	ci right 7.497062e-02	k: 698	n:10000
Cons ci ratio: 4.204869e-02	ci left: 4.550858e-01	ci right 4.747347e-01	k: 4649	n:10000
KS ci ratio: 2.408683e-01	ci left: 2.268733e-02	ci right 2.899301e-02	k: 257	n:10000
PRRG1   10000 perm   2 sec   (6543 perm/sec)   p_kst 2.570000e-02   p_cons 4.649000e-01   p_joint 6.980000e-02

Joint ci ratio: 8.530316e-02	ci left: 9.141174e-02	ci right 9.960629e-02	k: 1909	n:20000
Cons ci ratio: 2.967566e-02	ci left: 4.589670e-01	ci right 4.728429e-01	k: 9318	n:20000
KS ci ratio: 1.725682e-01	ci left: 2.297630e-02	ci right 2.736323e-02	k: 502	n:20000
PRRG1   20000 perm   3 sec   (5921 perm/sec)   p_kst 2.510000e-02   p_cons 4.659000e-01   p_joint 9.545000e-02

Joint ci ratio: 6.907853e-02	ci left: 9.357501e-02	ci right 1.003033e-01	k: 2907	n:30000
Cons ci ratio: 2.421776e-02	ci left: 4.605085e-01	ci right 4.718313e-01	k: 13985	n:30000
KS ci ratio: 1.424101e-01	ci left: 2.287663e-02	ci right 2.641625e-02	k: 738	n:30000
PRRG1   30000 perm   5 sec   (5680 perm/sec)   p_kst 2.460000e-02   p_cons 4.661667e-01   p_joint 9.690000e-02

Joint ci ratio: 5.982681e-02	ci left: 9.401784e-02	ci right 9.984083e-02	k: 3876	n:40000
Cons ci ratio: 2.094050e-02	ci left: 4.620509e-01	ci right 4.718539e-01	k: 18678	n:40000
KS ci ratio: 1.243924e-01	ci left: 2.271618e-02	ci right 2.575343e-02	k: 968	n:40000
PRRG1   40000 perm   7 sec   (5526 perm/sec)   p_kst 2.420000e-02   p_cons 4.669500e-01   p_joint 9.690000e-02

Joint ci ratio: 5.328738e-02	ci left: 9.505165e-02	ci right 1.002752e-01	k: 4882	n:50000
Cons ci ratio: 1.866495e-02	ci left: 4.642979e-01	ci right 4.730657e-01	k: 23434	n:50000
KS ci ratio: 1.102500e-01	ci left: 2.329882e-02	ci right 2.603675e-02	k: 1232	n:50000
PRRG1   50000 perm   9 sec   (5383 perm/sec)   p_kst 2.464000e-02   p_cons 4.686800e-01   p_joint 9.764000e-02

Joint ci ratio: 4.899093e-02	ci left: 9.404967e-02	ci right 9.878945e-02	k: 5784	n:60000
Cons ci ratio: 1.706777e-02	ci left: 4.638342e-01	ci right 4.718356e-01	k: 28070	n:60000
KS ci ratio: 1.018360e-01	ci left: 2.287136e-02	ci right 2.534163e-02	k: 1445	n:60000
PRRG1   60000 perm   11 sec   (5228 perm/sec)   p_kst 2.408333e-02   p_cons 4.678333e-01   p_joint 9.640000e-02

Joint ci ratio: 4.555943e-02	ci left: 9.345968e-02	ci right 9.783105e-02	k: 6694	n:70000
Cons ci ratio: 1.582913e-02	ci left: 4.632698e-01	ci right 4.706758e-01	k: 32688	n:70000
KS ci ratio: 9.371421e-02	ci left: 2.324173e-02	ci right 2.554078e-02	k: 1706	n:70000
PRRG1   70000 perm   14 sec   (5107 perm/sec)   p_kst 2.437143e-02   p_cons 4.669714e-01   p_joint 9.562857e-02

Outputting figure to mutsig2_images.part000000000138/PRRG1.2_751_70000_0.024371_0.46697_0.095629.png
                gene_name: PRRG1
               theta_stop: 0.094 
                    nperm: 70000 
                     p_ks: 0.024 
        ci_ks_bounds_left: 0.023 
       ci_ks_bounds_right: 0.026 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.096 
     ci_joint_bounds_left: 0.093 
    ci_joint_bounds_right: 0.098 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000138
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 138 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4398261: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000139> was used as the working directory.
Started at Wed Oct 24 16:15:40 2012
Results reported at Wed Oct 24 16:17:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000139.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000139.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 139  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000139.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     97.23 sec.
    Max Memory :      1425 MB
    Max Swap   :      4074 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
139
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 139
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 139: processing genes 12381 - 12470
Calculating significance of each gene.
Using projection method.
12381	PRRX2	1
12382	PRSS1	1
12383	PRSS12	1
12384	PRSS16	1
12385	PRSS21	1
12386	PRSS22	1
12387	PRSS23	1
12388	PRSS27	1
12389	PRSS3	1
12390	PRSS33	1
12391	PRSS35	1
12392	PRSS36	1
12393	PRSS37	6.764711e-02
12394	PRSS38	1
12395	PRSS42	1
12396	PRSS45	1
12397	PRSS48	1
12398	PRSS50	1
12399	PRSS53	1
12400	PRSS54	1
12401	PRSS55	1
12402	PRSS8	1
12403	PRSSL1	1
12404	PRTFDC1	1
12405	PRTG	2.003359e-01
12406	PRUNE	1.348962e-01
12407	PRUNE2	1.357388e-01
12408	PRX	4.088839e-01
12409	PSAP	1
12410	PSAT1	1
12411	PSCA	1
12412	PSD	1.602456e-01
12413	PSD2	3.668604e-01
12414	PSD3	1
12415	PSD4	1
12416	PSEN1	4.984876e-03
12417	PSEN2	7.738845e-02
12418	PSENEN	1
12419	PSG1	1
12420	PSG11	1
12421	PSG2	1
12422	PSG3	1
12423	PSG4	1
12424	PSG5	1
12425	PSG6	2.105251e-02
12426	PSG7	1
12427	PSG8	1
12428	PSG9	1
12429	PSIP1	1
12430	PSKH1	1
12431	PSKH2	1.297701e-01
12432	PSMA1	1
12433	PSMA2	1
12434	PSMA3	1
12435	PSMA4	1
12436	PSMA5	1
12437	PSMA6	8.045194e-02
12438	PSMA7	1
12439	PSMA8	5.600191e-02
12440	PSMB1	1
12441	PSMB10	1
12442	PSMB11	1
12443	PSMB2	1
12444	PSMB3	1
12445	PSMB4	1
12446	PSMB5	1
12447	PSMB6	1
12448	PSMB7	1
12449	PSMB8	4.943620e-03
12450	PSMB9	1
12451	PSMC1	1
12452	PSMC2	1.131786e-01
12453	PSMC3	1.675852e-01
12454	PSMC3IP	1
12455	PSMC4	1
12456	PSMC5	1
12457	PSMC6	1
12458	PSMD1	1
12459	PSMD10	3.963727e-02
12460	PSMD11	1
12461	PSMD12	1
12462	PSMD13	1
12463	PSMD14	1
12464	PSMD2	2.202799e-01
12465	PSMD3	1
12466	PSMD4	1
12467	PSMD5	1
12468	PSMD6	1
12469	PSMD7	1
12470	PSMD8	1
Done

Running MutSig 2:
Scatter job 139: processing genes 12381 - 12470
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PRUNE2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.007379e-01	ci left: 1.248365e-01	ci right 1.381789e-01	k: 1314	n:10000
Cons ci ratio: 8.243893e-02	ci left: 1.767434e-01	ci right 1.920409e-01	k: 1843	n:10000
KS ci ratio: 1.021741e-01	ci left: 1.217066e-01	ci right 1.349108e-01	k: 1282	n:10000
PRUNE2   10000 perm   3 sec   (3674 perm/sec)   p_kst 1.282000e-01   p_cons 1.843000e-01   p_joint 1.314000e-01

Joint ci ratio: 8.430639e-02	ci left: 9.342261e-02	ci right 1.016948e-01	k: 1950	n:20000
Cons ci ratio: 6.040261e-02	ci left: 1.686698e-01	ci right 1.792252e-01	k: 3478	n:20000
KS ci ratio: 7.242749e-02	ci left: 1.231038e-01	ci right 1.324047e-01	k: 2554	n:20000
PRUNE2   20000 perm   8 sec   (2641 perm/sec)   p_kst 1.277000e-01   p_cons 1.739000e-01   p_joint 9.750000e-02

Outputting figure to mutsig2_images.part000000000139/PRUNE2.2_9343_20000_0.1277_0.1739_0.0975.png
                gene_name: PRUNE2
               theta_stop: 0.084 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.098 
     ci_joint_bounds_left: 0.093 
    ci_joint_bounds_right: 0.10 

Current progress: 33 percent done.
PSEN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.901168e-03	ci left: 9.352693e-01	ci right 9.446723e-01	k: 9401	n:10000
Cons ci ratio: 1.454018e-02	ci left: 8.725497e-01	ci right 8.854286e-01	k: 8791	n:10000
KS ci ratio: 1.813050e-02	ci left: 8.161888e-01	ci right 8.312222e-01	k: 8238	n:10000
PSEN1   10000 perm   2 sec   (6592 perm/sec)   p_kst 8.238000e-01   p_cons 8.791000e-01   p_joint 9.401000e-01

Outputting figure to mutsig2_images.part000000000139/PSEN1.2_1444_10000_0.8238_0.8791_0.9401.png
                gene_name: PSEN1
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.94 

Current progress: 67 percent done.
PSMB8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.692213e-02	ci left: 1.616039e-01	ci right 1.763894e-01	k: 1689	n:10000
Cons ci ratio: 1.881357e-02	ci left: 8.050140e-01	ci right 8.204033e-01	k: 8128	n:10000
KS ci ratio: 2.209987e-01	ci left: 2.712237e-02	ci right 3.395474e-02	k: 304	n:10000
PSMB8   10000 perm   1 sec   (6760 perm/sec)   p_kst 3.040000e-02   p_cons 8.128000e-01   p_joint 1.689000e-01

Joint ci ratio: 6.632081e-02	ci left: 1.437461e-01	ci right 1.536563e-01	k: 2973	n:20000
Cons ci ratio: 1.334871e-02	ci left: 8.062622e-01	ci right 8.171471e-01	k: 16235	n:20000
KS ci ratio: 1.545824e-01	ci left: 2.873760e-02	ci right 3.359997e-02	k: 622	n:20000
PSMB8   20000 perm   3 sec   (5940 perm/sec)   p_kst 3.110000e-02   p_cons 8.117500e-01   p_joint 1.486500e-01

Joint ci ratio: 6.987964e-02	ci left: 9.160626e-02	ci right 9.827242e-02	k: 2847	n:30000
Cons ci ratio: 1.097567e-02	ci left: 8.051106e-01	ci right 8.140293e-01	k: 24288	n:30000
KS ci ratio: 1.275258e-01	ci left: 2.858305e-02	ci right 3.250857e-02	k: 915	n:30000
PSMB8   30000 perm   5 sec   (5663 perm/sec)   p_kst 3.050000e-02   p_cons 8.096000e-01   p_joint 9.490000e-02

Joint ci ratio: 1.047114e-01	ci left: 3.207481e-02	ci right 3.564328e-02	k: 1353	n:40000
Cons ci ratio: 9.559851e-03	ci left: 8.039290e-01	ci right 8.116763e-01	k: 32313	n:40000
KS ci ratio: 1.098548e-01	ci left: 2.915279e-02	ci right 3.256576e-02	k: 1233	n:40000
PSMB8   40000 perm   7 sec   (5471 perm/sec)   p_kst 3.082500e-02   p_cons 8.078250e-01   p_joint 3.382500e-02

Joint ci ratio: 5.204996e-02	ci left: 9.922200e-02	ci right 1.045443e-01	k: 5093	n:50000
Cons ci ratio: 8.199179e-03	ci left: 8.171277e-01	ci right 8.238750e-01	k: 41026	n:50000
KS ci ratio: 9.827376e-02	ci left: 2.932240e-02	ci right 3.237239e-02	k: 1541	n:50000
PSMB8   50000 perm   9 sec   (5315 perm/sec)   p_kst 3.082000e-02   p_cons 8.205200e-01   p_joint 1.018600e-01

Outputting figure to mutsig2_images.part000000000139/PSMB8.2_994_50000_0.03082_0.82052_0.10186.png
                gene_name: PSMB8
               theta_stop: 0.098 
                    nperm: 50000 
                     p_ks: 0.031 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.82 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.099 
    ci_joint_bounds_right: 0.10 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000139
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 139 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 4398265: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000140> was used as the working directory.
Started at Wed Oct 24 16:15:45 2012
Results reported at Wed Oct 24 16:17:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000140.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000140.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 140  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000140.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    130.18 sec.
    Max Memory :      1095 MB
    Max Swap   :      4042 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
140
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 140
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 140: processing genes 12471 - 12559
Calculating significance of each gene.
Using projection method.
12471	PSMD9	1
12472	PSME1	1
12473	PSME2	1
12474	PSME3	7.716340e-02
12475	PSME4	1
12476	PSMF1	1
12477	PSMG1	1
12478	PSMG2	1
12479	PSMG3	1
12480	PSORS1C1	1
12481	PSORS1C2	1
12482	PSPC1	1
12483	PSPH	8.387574e-02
12484	PSPN	1
12485	PSRC1	1
12486	PSTK	1
12487	PSTPIP1	1
12488	PSTPIP2	1
12489	PTAFR	1
12490	PTAR1	3.161707e-02
12491	PTBP1	1
12492	PTBP2	1
12493	PTCD1	2.563809e-01
12494	PTCD2	1.085993e-01
12495	PTCD3	1
12496	PTCH1	5.449786e-01
12497	PTCH2	1
12498	PTCHD1	1
12499	PTCHD2	1
12500	PTCHD3	1.335253e-01
12501	PTCRA	1
12502	PTDSS1	1
12503	PTDSS2	1.716720e-02
12504	PTEN	3.989097e-05
12505	PTER	1
12506	PTF1A	1
12507	PTGDR	1
12508	PTGDS	1
12509	PTGER2	1
12510	PTGER3	1
12511	PTGER4	1
12512	PTGES	1
12513	PTGES2	1
12514	PTGES3	1
12515	PTGFR	1
12516	PTGFRN	1
12517	PTGIR	1
12518	PTGIS	1
12519	PTGR1	1
12520	PTGR2	1
12521	PTGS1	1
12522	PTGS2	1
12523	PTH	1
12524	PTH1R	7.282227e-02
12525	PTH2	1.277738e-02
12526	PTH2R	1
12527	PTHLH	1
12528	PTK2	3.765453e-01
12529	PTK2B	1
12530	PTK6	1
12531	PTK7	1
12532	PTMA	1
12533	PTMS	1
12534	PTN	1
12535	PTOV1	1
12536	PTP4A1	1
12537	PTP4A2	1
12538	PTP4A3	1
12539	PTPDC1	1
12540	PTPLA	6.654125e-02
12541	PTPLAD1	1
12542	PTPLAD2	1
12543	PTPLB	1
12544	PTPMT1	1
12545	PTPN1	1
12546	PTPN11	1
12547	PTPN12	1.115240e-01
12548	PTPN13	6.989980e-04
12549	PTPN14	1.305355e-01
12550	PTPN18	1
12551	PTPN2	1.630909e-01
12552	PTPN21	4.068311e-01
12553	PTPN22	1
12554	PTPN23	1
12555	PTPN3	2.722064e-01
12556	PTPN4	1
12557	PTPN5	1
12558	PTPN6	1
12559	PTPN7	1
Done

Running MutSig 2:
Scatter job 140: processing genes 12471 - 12559
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PTPN13
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.370375e-02	ci left: 3.381626e-01	ci right 3.569262e-01	k: 3475	n:10000
Cons ci ratio: 1.515566e-02	ci left: 8.632507e-01	ci right 8.765330e-01	k: 8700	n:10000
KS ci ratio: 8.341096e-02	ci left: 1.733008e-01	ci right 1.884856e-01	k: 1808	n:10000
PTPN13   10000 perm   2 sec   (4104 perm/sec)   p_kst 1.808000e-01   p_cons 8.700000e-01   p_joint 3.475000e-01

Outputting figure to mutsig2_images.part000000000140/PTPN13.5_7661_10000_0.1808_0.87_0.3475.png
                gene_name: PTPN13
               theta_stop: 0.083 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.88 
                  p_joint: 0.35 
     ci_joint_bounds_left: 0.34 
    ci_joint_bounds_right: 0.36 

Current progress: 33 percent done.
PTEN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.164895e-02	ci left: 3.559523e-01	ci right 3.749262e-01	k: 3654	n:10000
Cons ci ratio: 1.968641e-02	ci left: 7.906032e-01	ci right 8.064225e-01	k: 7986	n:10000
KS ci ratio: 6.374371e-02	ci left: 2.655721e-01	ci right 2.831595e-01	k: 2743	n:10000
PTEN   10000 perm   2 sec   (6318 perm/sec)   p_kst 2.743000e-01   p_cons 7.986000e-01   p_joint 3.654000e-01

Outputting figure to mutsig2_images.part000000000140/PTEN.3_1248_10000_0.2743_0.7986_0.3654.png
                gene_name: PTEN
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 67 percent done.
PTDSS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.112967e-02	ci left: 3.606257e-01	ci right 3.796501e-01	k: 3701	n:10000
Cons ci ratio: 5.744651e-02	ci left: 3.084797e-01	ci right 3.268266e-01	k: 3176	n:10000
KS ci ratio: 5.132760e-02	ci left: 3.588357e-01	ci right 3.778410e-01	k: 3683	n:10000
PTDSS2   10000 perm   1 sec   (6686 perm/sec)   p_kst 3.683000e-01   p_cons 3.176000e-01   p_joint 3.701000e-01

Outputting figure to mutsig2_images.part000000000140/PTDSS2.2_1512_10000_0.3683_0.3176_0.3701.png
                gene_name: PTDSS2
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.38 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000140
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 140 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4398269: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000141> was used as the working directory.
Started at Wed Oct 24 16:15:55 2012
Results reported at Wed Oct 24 16:19:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000141.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000141.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 141  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000141.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    217.53 sec.
    Max Memory :      1577 MB
    Max Swap   :      3986 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
141
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 141
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 141: processing genes 12560 - 12649
Calculating significance of each gene.
Using projection method.
12560	PTPN9	1
12561	PTPRA	1
12562	PTPRB	1
12563	PTPRC	1
12564	PTPRCAP	1
12565	PTPRD	1
12566	PTPRE	1
12567	PTPRF	1.084705e-01
12568	PTPRG	2.925313e-01
12569	PTPRH	1
12570	PTPRJ	1
12571	PTPRK	4.185667e-01
12572	PTPRM	5.624689e-02
12573	PTPRN	1
12574	PTPRN2	7.248498e-03
12575	PTPRO	1
12576	PTPRR	1
12577	PTPRS	1
12578	PTPRT	3.909106e-01
12579	PTPRU	1
12580	PTPRZ1	5.672254e-01
12581	PTRF	1
12582	PTRH1	1.271047e-02
12583	PTRH2	1
12584	PTS	1
12585	PTTG1	1
12586	PTTG1IP	1
12587	PTTG2	1
12588	PTX3	1
12589	PTX4	1
12590	PUF60	1
12591	PUM1	1.428846e-02
12592	PUM2	2.731634e-01
12593	PURA	1
12594	PURB	1
12595	PURG	1
12596	PUS1	1
12597	PUS10	1
12598	PUS3	1
12599	PUS7	1
12600	PUS7L	1
12601	PUSL1	1
12602	PVALB	1
12603	PVR	1
12604	PVRIG	1
12605	PVRL1	1
12606	PVRL2	1
12607	PVRL3	2.825874e-02
12608	PVRL4	1
12609	PWP1	1
12610	PWP2	6.774556e-03
12611	PWWP2A	1
12612	PWWP2B	1.311475e-01
12613	PXDN	2.428760e-02
12614	PXDNL	1
12615	PXK	2.663417e-01
12616	PXMP2	1
12617	PXMP4	1
12618	PXN	1
12619	PXT1	1
12620	PYCARD	1
12621	PYCR1	1
12622	PYCR2	1
12623	PYCRL	1
12624	PYDC1	1
12625	PYDC2	1
12626	PYGB	1.476193e-01
12627	PYGL	1
12628	PYGM	1.101735e-01
12629	PYGO1	1
12630	PYGO2	1
12631	PYHIN1	2.032322e-01
12632	PYROXD1	1.726887e-01
12633	PYROXD2	1
12634	PYY	1
12635	PZP	3.726245e-01
12636	ProSAPiP1	1
12637	QARS	1
12638	QDPR	1
12639	QKI	1
12640	QPCT	9.416708e-02
12641	QPCTL	1.111917e-01
12642	QPRT	1
12643	QRFP	1
12644	QRFPR	1
12645	QRICH1	1
12646	QRICH2	7.542848e-02
12647	QRSL1	1
12648	QSER1	1
12649	QSOX1	1
Done

Running MutSig 2:
Scatter job 141: processing genes 12560 - 12649
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PTPRN2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.653334e-02	ci left: 5.252653e-01	ci right 5.449142e-01	k: 5351	n:10000
Cons ci ratio: 2.402065e-02	ci left: 7.181531e-01	ci right 7.357145e-01	k: 7270	n:10000
KS ci ratio: 6.356810e-02	ci left: 2.666610e-01	ci right 2.842700e-01	k: 2754	n:10000
PTPRN2   10000 perm   2 sec   (5467 perm/sec)   p_kst 2.754000e-01   p_cons 7.270000e-01   p_joint 5.351000e-01

Outputting figure to mutsig2_images.part000000000141/PTPRN2.3_3140_10000_0.2754_0.727_0.5351.png
                gene_name: PTPRN2
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.54 

Current progress: 12 percent done.
PUM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.845979e-02	ci left: 6.453876e-01	ci right 6.641221e-01	k: 6548	n:10000
KS ci ratio: 1.189849e-02	ci left: 9.100826e-01	ci right 9.210739e-01	k: 9157	n:10000
PUM1   10000 perm   2 sec   (5589 perm/sec)   p_kst 9.157000e-01   p_cons 6.548000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000141/PUM1.3_3651_10000_0.9157_0.6548_1.png
                gene_name: PUM1
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.66 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
PWP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.170758e-01	ci left: 9.486876e-02	ci right 1.067649e-01	k: 1007	n:10000
Cons ci ratio: 3.715456e-02	ci left: 5.168576e-01	ci right 5.365269e-01	k: 5267	n:10000
KS ci ratio: 1.985870e-01	ci left: 3.376644e-02	ci right 4.130605e-02	k: 374	n:10000
PWP2   10000 perm   2 sec   (5819 perm/sec)   p_kst 3.740000e-02   p_cons 5.267000e-01   p_joint 1.007000e-01

Joint ci ratio: 8.803028e-02	ci left: 8.621560e-02	ci right 9.420400e-02	k: 1803	n:20000
Cons ci ratio: 2.677096e-02	ci left: 5.103976e-01	ci right 5.242974e-01	k: 10347	n:20000
KS ci ratio: 1.439520e-01	ci left: 3.317126e-02	ci right 3.836483e-02	k: 714	n:20000
PWP2   20000 perm   4 sec   (5224 perm/sec)   p_kst 3.570000e-02   p_cons 5.173500e-01   p_joint 9.015000e-02

Joint ci ratio: 7.638557e-02	ci left: 7.760915e-02	ci right 8.380567e-02	k: 2420	n:30000
Cons ci ratio: 2.198399e-02	ci left: 5.088266e-01	ci right 5.201706e-01	k: 15435	n:30000
KS ci ratio: 1.167214e-01	ci left: 3.411469e-02	ci right 3.837573e-02	k: 1086	n:30000
PWP2   30000 perm   6 sec   (4960 perm/sec)   p_kst 3.620000e-02   p_cons 5.145000e-01   p_joint 8.066667e-02

Joint ci ratio: 5.785582e-02	ci left: 9.996362e-02	ci right 1.059442e-01	k: 4117	n:40000
Cons ci ratio: 1.902749e-02	ci left: 5.098888e-01	ci right 5.197090e-01	k: 20592	n:40000
KS ci ratio: 1.014234e-01	ci left: 3.417125e-02	ci right 3.784651e-02	k: 1439	n:40000
PWP2   40000 perm   8 sec   (4803 perm/sec)   p_kst 3.597500e-02   p_cons 5.148000e-01   p_joint 1.029250e-01

Joint ci ratio: 5.236529e-02	ci left: 9.813480e-02	ci right 1.034316e-01	k: 5038	n:50000
Cons ci ratio: 1.705429e-02	ci left: 5.093684e-01	ci right 5.181500e-01	k: 25688	n:50000
KS ci ratio: 9.009486e-02	ci left: 3.483408e-02	ci right 3.814002e-02	k: 1823	n:50000
PWP2   50000 perm   11 sec   (4677 perm/sec)   p_kst 3.646000e-02   p_cons 5.137600e-01   p_joint 1.007600e-01

Outputting figure to mutsig2_images.part000000000141/PWP2.3_2844_50000_0.03646_0.51376_0.10076.png
                gene_name: PWP2
               theta_stop: 0.090 
                    nperm: 50000 
                     p_ks: 0.036 
        ci_ks_bounds_left: 0.035 
       ci_ks_bounds_right: 0.038 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.098 
    ci_joint_bounds_right: 0.10 

Current progress: 38 percent done.
PXDN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.460375e-02	ci left: 3.307132e-01	ci right 3.493801e-01	k: 3400	n:10000
Cons ci ratio: 1.438733e-01	ci left: 6.410846e-02	ci right 7.414431e-02	k: 690	n:10000
KS ci ratio: 4.569972e-02	ci left: 4.140880e-01	ci right 4.335564e-01	k: 4238	n:10000
PXDN   10000 perm   2 sec   (5139 perm/sec)   p_kst 4.238000e-01   p_cons 6.900000e-02   p_joint 3.400000e-01

Joint ci ratio: 3.376179e-02	ci left: 3.957928e-01	ci right 4.094355e-01	k: 8052	n:20000
Cons ci ratio: 1.016964e-01	ci left: 6.562284e-02	ci right 7.270304e-02	k: 1382	n:20000
KS ci ratio: 3.156481e-02	ci left: 4.284635e-01	ci right 4.422553e-01	k: 8707	n:20000
PXDN   20000 perm   4 sec   (4657 perm/sec)   p_kst 4.353500e-01   p_cons 6.910000e-02   p_joint 4.026000e-01

Joint ci ratio: 3.390772e-02	ci left: 3.029438e-01	ci right 3.134267e-01	k: 9245	n:30000
Cons ci ratio: 8.201010e-02	ci left: 6.785719e-02	ci right 7.369293e-02	k: 2122	n:30000
KS ci ratio: 2.582493e-02	ci left: 4.287476e-01	ci right 4.399984e-01	k: 13031	n:30000
PXDN   30000 perm   7 sec   (4468 perm/sec)   p_kst 4.343667e-01   p_cons 7.073333e-02   p_joint 3.081667e-01

Outputting figure to mutsig2_images.part000000000141/PXDN.3_4532_30000_0.43437_0.070733_0.30817.png
                gene_name: PXDN
               theta_stop: 0.082 
                    nperm: 30000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.071 
      ci_cons_bounds_left: 0.068 
     ci_cons_bounds_right: 0.074 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.31 

Current progress: 50 percent done.
PTPRF
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.824171e-01	ci left: 1.622887e-02	ci right 2.165650e-02	k: 188	n:10000
Cons ci ratio: 3.294486e-02	ci left: 5.762723e-01	ci right 5.956776e-01	k: 5860	n:10000
KS ci ratio: 3.842359e-01	ci left: 8.324320e-03	ci right 1.236857e-02	k: 102	n:10000
PTPRF   10000 perm   2 sec   (5037 perm/sec)   p_kst 1.020000e-02   p_cons 5.860000e-01   p_joint 1.880000e-02

Joint ci ratio: 2.764887e-01	ci left: 8.574499e-03	ci right 1.137073e-02	k: 198	n:20000
Cons ci ratio: 2.328487e-02	ci left: 5.793872e-01	ci right 5.930877e-01	k: 11725	n:20000
KS ci ratio: 2.764887e-01	ci left: 8.574499e-03	ci right 1.137073e-02	k: 198	n:20000
PTPRF   20000 perm   4 sec   (4450 perm/sec)   p_kst 9.900000e-03   p_cons 5.862500e-01   p_joint 9.900000e-03

Joint ci ratio: 2.263290e-01	ci left: 8.779206e-03	ci right 1.105055e-02	k: 296	n:30000
Cons ci ratio: 1.897126e-02	ci left: 5.817041e-01	ci right 5.928790e-01	k: 17619	n:30000
KS ci ratio: 2.263290e-01	ci left: 8.779206e-03	ci right 1.105055e-02	k: 296	n:30000
PTPRF   30000 perm   7 sec   (4296 perm/sec)   p_kst 9.866667e-03   p_cons 5.873000e-01   p_joint 9.866667e-03

Joint ci ratio: 1.947694e-01	ci left: 9.048130e-03	ci right 1.102398e-02	k: 400	n:40000
Cons ci ratio: 1.635361e-02	ci left: 5.847105e-01	ci right 5.943765e-01	k: 23582	n:40000
KS ci ratio: 1.947694e-01	ci left: 9.048130e-03	ci right 1.102398e-02	k: 400	n:40000
PTPRF   40000 perm   10 sec   (4190 perm/sec)   p_kst 1.000000e-02   p_cons 5.895500e-01   p_joint 1.000000e-02

Joint ci ratio: 1.701806e-01	ci left: 9.605911e-03	ci right 1.141160e-02	k: 524	n:50000
Cons ci ratio: 1.458703e-02	ci left: 5.865552e-01	ci right 5.951942e-01	k: 29544	n:50000
KS ci ratio: 1.701806e-01	ci left: 9.605911e-03	ci right 1.141160e-02	k: 524	n:50000
PTPRF   50000 perm   12 sec   (4098 perm/sec)   p_kst 1.048000e-02   p_cons 5.908800e-01   p_joint 1.048000e-02

Joint ci ratio: 1.107576e-01	ci left: 1.931621e-02	ci right 2.159718e-02	k: 1226	n:60000
Cons ci ratio: 1.329172e-02	ci left: 5.878212e-01	ci right 5.957033e-01	k: 35506	n:60000
KS ci ratio: 1.529187e-01	ci left: 1.000439e-02	ci right 1.167676e-02	k: 649	n:60000
PTPRF   60000 perm   15 sec   (4019 perm/sec)   p_kst 1.081667e-02   p_cons 5.917667e-01   p_joint 2.043333e-02

Joint ci ratio: 1.021238e-01	ci left: 1.956053e-02	ci right 2.167947e-02	k: 1442	n:70000
Cons ci ratio: 1.230420e-02	ci left: 5.881767e-01	ci right 5.954728e-01	k: 41428	n:70000
KS ci ratio: 1.409503e-01	ci left: 1.015778e-02	ci right 1.171173e-02	k: 764	n:70000
PTPRF   70000 perm   18 sec   (3947 perm/sec)   p_kst 1.091429e-02   p_cons 5.918286e-01   p_joint 2.060000e-02

Joint ci ratio: 5.013703e-02	ci left: 6.920495e-02	ci right 7.277624e-02	k: 5678	n:80000
Cons ci ratio: 1.149564e-02	ci left: 5.889979e-01	ci right 5.958204e-01	k: 47393	n:80000
KS ci ratio: 1.322519e-01	ci left: 1.014366e-02	ci right 1.159214e-02	k: 868	n:80000
PTPRF   80000 perm   21 sec   (3830 perm/sec)   p_kst 1.085000e-02   p_cons 5.924125e-01   p_joint 7.097500e-02

Joint ci ratio: 4.718972e-02	ci left: 6.952821e-02	ci right 7.289949e-02	k: 6408	n:90000
Cons ci ratio: 1.083401e-02	ci left: 5.893814e-01	ci right 5.958126e-01	k: 53334	n:90000
KS ci ratio: 1.245998e-01	ci left: 1.019958e-02	ci right 1.156556e-02	k: 978	n:90000
PTPRF   90000 perm   25 sec   (3632 perm/sec)   p_kst 1.086667e-02   p_cons 5.926000e-01   p_joint 7.120000e-02

Joint ci ratio: 4.115617e-03	ci left: 8.988499e-01	ci right 9.025668e-01	k: 90072	n:100000
Cons ci ratio: 1.027018e-02	ci left: 5.899174e-01	ci right 5.960172e-01	k: 59297	n:100000
KS ci ratio: 1.185245e-01	ci left: 1.017830e-02	ci right 1.147031e-02	k: 1081	n:100000
PTPRF   100000 perm   28 sec   (3536 perm/sec)   p_kst 1.081000e-02   p_cons 5.929700e-01   p_joint 9.007200e-01

Joint ci ratio: 3.924316e-03	ci left: 8.989267e-01	ci right 9.024703e-01	k: 99078	n:110000
Cons ci ratio: 9.773389e-03	ci left: 5.909908e-01	ci right 5.968042e-01	k: 65329	n:110000
KS ci ratio: 1.131626e-01	ci left: 1.017990e-02	ci right 1.140974e-02	k: 1186	n:110000
PTPRF   110000 perm   32 sec   (3430 perm/sec)   p_kst 1.078182e-02   p_cons 5.939000e-01   p_joint 9.007091e-01

Joint ci ratio: 3.757954e-03	ci left: 8.989689e-01	ci right 9.023617e-01	k: 108081	n:120000
Cons ci ratio: 9.354729e-03	ci left: 5.912484e-01	ci right 5.968137e-01	k: 71284	n:120000
KS ci ratio: 1.085532e-01	ci left: 1.016611e-02	ci right 1.134105e-02	k: 1289	n:120000
PTPRF   120000 perm   35 sec   (3399 perm/sec)   p_kst 1.074167e-02   p_cons 5.940333e-01   p_joint 9.006750e-01

Joint ci ratio: 3.613583e-03	ci left: 8.988833e-01	ci right 9.021450e-01	k: 117068	n:130000
Cons ci ratio: 8.991944e-03	ci left: 5.911321e-01	ci right 5.964791e-01	k: 77195	n:130000
KS ci ratio: 1.049225e-01	ci left: 1.006538e-02	ci right 1.118738e-02	k: 1380	n:130000
PTPRF   130000 perm   39 sec   (3307 perm/sec)   p_kst 1.061538e-02   p_cons 5.938077e-01   p_joint 9.005231e-01

Joint ci ratio: 3.488960e-03	ci left: 8.985893e-01	ci right 9.017370e-01	k: 126024	n:140000
Cons ci ratio: 8.663843e-03	ci left: 5.912862e-01	ci right 5.964384e-01	k: 83141	n:140000
KS ci ratio: 1.012860e-01	ci left: 1.004925e-02	ci right 1.112831e-02	k: 1481	n:140000
PTPRF   140000 perm   44 sec   (3199 perm/sec)   p_kst 1.057857e-02   p_cons 5.938643e-01   p_joint 9.001714e-01

Joint ci ratio: 3.373740e-03	ci left: 8.984775e-01	ci right 9.015204e-01	k: 135001	n:150000
Cons ci ratio: 8.375469e-03	ci left: 5.910626e-01	ci right 5.960405e-01	k: 89033	n:150000
KS ci ratio: 9.769185e-02	ci left: 1.010090e-02	ci right 1.114481e-02	k: 1592	n:150000
PTPRF   150000 perm   47 sec   (3175 perm/sec)   p_kst 1.061333e-02   p_cons 5.935533e-01   p_joint 9.000067e-01

Outputting figure to mutsig2_images.part000000000141/PTPRF.2_5852_150000_0.010613_0.59355_0.90001.png
                gene_name: PTPRF
               theta_stop: 0.098 
                    nperm: 150000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.90 

Current progress: 62 percent done.
PTPRM
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.026571e-02	ci left: 2.882526e-01	ci right 3.062657e-01	k: 2972	n:10000
KS ci ratio: 4.199803e-02	ci left: 4.556848e-01	ci right 4.753353e-01	k: 4655	n:10000
PTPRM   10000 perm   3 sec   (3738 perm/sec)   p_kst 4.655000e-01   p_cons 2.972000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000141/PTPRM.2_4530_10000_0.4655_0.2972_1.png
                gene_name: PTPRM
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.30 
      ci_cons_bounds_left: 0.29 
     ci_cons_bounds_right: 0.31 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
PVRL3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.628610e-03	ci left: 9.896106e-01	ci right 9.932945e-01	k: 9916	n:10000
Cons ci ratio: 4.475820e-02	ci left: 4.242563e-01	ci right 4.437821e-01	k: 4340	n:10000
KS ci ratio: 2.042418e-02	ci left: 7.783356e-01	ci right 7.944972e-01	k: 7865	n:10000
PVRL3   10000 perm   2 sec   (4415 perm/sec)   p_kst 7.865000e-01   p_cons 4.340000e-01   p_joint 9.916000e-01

Outputting figure to mutsig2_images.part000000000141/PVRL3.2_1674_10000_0.7865_0.434_0.9916.png
                gene_name: PVRL3
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 88 percent done.
QRICH2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.114346e-02	ci left: 6.033719e-01	ci right 6.225622e-01	k: 6130	n:10000
Cons ci ratio: 4.004187e-02	ci left: 4.794567e-01	ci right 4.991495e-01	k: 4893	n:10000
KS ci ratio: 5.841444e-02	ci left: 3.013384e-01	ci right 3.195722e-01	k: 3104	n:10000
QRICH2   10000 perm   2 sec   (4687 perm/sec)   p_kst 3.104000e-01   p_cons 4.893000e-01   p_joint 6.130000e-01

Outputting figure to mutsig2_images.part000000000141/QRICH2.2_5068_10000_0.3104_0.4893_0.613.png
                gene_name: QRICH2
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000141
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 141 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4398271: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000142> was used as the working directory.
Started at Wed Oct 24 16:15:55 2012
Results reported at Wed Oct 24 16:17:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000142.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000142.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 142  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000142.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     76.78 sec.
    Max Memory :      1163 MB
    Max Swap   :      3956 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
142
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 142
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 142: processing genes 12650 - 12739
Calculating significance of each gene.
Using projection method.
12650	QSOX2	1
12651	QTRT1	1
12652	QTRTD1	1
12653	R3HDM1	1
12654	R3HDM2	1
12655	R3HDML	1
12656	RAB10	1
12657	RAB11A	1
12658	RAB11B	1
12659	RAB11FIP1	1
12660	RAB11FIP2	1
12661	RAB11FIP3	1
12662	RAB11FIP4	1
12663	RAB11FIP5	1
12664	RAB12	1
12665	RAB13	1
12666	RAB14	6.559788e-02
12667	RAB15	1
12668	RAB17	1
12669	RAB18	1
12670	RAB19	1
12671	RAB1A	1
12672	RAB1B	1
12673	RAB20	1
12674	RAB21	1
12675	RAB22A	1
12676	RAB23	1
12677	RAB24	1
12678	RAB25	1
12679	RAB26	1
12680	RAB27A	1
12681	RAB27B	1
12682	RAB28	1
12683	RAB2A	1
12684	RAB2B	1
12685	RAB30	1
12686	RAB31	1
12687	RAB32	1
12688	RAB33A	1
12689	RAB33B	1
12690	RAB34	1
12691	RAB35	1
12692	RAB36	8.544390e-02
12693	RAB37	1
12694	RAB38	1
12695	RAB39	1
12696	RAB39B	1
12697	RAB3A	1
12698	RAB3B	1
12699	RAB3C	1
12700	RAB3D	1.197871e-01
12701	RAB3GAP1	1
12702	RAB3GAP2	4.432379e-01
12703	RAB3IL1	1
12704	RAB3IP	5.959518e-02
12705	RAB40A	1
12706	RAB40AL	1
12707	RAB40B	1
12708	RAB40C	1
12709	RAB41	1
12710	RAB42	1
12711	RAB43	1
12712	RAB4A	1
12713	RAB4B	1
12714	RAB5A	1
12715	RAB5B	1
12716	RAB5C	1
12717	RAB6A	1
12718	RAB6B	1
12719	RAB6C	1
12720	RAB7A	3.605201e-02
12721	RAB7L1	1
12722	RAB8A	1
12723	RAB8B	1
12724	RAB9A	1
12725	RAB9B	1
12726	RABAC1	1
12727	RABEP1	1
12728	RABEP2	1
12729	RABEPK	1.877738e-01
12730	RABGAP1	1
12731	RABGAP1L	1.609290e-01
12732	RABGEF1	1.538042e-01
12733	RABGGTA	1
12734	RABGGTB	1
12735	RABIF	1
12736	RABL2A	1
12737	RABL2B	1
12738	RABL3	1
12739	RABL5	1
Done

Running MutSig 2:
Scatter job 142: processing genes 12650 - 12739
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RAB3GAP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.287024e-02	ci left: 5.773758e-01	ci right 5.967734e-01	k: 5871	n:10000
Cons ci ratio: 4.472179e-02	ci left: 4.246552e-01	ci right 4.441830e-01	k: 4344	n:10000
KS ci ratio: 7.152117e-02	ci left: 2.226698e-01	ci right 2.392872e-01	k: 2309	n:10000
RAB3GAP2   10000 perm   2 sec   (5309 perm/sec)   p_kst 2.309000e-01   p_cons 4.344000e-01   p_joint 5.871000e-01

Outputting figure to mutsig2_images.part000000000142/RAB3GAP2.2_4322_10000_0.2309_0.4344_0.5871.png
                gene_name: RAB3GAP2
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000142
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 142 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 4398275: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000143> was used as the working directory.
Started at Wed Oct 24 16:15:57 2012
Results reported at Wed Oct 24 16:18:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000143.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000143.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 143  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000143.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    156.31 sec.
    Max Memory :      1483 MB
    Max Swap   :      4020 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
143
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 143
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 143: processing genes 12740 - 12829
Calculating significance of each gene.
Using projection method.
12740	RAC1	1
12741	RAC2	1
12742	RAC3	1
12743	RACGAP1	1
12744	RAD1	1
12745	RAD17	1
12746	RAD18	1
12747	RAD21	1
12748	RAD23A	1
12749	RAD23B	2.103987e-02
12750	RAD50	1
12751	RAD51	1
12752	RAD51AP1	1
12753	RAD51AP2	1
12754	RAD51C	1
12755	RAD51L1	1
12756	RAD51L3	1
12757	RAD52	1
12758	RAD54B	1
12759	RAD54L	2.241795e-01
12760	RAD54L2	2.495745e-01
12761	RAD9A	1
12762	RAD9B	1
12763	RADIL	1
12764	RAE1	1
12765	RAET1E	1
12766	RAET1G	1
12767	RAET1L	1
12768	RAF1	1
12769	RAG1	1
12770	RAG1AP1	1
12771	RAG2	1
12772	RAGE	1
12773	RAI1	2.553032e-01
12774	RAI14	1
12775	RAI2	1
12776	RALA	1
12777	RALB	1
12778	RALBP1	1
12779	RALGAPA1	4.187682e-01
12780	RALGAPA2	1
12781	RALGAPB	3.803475e-01
12782	RALGDS	1
12783	RALGPS1	1
12784	RALGPS2	1.487184e-01
12785	RALY	1
12786	RALYL	1
12787	RAMP1	1.351720e-02
12788	RAMP2	1
12789	RAMP3	1
12790	RAN	1.152473e-02
12791	RANBP1	1
12792	RANBP10	1
12793	RANBP17	1
12794	RANBP2	5.798552e-01
12795	RANBP3	1
12796	RANBP3L	1
12797	RANBP6	1.095986e-01
12798	RANBP9	1
12799	RANGAP1	1
12800	RANGRF	1
12801	RAP1A	1
12802	RAP1B	1
12803	RAP1GAP	1.142192e-01
12804	RAP1GAP2	1
12805	RAP1GDS1	2.648766e-01
12806	RAP2A	1
12807	RAP2B	1
12808	RAP2C	1
12809	RAPGEF1	1
12810	RAPGEF2	7.087515e-02
12811	RAPGEF3	1
12812	RAPGEF4	1
12813	RAPGEF5	1
12814	RAPGEF6	1
12815	RAPGEFL1	1
12816	RAPH1	1.556641e-01
12817	RAPSN	1
12818	RARA	1
12819	RARB	1.453608e-01
12820	RARG	1
12821	RARRES1	1
12822	RARRES2	1
12823	RARRES3	1
12824	RARS	1
12825	RARS2	2.765449e-01
12826	RASA1	1.953717e-01
12827	RASA2	2.052594e-01
12828	RASA3	1
12829	RASAL1	1
Done

Running MutSig 2:
Scatter job 143: processing genes 12740 - 12829
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RAD23B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.942915e-02	ci left: 7.948639e-01	ci right 8.105594e-01	k: 8028	n:10000
Cons ci ratio: 2.429909e-02	ci left: 7.135091e-01	ci right 7.311612e-01	k: 7224	n:10000
KS ci ratio: 5.983582e-02	ci left: 2.912258e-01	ci right 3.092906e-01	k: 3002	n:10000
RAD23B   10000 perm   2 sec   (6298 perm/sec)   p_kst 3.002000e-01   p_cons 7.224000e-01   p_joint 8.028000e-01

Outputting figure to mutsig2_images.part000000000143/RAD23B.2_1270_10000_0.3002_0.7224_0.8028.png
                gene_name: RAD23B
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.80 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.81 

Current progress: 25 percent done.
RALGAPA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.165041e-02	ci left: 9.133766e-01	ci right 9.241779e-01	k: 9189	n:10000
Cons ci ratio: 6.138026e-02	ci left: 2.807224e-01	ci right 2.986003e-01	k: 2896	n:10000
KS ci ratio: 1.422220e-01	ci left: 6.555836e-02	ci right 7.569349e-02	k: 705	n:10000
RALGAPA1   10000 perm   2 sec   (4782 perm/sec)   p_kst 7.050000e-02   p_cons 2.896000e-01   p_joint 9.189000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 4.393048e-02	ci left: 2.784525e-01	ci right 2.910102e-01	k: 5694	n:20000
KS ci ratio: 1.009534e-01	ci left: 6.655043e-02	ci right 7.367517e-02	k: 1401	n:20000
RALGAPA1   20000 perm   5 sec   (4266 perm/sec)   p_kst 7.005000e-02   p_cons 2.847000e-01   p_joint 1

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 3.628301e-02	ci left: 2.749903e-01	ci right 2.851856e-01	k: 8402	n:30000
KS ci ratio: 8.201010e-02	ci left: 6.785719e-02	ci right 7.369293e-02	k: 2122	n:30000
RALGAPA1   30000 perm   7 sec   (4082 perm/sec)   p_kst 7.073333e-02   p_cons 2.800667e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000143/RALGAPA1.2_6424_30000_0.070733_0.28007_1.png
                gene_name: RALGAPA1
               theta_stop: 0.082 
                    nperm: 30000 
                     p_ks: 0.071 
        ci_ks_bounds_left: 0.068 
       ci_ks_bounds_right: 0.074 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
RANBP6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.558433e-01	ci left: 5.484605e-02	ci right 6.421259e-02	k: 594	n:10000
Cons ci ratio: 5.129453e-02	ci left: 3.591340e-01	ci right 3.781425e-01	k: 3686	n:10000
KS ci ratio: 2.716280e-01	ci left: 1.762636e-02	ci right 2.325787e-02	k: 203	n:10000
RANBP6   10000 perm   2 sec   (5736 perm/sec)   p_kst 2.030000e-02   p_cons 3.686000e-01   p_joint 5.940000e-02

Joint ci ratio: 1.121161e-01	ci left: 5.436186e-02	ci right 6.086750e-02	k: 1151	n:20000
Cons ci ratio: 3.626666e-02	ci left: 3.620082e-01	ci right 3.754300e-01	k: 7374	n:20000
KS ci ratio: 1.865486e-01	ci left: 1.958233e-02	ci right 2.365841e-02	k: 431	n:20000
RANBP6   20000 perm   4 sec   (5096 perm/sec)   p_kst 2.155000e-02   p_cons 3.687000e-01   p_joint 5.755000e-02

Joint ci ratio: 8.548467e-02	ci left: 6.269323e-02	ci right 6.832461e-02	k: 1964	n:30000
Cons ci ratio: 2.955546e-02	ci left: 3.641341e-01	ci right 3.750912e-01	k: 11088	n:30000
KS ci ratio: 1.544004e-01	ci left: 1.940733e-02	ci right 2.268634e-02	k: 630	n:30000
RANBP6   30000 perm   6 sec   (4871 perm/sec)   p_kst 2.100000e-02   p_cons 3.696000e-01   p_joint 6.546667e-02

Joint ci ratio: 7.407755e-02	ci left: 6.299630e-02	ci right 6.786702e-02	k: 2616	n:40000
Cons ci ratio: 2.552087e-02	ci left: 3.662380e-01	ci right 3.757307e-01	k: 14839	n:40000
KS ci ratio: 1.334185e-01	ci left: 1.971394e-02	ci right 2.255618e-02	k: 844	n:40000
RANBP6   40000 perm   8 sec   (4739 perm/sec)   p_kst 2.110000e-02   p_cons 3.709750e-01   p_joint 6.540000e-02

Joint ci ratio: 6.065234e-02	ci left: 7.475675e-02	ci right 7.945248e-02	k: 3854	n:50000
Cons ci ratio: 2.283144e-02	ci left: 3.666436e-01	ci right 3.751314e-01	k: 18544	n:50000
KS ci ratio: 1.196375e-01	ci left: 1.976107e-02	ci right 2.229496e-02	k: 1050	n:50000
RANBP6   50000 perm   11 sec   (4561 perm/sec)   p_kst 2.100000e-02   p_cons 3.708800e-01   p_joint 7.708000e-02

Joint ci ratio: 5.534192e-02	ci left: 7.502711e-02	ci right 7.931389e-02	k: 4629	n:60000
Cons ci ratio: 2.086972e-02	ci left: 3.664009e-01	ci right 3.741449e-01	k: 22216	n:60000
KS ci ratio: 1.084781e-01	ci left: 2.014336e-02	ci right 2.246993e-02	k: 1277	n:60000
RANBP6   60000 perm   13 sec   (4470 perm/sec)   p_kst 2.128333e-02   p_cons 3.702667e-01   p_joint 7.715000e-02

Joint ci ratio: 5.101022e-02	ci left: 7.581199e-02	ci right 7.979451e-02	k: 5445	n:70000
Cons ci ratio: 1.937013e-02	ci left: 3.655235e-01	ci right 3.726873e-01	k: 25837	n:70000
KS ci ratio: 9.971613e-02	ci left: 2.052186e-02	ci right 2.268947e-02	k: 1511	n:70000
RANBP6   70000 perm   16 sec   (4381 perm/sec)   p_kst 2.158571e-02   p_cons 3.691000e-01   p_joint 7.778571e-02

Outputting figure to mutsig2_images.part000000000143/RANBP6.2_3322_70000_0.021586_0.3691_0.077786.png
                gene_name: RANBP6
               theta_stop: 0.100 
                    nperm: 70000 
                     p_ks: 0.022 
        ci_ks_bounds_left: 0.021 
       ci_ks_bounds_right: 0.023 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.078 
     ci_joint_bounds_left: 0.076 
    ci_joint_bounds_right: 0.080 

Current progress: 75 percent done.
RAPGEF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.383424e-02	ci left: 3.370699e-01	ci right 3.558196e-01	k: 3464	n:10000
KS ci ratio: 3.644533e-02	ci left: 5.264667e-01	ci right 5.461122e-01	k: 5363	n:10000
RAPGEF2   10000 perm   2 sec   (4864 perm/sec)   p_kst 5.363000e-01   p_cons 3.464000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000143/RAPGEF2.2_4596_10000_0.5363_0.3464_1.png
                gene_name: RAPGEF2
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000143
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 143 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1547>
Subject: Job 4398278: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000144> was used as the working directory.
Started at Wed Oct 24 16:16:07 2012
Results reported at Wed Oct 24 16:18:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000144.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000144.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 144  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000144.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    185.22 sec.
    Max Memory :      1536 MB
    Max Swap   :      3985 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
144
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 144
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 144: processing genes 12830 - 12918
Calculating significance of each gene.
Using projection method.
12830	RASAL2	1
12831	RASAL3	1.243651e-01
12832	RASD1	1
12833	RASD2	1
12834	RASEF	1
12835	RASGEF1A	3.636696e-03
12836	RASGEF1B	1
12837	RASGEF1C	1
12838	RASGRF1	1
12839	RASGRF2	1
12840	RASGRP1	1
12841	RASGRP2	1
12842	RASGRP3	1
12843	RASGRP4	2.405434e-01
12844	RASIP1	1
12845	RASL10B	1
12846	RASL11A	1
12847	RASL11B	1
12848	RASL12	1
12849	RASSF1	8.849088e-02
12850	RASSF2	1.344757e-01
12851	RASSF3	1.665422e-02
12852	RASSF4	1
12853	RASSF5	1
12854	RASSF6	1
12855	RASSF7	1
12856	RASSF8	1
12857	RASSF9	1
12858	RAVER1	1
12859	RAVER2	1
12860	RAX	1
12861	RAX2	1
12862	RB1	1
12863	RB1CC1	4.294052e-01
12864	RBAK	1
12865	RBBP4	1
12866	RBBP5	1.906931e-01
12867	RBBP6	1
12868	RBBP7	1
12869	RBBP8	5.242272e-02
12870	RBBP9	1
12871	RBCK1	8.869282e-02
12872	RBKS	1
12873	RBL1	1
12874	RBL2	3.756650e-01
12875	RBM10	1
12876	RBM11	1
12877	RBM12	1
12878	RBM12B	1
12879	RBM14	1
12880	RBM15	1.804060e-01
12881	RBM15B	1
12882	RBM16	1
12883	RBM17	2.165395e-01
12884	RBM18	1
12885	RBM19	1
12886	RBM22	1
12887	RBM23	1.811771e-01
12888	RBM24	1
12889	RBM25	1.725126e-01
12890	RBM26	1.715584e-01
12891	RBM27	1
12892	RBM28	1.417068e-01
12893	RBM3	1
12894	RBM33	3.702990e-01
12895	RBM34	1.605339e-01
12896	RBM38	1
12897	RBM39	1.868222e-01
12898	RBM4	4.392758e-02
12899	RBM41	1
12900	RBM42	1
12901	RBM43	1
12902	RBM44	9.054346e-02
12903	RBM45	1
12904	RBM46	1
12905	RBM47	1
12906	RBM4B	1
12907	RBM5	7.529283e-02
12908	RBM6	2.001540e-01
12909	RBM7	1
12910	RBM8A	1
12911	RBM9	1.514425e-01
12912	RBMS1	1
12913	RBMS2	1
12914	RBMS3	1
12915	RBMX	1.538096e-01
12916	RBMX2	1
12917	RBMXL1	1
12918	RBMXL2	1
Done

Running MutSig 2:
Scatter job 144: processing genes 12830 - 12918
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RBM5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.755631e-03	ci left: 9.889489e-01	ci right 9.927569e-01	k: 9910	n:10000
Cons ci ratio: 5.785981e-02	ci left: 3.054047e-01	ci right 3.237035e-01	k: 3145	n:10000
KS ci ratio: 2.980685e-02	ci left: 6.240687e-01	ci right 6.430535e-01	k: 6336	n:10000
RBM5   10000 perm   2 sec   (5625 perm/sec)   p_kst 6.336000e-01   p_cons 3.145000e-01   p_joint 9.910000e-01

Outputting figure to mutsig2_images.part000000000144/RBM5.3_2544_10000_0.6336_0.3145_0.991.png
                gene_name: RBM5
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 17 percent done.
RASGEF1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.019958e-02	ci left: 6.179381e-01	ci right 6.369876e-01	k: 6275	n:10000
Cons ci ratio: 1.701452e-02	ci left: 8.341928e-01	ci right 8.486078e-01	k: 8415	n:10000
KS ci ratio: 3.620425e-02	ci left: 5.297706e-01	ci right 5.494063e-01	k: 5396	n:10000
RASGEF1A   10000 perm   2 sec   (6347 perm/sec)   p_kst 5.396000e-01   p_cons 8.415000e-01   p_joint 6.275000e-01

Outputting figure to mutsig2_images.part000000000144/RASGEF1A.2_1494_10000_0.5396_0.8415_0.6275.png
                gene_name: RASGEF1A
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 33 percent done.
RASSF3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.780486e-02	ci left: 2.419322e-01	ci right 2.590133e-01	k: 2504	n:10000
Cons ci ratio: 8.146546e-02	ci left: 1.802855e-01	ci right 1.956967e-01	k: 1879	n:10000
KS ci ratio: 6.710789e-02	ci left: 2.457875e-01	ci right 2.629558e-01	k: 2543	n:10000
RASSF3   10000 perm   1 sec   (7289 perm/sec)   p_kst 2.543000e-01   p_cons 1.879000e-01   p_joint 2.504000e-01

Outputting figure to mutsig2_images.part000000000144/RASSF3.2_737_10000_0.2543_0.1879_0.2504.png
                gene_name: RASSF3
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.26 

Current progress: 50 percent done.
RB1CC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.061251e-02	ci left: 7.751944e-01	ci right 7.914402e-01	k: 7834	n:10000
Cons ci ratio: 1.060242e-02	ci left: 9.267855e-01	ci right 9.367612e-01	k: 9319	n:10000
KS ci ratio: 3.151877e-02	ci left: 5.976484e-01	ci right 6.168891e-01	k: 6073	n:10000
RB1CC1   10000 perm   2 sec   (4473 perm/sec)   p_kst 6.073000e-01   p_cons 9.319000e-01   p_joint 7.834000e-01

Outputting figure to mutsig2_images.part000000000144/RB1CC1.2_4873_10000_0.6073_0.9319_0.7834.png
                gene_name: RB1CC1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.79 

Current progress: 67 percent done.
RBBP5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.592830e-02	ci left: 5.335757e-01	ci right 5.531990e-01	k: 5434	n:10000
KS ci ratio: 6.470164e-02	ci left: 2.597333e-01	ci right 2.772017e-01	k: 2684	n:10000
RBBP5   10000 perm   2 sec   (6299 perm/sec)   p_kst 2.684000e-01   p_cons 5.434000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000144/RBBP5.2_1673_10000_0.2684_0.5434_1.png
                gene_name: RBBP5
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
RBM26
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.783046e-02	ci left: 1.587554e-01	ci right 1.734397e-01	k: 1660	n:10000
Cons ci ratio: 1.787134e-01	ci left: 4.178548e-02	ci right 5.008162e-02	k: 458	n:10000
KS ci ratio: 2.835287e-02	ci left: 6.470981e-01	ci right 6.658107e-01	k: 6565	n:10000
RBM26   10000 perm   2 sec   (5541 perm/sec)   p_kst 6.565000e-01   p_cons 4.580000e-02   p_joint 1.660000e-01

Joint ci ratio: 8.242343e-02	ci left: 9.739693e-02	ci right 1.058193e-01	k: 2031	n:20000
Cons ci ratio: 1.273938e-01	ci left: 4.231371e-02	ci right 4.811944e-02	k: 903	n:20000
KS ci ratio: 1.985188e-02	ci left: 6.543413e-01	ci right 6.675119e-01	k: 13219	n:20000
RBM26   20000 perm   4 sec   (4965 perm/sec)   p_kst 6.609500e-01   p_cons 4.515000e-02   p_joint 1.015500e-01

Joint ci ratio: 1.030266e-01	ci left: 4.365689e-02	ci right 4.843152e-02	k: 1380	n:30000
Cons ci ratio: 1.059128e-01	ci left: 4.134938e-02	ci right 4.600618e-02	k: 1309	n:30000
KS ci ratio: 1.618329e-02	ci left: 6.562805e-01	ci right 6.670215e-01	k: 19850	n:30000
RBM26   30000 perm   6 sec   (4780 perm/sec)   p_kst 6.616667e-01   p_cons 4.363333e-02   p_joint 4.600000e-02

Joint ci ratio: 8.905511e-02	ci left: 4.413888e-02	ci right 4.827732e-02	k: 1847	n:40000
Cons ci ratio: 9.163214e-02	ci left: 4.174179e-02	ci right 4.577478e-02	k: 1749	n:40000
KS ci ratio: 1.401654e-02	ci left: 6.569640e-01	ci right 6.662625e-01	k: 26465	n:40000
RBM26   40000 perm   9 sec   (4619 perm/sec)   p_kst 6.616250e-01   p_cons 4.372500e-02   p_joint 4.617500e-02

Outputting figure to mutsig2_images.part000000000144/RBM26.2_3027_40000_0.66163_0.043725_0.046175.png
                gene_name: RBM26
               theta_stop: 0.092 
                    nperm: 40000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.044 
      ci_cons_bounds_left: 0.042 
     ci_cons_bounds_right: 0.046 
                  p_joint: 0.046 
     ci_joint_bounds_left: 0.044 
    ci_joint_bounds_right: 0.048 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000144
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 144 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4398281: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000145> was used as the working directory.
Started at Wed Oct 24 16:16:09 2012
Results reported at Wed Oct 24 16:18:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000145.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000145.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 145  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000145.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    144.43 sec.
    Max Memory :      1204 MB
    Max Swap   :      3925 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
145
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 145
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 145: processing genes 12919 - 13008
Calculating significance of each gene.
Using projection method.
12919	RBP1	1
12920	RBP2	1
12921	RBP3	4.837894e-01
12922	RBP4	1
12923	RBP5	1
12924	RBP7	1
12925	RBPJ	1.904337e-01
12926	RBPJL	1
12927	RBPMS	1
12928	RBPMS2	1
12929	RBX1	1
12930	RC3H1	1
12931	RC3H2	1.153477e-01
12932	RCAN1	1
12933	RCAN2	1
12934	RCAN3	7.457375e-03
12935	RCBTB1	1
12936	RCBTB2	1
12937	RCC1	1
12938	RCC2	1
12939	RCCD1	1
12940	RCE1	8.574641e-02
12941	RCHY1	7.392049e-02
12942	RCL1	1
12943	RCN1	1
12944	RCN2	1
12945	RCN3	1
12946	RCOR1	1
12947	RCOR2	1
12948	RCOR3	1
12949	RCSD1	1.886998e-01
12950	RCVRN	1
12951	RD3	1
12952	RDBP	1
12953	RDH10	1
12954	RDH11	1
12955	RDH12	1
12956	RDH13	1
12957	RDH14	1
12958	RDH16	1
12959	RDH5	1.053294e-01
12960	RDH8	1
12961	RDM1	1
12962	RDX	1
12963	REC8	1
12964	RECK	1.477954e-01
12965	RECQL	1
12966	RECQL4	1
12967	RECQL5	6.030736e-03
12968	REEP1	1
12969	REEP2	1
12970	REEP3	1
12971	REEP4	1
12972	REEP5	1
12973	REEP6	1
12974	REG1A	2.464487e-02
12975	REG1B	3.570818e-02
12976	REG3A	7.683151e-02
12977	REG3G	1
12978	REG4	1
12979	REL	1.034874e-01
12980	RELA	1
12981	RELB	1.308196e-01
12982	RELL1	1
12983	RELL2	1
12984	RELN	3.821530e-01
12985	RELT	1
12986	REM1	8.463206e-02
12987	REM2	1
12988	REN	1
12989	RENBP	1
12990	REP15	4.081403e-02
12991	REPIN1	7.621694e-03
12992	REPS1	7.313857e-02
12993	REPS2	1
12994	RER1	1
12995	RERE	4.072012e-01
12996	RERG	1
12997	RERGL	1
12998	REST	1
12999	RET	1
13000/17942 13000	RETN	1
13001	RETNLB	1
13002	RETSAT	1
13003	REV1	1
13004	REV3L	5.975217e-01
13005	REXO1	1.436890e-01
13006	REXO2	7.347843e-02
13007	REXO4	1
13008	RFC1	4.649768e-01
Done

Running MutSig 2:
Scatter job 145: processing genes 12919 - 13008
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RECQL5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.395331e-02	ci left: 3.360765e-01	ci right 3.548136e-01	k: 3454	n:10000
Cons ci ratio: 1.365803e-01	ci left: 7.088017e-02	ci right 8.136835e-02	k: 760	n:10000
KS ci ratio: 1.356558e-02	ci left: 8.868791e-01	ci right 8.990909e-01	k: 8931	n:10000
RECQL5   10000 perm   3 sec   (3411 perm/sec)   p_kst 8.931000e-01   p_cons 7.600000e-02   p_joint 3.454000e-01

Joint ci ratio: 5.360787e-02	ci left: 2.052636e-01	ci right 2.166206e-01	k: 4218	n:20000
Cons ci ratio: 9.695863e-02	ci left: 7.187539e-02	ci right 7.924857e-02	k: 1510	n:20000
KS ci ratio: 9.525663e-03	ci left: 8.900583e-01	ci right 8.986267e-01	k: 17888	n:20000
RECQL5   20000 perm   8 sec   (2542 perm/sec)   p_kst 8.944000e-01   p_cons 7.550000e-02   p_joint 2.109000e-01

Outputting figure to mutsig2_images.part000000000145/RECQL5.3_3139_20000_0.8944_0.0755_0.2109.png
                gene_name: RECQL5
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.075 
      ci_cons_bounds_left: 0.072 
     ci_cons_bounds_right: 0.079 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 20 percent done.
RCAN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.159954e-02	ci left: 7.586885e-01	ci right 7.753556e-01	k: 7671	n:10000
Cons ci ratio: 4.524428e-02	ci left: 4.189723e-01	ci right 4.384693e-01	k: 4287	n:10000
KS ci ratio: 3.382151e-02	ci left: 5.634356e-01	ci right 5.829217e-01	k: 5732	n:10000
RCAN3   10000 perm   2 sec   (6615 perm/sec)   p_kst 5.732000e-01   p_cons 4.287000e-01   p_joint 7.671000e-01

Outputting figure to mutsig2_images.part000000000145/RCAN3.2_742_10000_0.5732_0.4287_0.7671.png
                gene_name: RCAN3
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.78 

Current progress: 40 percent done.
RELN
Processing conservation and coverage...
93% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.944204e-02	ci left: 6.297987e-01	ci right 6.487201e-01	k: 6393	n:10000
KS ci ratio: 4.474909e-02	ci left: 4.243561e-01	ci right 4.438824e-01	k: 4341	n:10000
RELN   10000 perm   3 sec   (3657 perm/sec)   p_kst 4.341000e-01   p_cons 6.393000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000145/RELN.2_10643_10000_0.4341_0.6393_1.png
                gene_name: RELN
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
REPIN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.989902e-02	ci left: 1.861912e-01	ci right 2.017874e-01	k: 1939	n:10000
Cons ci ratio: 8.717051e-02	ci left: 1.608181e-01	ci right 1.755758e-01	k: 1681	n:10000
KS ci ratio: 4.273097e-02	ci left: 4.471004e-01	ci right 4.667247e-01	k: 4569	n:10000
REPIN1   10000 perm   2 sec   (6205 perm/sec)   p_kst 4.569000e-01   p_cons 1.681000e-01   p_joint 1.939000e-01

Outputting figure to mutsig2_images.part000000000145/REPIN1.2_1883_10000_0.4569_0.1681_0.1939.png
                gene_name: REPIN1
               theta_stop: 0.087 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 80 percent done.
RERE
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.014468e-02	ci left: 9.323699e-01	ci right 9.419735e-01	k: 9373	n:10000
Cons ci ratio: 4.226054e-02	ci left: 4.525901e-01	ci right 4.722318e-01	k: 4624	n:10000
KS ci ratio: 2.506374e-02	ci left: 7.007944e-01	ci right 7.186833e-01	k: 7098	n:10000
RERE   10000 perm   2 sec   (4433 perm/sec)   p_kst 7.098000e-01   p_cons 4.624000e-01   p_joint 9.373000e-01

Outputting figure to mutsig2_images.part000000000145/RERE.2_4789_10000_0.7098_0.4624_0.9373.png
                gene_name: RERE
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000145
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 145 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 4398285: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000146> was used as the working directory.
Started at Wed Oct 24 16:16:09 2012
Results reported at Wed Oct 24 16:19:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000146.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000146.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 146  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000146.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    221.34 sec.
    Max Memory :      1405 MB
    Max Swap   :      3991 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
146
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 146
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 146: processing genes 13009 - 13098
Calculating significance of each gene.
Using projection method.
13009	RFC2	8.437227e-02
13010	RFC3	1
13011	RFC4	1
13012	RFC5	1
13013	RFESD	1
13014	RFFL	5.526219e-02
13015	RFK	1
13016	RFNG	1
13017	RFPL1	1
13018	RFPL2	1
13019	RFPL3	9.579917e-02
13020	RFPL4B	5.256419e-02
13021	RFT1	1
13022	RFTN1	1
13023	RFTN2	1
13024	RFWD2	1
13025	RFWD3	2.944405e-01
13026	RFX1	2.489261e-01
13027	RFX2	1
13028	RFX3	2.234654e-01
13029	RFX4	1
13030	RFX5	1
13031	RFX6	1
13032	RFX7	1
13033	RFXANK	1
13034	RFXAP	1
13035	RG9MTD1	1.479245e-01
13036	RG9MTD2	1
13037	RG9MTD3	1
13038	RGAG1	8.035046e-02
13039	RGAG4	1
13040	RGL1	1
13041	RGL2	3.391082e-01
13042	RGL3	1
13043	RGL4	1
13044	RGMA	1
13045	RGMB	1
13046	RGN	1
13047	RGNEF	1
13048	RGP1	3.119782e-02
13049	RGR	1
13050	RGS1	1
13051	RGS10	1
13052	RGS11	1
13053	RGS12	1
13054	RGS13	6.682885e-02
13055	RGS14	1
13056	RGS16	1
13057	RGS17	5.911638e-03
13058	RGS18	1
13059	RGS19	1
13060	RGS2	8.426371e-03
13061	RGS20	1.433767e-01
13062	RGS21	1
13063	RGS22	4.909937e-01
13064	RGS3	5.382151e-01
13065	RGS4	1
13066	RGS5	1
13067	RGS6	1
13068	RGS7	1
13069	RGS7BP	1
13070	RGS8	1
13071	RGS9	1
13072	RGS9BP	1
13073	RHAG	4.279735e-02
13074	RHBDD1	1
13075	RHBDD2	1
13076	RHBDD3	1
13077	RHBDF1	2.734543e-01
13078	RHBDF2	1.233952e-02
13079	RHBDL1	1
13080	RHBDL2	1
13081	RHBDL3	1
13082	RHBG	1
13083	RHCE	1
13084	RHCG	1
13085	RHD	1
13086	RHEB	1
13087	RHEBL1	1
13088	RHO	1
13089	RHOA	1.055381e-01
13090	RHOB	1
13091	RHOBTB1	1.087694e-01
13092	RHOBTB2	1
13093	RHOBTB3	1
13094	RHOC	1
13095	RHOD	1
13096	RHOF	1
13097	RHOG	1
13098	RHOH	1
Done

Running MutSig 2:
Scatter job 146: processing genes 13009 - 13098
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RFX3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.113205e-01	ci left: 7.153353e-03	ci right 1.094096e-02	k: 89	n:10000
Cons ci ratio: 7.557379e-02	ci left: 2.039253e-01	ci right 2.200428e-01	k: 2119	n:10000
KS ci ratio: 4.113205e-01	ci left: 7.153353e-03	ci right 1.094096e-02	k: 89	n:10000
RFX3   10000 perm   2 sec   (5681 perm/sec)   p_kst 8.900000e-03   p_cons 2.119000e-01   p_joint 8.900000e-03

Joint ci ratio: 2.723712e-01	ci left: 8.854025e-03	ci right 1.169107e-02	k: 204	n:20000
Cons ci ratio: 5.931176e-02	ci left: 1.739067e-01	ci right 1.845867e-01	k: 3584	n:20000
KS ci ratio: 2.723712e-01	ci left: 8.854025e-03	ci right 1.169107e-02	k: 204	n:20000
RFX3   20000 perm   6 sec   (3390 perm/sec)   p_kst 1.020000e-02   p_cons 1.792000e-01   p_joint 1.020000e-02

Joint ci ratio: 2.259452e-01	ci left: 8.810667e-03	ci right 1.108575e-02	k: 297	n:30000
Cons ci ratio: 4.827774e-02	ci left: 1.757991e-01	ci right 1.845296e-01	k: 5404	n:30000
KS ci ratio: 2.259452e-01	ci left: 8.810667e-03	ci right 1.108575e-02	k: 297	n:30000
RFX3   30000 perm   8 sec   (3675 perm/sec)   p_kst 9.900000e-03   p_cons 1.801333e-01   p_joint 9.900000e-03

Joint ci ratio: 1.937954e-01	ci left: 9.143308e-03	ci right 1.112878e-02	k: 404	n:40000
Cons ci ratio: 4.158712e-02	ci left: 1.779567e-01	ci right 1.855395e-01	k: 7269	n:40000
KS ci ratio: 1.937954e-01	ci left: 9.143308e-03	ci right 1.112878e-02	k: 404	n:40000
RFX3   40000 perm   10 sec   (3842 perm/sec)   p_kst 1.010000e-02   p_cons 1.817250e-01   p_joint 1.010000e-02

Joint ci ratio: 1.239854e-01	ci left: 1.838351e-02	ci right 2.083271e-02	k: 979	n:50000
Cons ci ratio: 3.715050e-02	ci left: 1.787258e-01	ci right 1.855112e-01	k: 9105	n:50000
KS ci ratio: 1.723502e-01	ci left: 9.356953e-03	ci right 1.114060e-02	k: 511	n:50000
RFX3   50000 perm   13 sec   (3930 perm/sec)   p_kst 1.022000e-02   p_cons 1.821000e-01   p_joint 1.958000e-02

Joint ci ratio: 1.568701e-01	ci left: 9.491530e-03	ci right 1.112303e-02	k: 617	n:60000
Cons ci ratio: 3.376300e-02	ci left: 1.803436e-01	ci right 1.865537e-01	k: 11006	n:60000
KS ci ratio: 1.568701e-01	ci left: 9.491530e-03	ci right 1.112303e-02	k: 617	n:60000
RFX3   60000 perm   15 sec   (3976 perm/sec)   p_kst 1.028333e-02   p_cons 1.834333e-01   p_joint 1.028333e-02

Joint ci ratio: 1.034867e-01	ci left: 1.904529e-02	ci right 2.113762e-02	k: 1405	n:70000
Cons ci ratio: 3.138802e-02	ci left: 1.793465e-01	ci right 1.850798e-01	k: 12754	n:70000
KS ci ratio: 1.431420e-01	ci left: 9.840773e-03	ci right 1.137163e-02	k: 741	n:70000
RFX3   70000 perm   18 sec   (3993 perm/sec)   p_kst 1.058571e-02   p_cons 1.822000e-01   p_joint 2.007143e-02

Joint ci ratio: 9.655365e-02	ci left: 1.921190e-02	ci right 2.117311e-02	k: 1614	n:80000
Cons ci ratio: 2.933024e-02	ci left: 1.798412e-01	ci right 1.852069e-01	k: 14601	n:80000
KS ci ratio: 1.337379e-01	ci left: 9.913980e-03	ci right 1.134684e-02	k: 849	n:80000
RFX3   80000 perm   20 sec   (3987 perm/sec)   p_kst 1.061250e-02   p_cons 1.825125e-01   p_joint 2.017500e-02

Joint ci ratio: 4.104418e-03	ci left: 9.083134e-01	ci right 9.120601e-01	k: 81918	n:90000
Cons ci ratio: 2.772848e-02	ci left: 1.791855e-01	ci right 1.842350e-01	k: 16353	n:90000
KS ci ratio: 1.270496e-01	ci left: 9.801280e-03	ci right 1.114167e-02	k: 941	n:90000
RFX3   90000 perm   23 sec   (3973 perm/sec)   p_kst 1.045556e-02   p_cons 1.817000e-01   p_joint 9.102000e-01

Joint ci ratio: 6.146001e-02	ci left: 3.788731e-02	ci right 4.029952e-02	k: 3908	n:100000
Cons ci ratio: 2.627473e-02	ci left: 1.796625e-01	ci right 1.844559e-01	k: 18205	n:100000
KS ci ratio: 1.209197e-01	ci left: 9.770757e-03	ci right 1.103788e-02	k: 1039	n:100000
RFX3   100000 perm   25 sec   (3949 perm/sec)   p_kst 1.039000e-02   p_cons 1.820500e-01   p_joint 3.908000e-02

Joint ci ratio: 3.715861e-03	ci left: 9.083484e-01	ci right 9.117390e-01	k: 100106	n:110000
Cons ci ratio: 2.502494e-02	ci left: 1.800946e-01	ci right 1.846676e-01	k: 20061	n:110000
KS ci ratio: 1.149882e-01	ci left: 9.853036e-03	ci right 1.106389e-02	k: 1149	n:110000
RFX3   110000 perm   28 sec   (3918 perm/sec)   p_kst 1.044545e-02   p_cons 1.823727e-01   p_joint 9.100545e-01

Joint ci ratio: 2.587820e-03	ci left: 9.490637e-01	ci right 9.515311e-01	k: 114037	n:120000
Cons ci ratio: 2.392135e-02	ci left: 1.806665e-01	ci right 1.850489e-01	k: 21942	n:120000
KS ci ratio: 1.100284e-01	ci left: 9.890441e-03	ci right 1.105007e-02	k: 1255	n:120000
RFX3   120000 perm   31 sec   (3883 perm/sec)   p_kst 1.045833e-02   p_cons 1.828500e-01   p_joint 9.503083e-01

Joint ci ratio: 2.483060e-03	ci left: 9.492369e-01	ci right 9.516045e-01	k: 123556	n:130000
Cons ci ratio: 2.301524e-02	ci left: 1.803347e-01	ci right 1.845411e-01	k: 23716	n:130000
KS ci ratio: 1.064924e-01	ci left: 9.765746e-03	ci right 1.087165e-02	k: 1340	n:130000
RFX3   130000 perm   34 sec   (3846 perm/sec)   p_kst 1.030769e-02   p_cons 1.824308e-01   p_joint 9.504308e-01

Joint ci ratio: 5.194622e-02	ci left: 3.806948e-02	ci right 4.010681e-02	k: 5471	n:140000
Cons ci ratio: 2.216975e-02	ci left: 1.805224e-01	ci right 1.845765e-01	k: 25556	n:140000
KS ci ratio: 1.026960e-01	ci left: 9.770752e-03	ci right 1.083539e-02	k: 1441	n:140000
RFX3   140000 perm   37 sec   (3808 perm/sec)   p_kst 1.029286e-02   p_cons 1.825429e-01   p_joint 3.907857e-02

Joint ci ratio: 2.309394e-03	ci left: 9.494104e-01	ci right 9.516121e-01	k: 142578	n:150000
Cons ci ratio: 2.144125e-02	ci left: 1.802693e-01	ci right 1.841830e-01	k: 27333	n:150000
KS ci ratio: 9.940904e-02	ci left: 9.749687e-03	ci right 1.077604e-02	k: 1538	n:150000
RFX3   150000 perm   40 sec   (3769 perm/sec)   p_kst 1.025333e-02   p_cons 1.822200e-01   p_joint 9.505200e-01

Outputting figure to mutsig2_images.part000000000146/RFX3.2_2470_150000_0.010253_0.18222_0.95052.png
                gene_name: RFX3
               theta_stop: 0.099 
                    nperm: 150000 
                     p_ks: 0.010 
        ci_ks_bounds_left: 0.0097 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.95 

Current progress: 25 percent done.
RGAG1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.437940e-01	ci left: 2.212298e-02	ci right 2.835777e-02	k: 251	n:10000
Cons ci ratio: 3.527114e-01	ci left: 1.005013e-02	ci right 1.444087e-02	k: 121	n:10000
KS ci ratio: 3.648198e-02	ci left: 5.259661e-01	ci right 5.456130e-01	k: 5358	n:10000
RGAG1   10000 perm   2 sec   (5469 perm/sec)   p_kst 5.358000e-01   p_cons 1.210000e-02   p_joint 2.510000e-02

Joint ci ratio: 2.007894e-01	ci left: 1.682030e-02	ci right 2.062146e-02	k: 373	n:20000
Cons ci ratio: 2.488949e-01	ci left: 1.072482e-02	ci right 1.381940e-02	k: 244	n:20000
KS ci ratio: 2.590490e-02	ci left: 5.268068e-01	ci right 5.406834e-01	k: 10675	n:20000
RGAG1   20000 perm   4 sec   (4927 perm/sec)   p_kst 5.337500e-01   p_cons 1.220000e-02   p_joint 1.865000e-02

Joint ci ratio: 1.745493e-01	ci left: 1.508879e-02	ci right 1.800592e-02	k: 495	n:30000
Cons ci ratio: 1.901594e-01	ci left: 1.263752e-02	ci right 1.532449e-02	k: 418	n:30000
KS ci ratio: 2.114112e-02	ci left: 5.283354e-01	ci right 5.396580e-01	k: 16020	n:30000
RGAG1   30000 perm   7 sec   (4614 perm/sec)   p_kst 5.340000e-01   p_cons 1.393333e-02   p_joint 1.650000e-02

Joint ci ratio: 1.513199e-01	ci left: 1.525024e-02	ci right 1.777065e-02	k: 659	n:40000
Cons ci ratio: 1.650836e-01	ci left: 1.275159e-02	ci right 1.506977e-02	k: 555	n:40000
KS ci ratio: 1.822910e-02	ci left: 5.312730e-01	ci right 5.410718e-01	k: 21447	n:40000
RGAG1   40000 perm   9 sec   (4497 perm/sec)   p_kst 5.361750e-01   p_cons 1.387500e-02   p_joint 1.647500e-02

Joint ci ratio: 1.350125e-01	ci left: 1.545955e-02	ci right 1.771708e-02	k: 828	n:50000
Cons ci ratio: 1.496330e-01	ci left: 1.252605e-02	ci right 1.457100e-02	k: 676	n:50000
KS ci ratio: 1.630979e-02	ci left: 5.316368e-01	ci right 5.403990e-01	k: 26801	n:50000
RGAG1   50000 perm   11 sec   (4400 perm/sec)   p_kst 5.360200e-01   p_cons 1.352000e-02   p_joint 1.656000e-02

Joint ci ratio: 1.320865e-01	ci left: 1.351033e-02	ci right 1.543705e-02	k: 867	n:60000
Cons ci ratio: 1.381909e-01	ci left: 1.231815e-02	ci right 1.416271e-02	k: 793	n:60000
KS ci ratio: 1.483362e-02	ci left: 5.338673e-01	ci right 5.418624e-01	k: 32272	n:60000
RGAG1   60000 perm   14 sec   (4309 perm/sec)   p_kst 5.378667e-01   p_cons 1.321667e-02   p_joint 1.445000e-02

Joint ci ratio: 1.320711e-01	ci left: 1.160715e-02	ci right 1.326221e-02	k: 869	n:70000
Cons ci ratio: 1.381475e-01	ci left: 1.058533e-02	ci right 1.216984e-02	k: 795	n:70000
KS ci ratio: 1.370833e-02	ci left: 5.350699e-01	ci right 5.424697e-01	k: 37714	n:70000
RGAG1   70000 perm   17 sec   (4227 perm/sec)   p_kst 5.387714e-01   p_cons 1.135714e-02   p_joint 1.241429e-02

Joint ci ratio: 1.260881e-01	ci left: 1.118430e-02	ci right 1.270140e-02	k: 954	n:80000
Cons ci ratio: 1.294929e-01	ci left: 1.059117e-02	ci right 1.206959e-02	k: 905	n:80000
KS ci ratio: 1.285131e-02	ci left: 5.342125e-01	ci right 5.411347e-01	k: 43014	n:80000
RGAG1   80000 perm   19 sec   (4152 perm/sec)   p_kst 5.376750e-01   p_cons 1.131250e-02   p_joint 1.192500e-02

Joint ci ratio: 1.145507e-01	ci left: 1.210817e-02	ci right 1.359015e-02	k: 1155	n:90000
Cons ci ratio: 1.227128e-01	ci left: 1.052271e-02	ci right 1.190907e-02	k: 1008	n:90000
KS ci ratio: 1.213146e-02	ci left: 5.337912e-01	ci right 5.403175e-01	k: 48335	n:90000
RGAG1   90000 perm   22 sec   (4079 perm/sec)   p_kst 5.370556e-01   p_cons 1.120000e-02   p_joint 1.283333e-02

Joint ci ratio: 1.136838e-01	ci left: 1.108159e-02	ci right 1.242695e-02	k: 1174	n:100000
Cons ci ratio: 1.163690e-01	ci left: 1.056667e-02	ci right 1.188191e-02	k: 1121	n:100000
KS ci ratio: 1.149703e-02	ci left: 5.344737e-01	ci right 5.406641e-01	k: 53757	n:100000
RGAG1   100000 perm   25 sec   (4012 perm/sec)   p_kst 5.375700e-01   p_cons 1.121000e-02   p_joint 1.174000e-02

Joint ci ratio: 1.067952e-01	ci left: 1.145339e-02	ci right 1.275434e-02	k: 1330	n:110000
Cons ci ratio: 1.106457e-01	ci left: 1.065721e-02	ci right 1.191421e-02	k: 1240	n:110000
KS ci ratio: 1.098019e-02	ci left: 5.337932e-01	ci right 5.396958e-01	k: 59042	n:110000
RGAG1   110000 perm   28 sec   (3954 perm/sec)   p_kst 5.367455e-01   p_cons 1.127273e-02   p_joint 1.209091e-02

Joint ci ratio: 1.029689e-01	ci left: 1.131849e-02	ci right 1.255527e-02	k: 1431	n:120000
Cons ci ratio: 1.062459e-01	ci left: 1.062037e-02	ci right 1.182010e-02	k: 1345	n:120000
KS ci ratio: 1.050349e-02	ci left: 5.343572e-01	ci right 5.400077e-01	k: 64462	n:120000
RGAG1   120000 perm   31 sec   (3893 perm/sec)   p_kst 5.371833e-01   p_cons 1.120833e-02   p_joint 1.192500e-02

Joint ci ratio: 9.949338e-02	ci left: 1.121256e-02	ci right 1.239398e-02	k: 1533	n:130000
Cons ci ratio: 1.020483e-01	ci left: 1.065002e-02	ci right 1.180271e-02	k: 1458	n:130000
KS ci ratio: 1.009313e-02	ci left: 5.343849e-01	ci right 5.398135e-01	k: 69823	n:130000
RGAG1   130000 perm   34 sec   (3837 perm/sec)   p_kst 5.371000e-01   p_cons 1.121538e-02   p_joint 1.179231e-02

Joint ci ratio: 9.534995e-02	ci left: 1.135947e-02	ci right 1.250374e-02	k: 1669	n:140000
Cons ci ratio: 9.872561e-02	ci left: 1.058564e-02	ci right 1.169189e-02	k: 1558	n:140000
KS ci ratio: 9.736894e-03	ci left: 5.339264e-01	ci right 5.391578e-01	k: 75116	n:140000
RGAG1   140000 perm   37 sec   (3784 perm/sec)   p_kst 5.365429e-01   p_cons 1.112857e-02   p_joint 1.192143e-02

Outputting figure to mutsig2_images.part000000000146/RGAG1.2_4175_140000_0.53654_0.011129_0.011921.png
                gene_name: RGAG1
               theta_stop: 0.099 
                    nperm: 140000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.011 
      ci_cons_bounds_left: 0.011 
     ci_cons_bounds_right: 0.012 
                  p_joint: 0.012 
     ci_joint_bounds_left: 0.011 
    ci_joint_bounds_right: 0.013 

Current progress: 50 percent done.
RGS17
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.433436e-02	ci left: 8.756178e-01	ci right 8.883587e-01	k: 8821	n:10000
KS ci ratio: 8.978231e-02	ci left: 1.528644e-01	ci right 1.673342e-01	k: 1600	n:10000
RGS17   10000 perm   1 sec   (7139 perm/sec)   p_kst 1.600000e-01   p_cons 8.821000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000146/RGS17.2_649_10000_0.16_0.8821_1.png
                gene_name: RGS17
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
RHBDF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.517934e-02	ci left: 6.988779e-01	ci right 7.168009e-01	k: 7079	n:10000
Cons ci ratio: 1.385488e-02	ci left: 8.826795e-01	ci right 8.950929e-01	k: 8890	n:10000
KS ci ratio: 4.854499e-02	ci left: 3.850022e-01	ci right 4.042592e-01	k: 3946	n:10000
RHBDF2   10000 perm   2 sec   (5943 perm/sec)   p_kst 3.946000e-01   p_cons 8.890000e-01   p_joint 7.079000e-01

Outputting figure to mutsig2_images.part000000000146/RHBDF2.2_2639_10000_0.3946_0.889_0.7079.png
                gene_name: RHBDF2
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000146
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 146 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4398287: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000147> was used as the working directory.
Started at Wed Oct 24 16:16:12 2012
Results reported at Wed Oct 24 16:17:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000147.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000147.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 147  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000147.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    122.08 sec.
    Max Memory :      1227 MB
    Max Swap   :      3940 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
147
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 147
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 147: processing genes 13099 - 13187
Calculating significance of each gene.
Using projection method.
13099	RHOJ	1
13100	RHOQ	1
13101	RHOT1	1
13102	RHOT2	3.211427e-02
13103	RHOU	7.350186e-02
13104	RHOV	4.143530e-02
13105	RHOXF1	5.465159e-03
13106	RHOXF2	1
13107	RHOXF2B	1
13108	RHPN1	1
13109	RHPN2	1
13110	RIBC1	1
13111	RIBC2	1
13112	RIC3	1
13113	RIC8A	1
13114	RIC8B	1
13115	RICH2	2.901505e-01
13116	RICTOR	5.956273e-01
13117	RIF1	1
13118	RILP	1
13119	RILPL1	1
13120	RILPL2	1
13121	RIMBP2	1
13122	RIMKLA	1
13123	RIMKLB	1
13124	RIMS1	2.235166e-01
13125	RIMS2	1
13126	RIMS3	1
13127	RIMS4	1
13128	RIN1	1
13129	RIN2	1
13130	RIN3	1
13131	RING1	1
13132	RINL	1
13133	RINT1	1
13134	RIOK1	2.637686e-01
13135	RIOK2	9.626679e-02
13136	RIOK3	1
13137	RIPK1	1
13138	RIPK2	1
13139	RIPK3	1
13140	RIPK4	1
13141	RIPPLY1	1
13142	RIPPLY2	1
13143	RIT1	4.481236e-02
13144	RIT2	1
13145	RLBP1	1
13146	RLF	4.035802e-01
13147	RLIM	1
13148	RLN1	1
13149	RLN2	1
13150	RLN3	1
13151	RLTPR	3.522774e-01
13152	RMI1	1
13153	RMND1	8.051739e-02
13154	RMND5A	1
13155	RMND5B	1
13156	RNASE1	1
13157	RNASE10	1
13158	RNASE11	1
13159	RNASE12	1
13160	RNASE13	1
13161	RNASE2	1
13162	RNASE3	1
13163	RNASE4	1
13164	RNASE6	1
13165	RNASE7	1
13166	RNASE8	1
13167	RNASE9	1
13168	RNASEH1	1.075468e-02
13169	RNASEH2A	1
13170	RNASEH2B	1
13171	RNASEH2C	1
13172	RNASEK	1
13173	RNASEL	1
13174	RNASEN	1
13175	RNASET2	1
13176	RND1	1
13177	RND2	1
13178	RND3	1
13179	RNF10	1
13180	RNF103	1
13181	RNF11	1
13182	RNF111	4.277577e-01
13183	RNF112	1
13184	RNF113A	1.008885e-01
13185	RNF113B	1
13186	RNF114	1
13187	RNF115	5.567379e-02
Done

Running MutSig 2:
Scatter job 147: processing genes 13099 - 13187
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RHOT2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.675160e-02	ci left: 3.137382e-01	ci right 3.321651e-01	k: 3229	n:10000
Cons ci ratio: 7.152117e-02	ci left: 2.226698e-01	ci right 2.392872e-01	k: 2309	n:10000
KS ci ratio: 6.463583e-02	ci left: 2.601291e-01	ci right 2.776057e-01	k: 2688	n:10000
RHOT2   10000 perm   2 sec   (6191 perm/sec)   p_kst 2.688000e-01   p_cons 2.309000e-01   p_joint 3.229000e-01

Outputting figure to mutsig2_images.part000000000147/RHOT2.2_1933_10000_0.2688_0.2309_0.3229.png
                gene_name: RHOT2
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000147
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 147 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4398290: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000148> was used as the working directory.
Started at Wed Oct 24 16:16:12 2012
Results reported at Wed Oct 24 16:18:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000148.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000148.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 148  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000148.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    165.31 sec.
    Max Memory :      1502 MB
    Max Swap   :      3966 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
148
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 148
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 148: processing genes 13188 - 13277
Calculating significance of each gene.
Using projection method.
13188	RNF121	1
13189	RNF122	1
13190	RNF123	9.598941e-03
13191	RNF125	1
13192	RNF126	2.445489e-02
13193	RNF128	1
13194	RNF13	1
13195	RNF130	1
13196	RNF133	1
13197	RNF135	5.935888e-02
13198	RNF138	1
13199	RNF139	1
13200	RNF14	1.687210e-02
13201	RNF141	1
13202	RNF144A	1
13203	RNF144B	1
13204	RNF145	1
13205	RNF146	1
13206	RNF148	1
13207	RNF149	1.443148e-01
13208	RNF150	9.488998e-02
13209	RNF151	3.141921e-02
13210	RNF152	1
13211	RNF157	1.810933e-02
13212	RNF160	1
13213	RNF165	1
13214	RNF166	1
13215	RNF167	1
13216	RNF168	1
13217	RNF169	1
13218	RNF17	5.726098e-01
13219	RNF170	1
13220	RNF175	1
13221	RNF180	1
13222	RNF181	1
13223	RNF182	1.307234e-01
13224	RNF183	1
13225	RNF185	1
13226	RNF186	3.505522e-02
13227	RNF19A	2.346653e-01
13228	RNF19B	1.078056e-01
13229	RNF2	1
13230	RNF20	1
13231	RNF207	1
13232	RNF208	1
13233	RNF212	1
13234	RNF213	1
13235	RNF214	1
13236	RNF215	1
13237	RNF216	1.996047e-01
13238	RNF217	1
13239	RNF219	1.267924e-01
13240	RNF220	8.013748e-02
13241	RNF24	1
13242	RNF25	1
13243	RNF26	1
13244	RNF31	1.520392e-01
13245	RNF32	1.899110e-01
13246	RNF34	1
13247	RNF38	1
13248	RNF39	4.227468e-02
13249	RNF4	1
13250	RNF40	2.037470e-01
13251	RNF41	1
13252	RNF43	1
13253	RNF44	1
13254	RNF5	1
13255	RNF6	1
13256	RNF7	1
13257	RNF8	1
13258	RNFT1	1
13259	RNFT2	1
13260	RNGTT	1
13261	RNH1	1
13262	RNLS	1
13263	RNMT	2.330576e-01
13264	RNMTL1	1.739417e-01
13265	RNPC3	1
13266	RNPEP	1
13267	RNPEPL1	1
13268	RNPS1	1
13269	ROBLD3	5.917230e-02
13270	ROBO1	1.698497e-01
13271	ROBO2	5.185638e-01
13272	ROBO3	6.934809e-02
13273	ROBO4	4.108565e-01
13274	ROCK1	3.318697e-03
13275	ROCK2	1.282371e-01
13276	ROD1	1
13277	ROGDI	1
Done

Running MutSig 2:
Scatter job 148: processing genes 13188 - 13277
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RNF123
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.613146e-02	ci left: 5.307719e-01	ci right 5.504044e-01	k: 5406	n:10000
Cons ci ratio: 9.727431e-02	ci left: 1.328630e-01	ci right 1.465476e-01	k: 1396	n:10000
KS ci ratio: 1.764158e-02	ci left: 8.241191e-01	ci right 8.388872e-01	k: 8316	n:10000
RNF123   10000 perm   2 sec   (4932 perm/sec)   p_kst 8.316000e-01   p_cons 1.396000e-01   p_joint 5.406000e-01

Outputting figure to mutsig2_images.part000000000148/RNF123.3_4097_10000_0.8316_0.1396_0.5406.png
                gene_name: RNF123
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.84 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 12 percent done.
ROCK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.564363e-02	ci left: 4.146860e-01	ci right 4.341580e-01	k: 4244	n:10000
Cons ci ratio: 3.476387e-02	ci left: 5.499041e-01	ci right 5.694611e-01	k: 5597	n:10000
KS ci ratio: 6.163475e-02	ci left: 2.790384e-01	ci right 2.968853e-01	k: 2879	n:10000
ROCK1   10000 perm   2 sec   (5032 perm/sec)   p_kst 2.879000e-01   p_cons 5.597000e-01   p_joint 4.244000e-01

Outputting figure to mutsig2_images.part000000000148/ROCK1.3_4197_10000_0.2879_0.5597_0.4244.png
                gene_name: ROCK1
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 25 percent done.
RNF14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.618837e-03	ci left: 9.839328e-01	ci right 9.885776e-01	k: 9864	n:10000
Cons ci ratio: 4.338240e-02	ci left: 4.396164e-01	ci right 4.592131e-01	k: 4494	n:10000
KS ci ratio: 1.811802e-02	ci left: 8.163920e-01	ci right 8.314188e-01	k: 8240	n:10000
RNF14   10000 perm   2 sec   (6348 perm/sec)   p_kst 8.240000e-01   p_cons 4.494000e-01   p_joint 9.864000e-01

Outputting figure to mutsig2_images.part000000000148/RNF14.2_1453_10000_0.824_0.4494_0.9864.png
                gene_name: RNF14
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 38 percent done.
RNF157
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.186533e-02	ci left: 7.542360e-01	ci right 7.710108e-01	k: 7627	n:10000
Cons ci ratio: 3.269431e-02	ci left: 5.799842e-01	ci right 5.993635e-01	k: 5897	n:10000
KS ci ratio: 3.659946e-02	ci left: 5.243644e-01	ci right 5.440157e-01	k: 5342	n:10000
RNF157   10000 perm   2 sec   (6383 perm/sec)   p_kst 5.342000e-01   p_cons 5.897000e-01   p_joint 7.627000e-01

Outputting figure to mutsig2_images.part000000000148/RNF157.2_2116_10000_0.5342_0.5897_0.7627.png
                gene_name: RNF157
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.76 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.77 

Current progress: 50 percent done.
RNF17
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.005121e-02	ci left: 6.202494e-01	ci right 6.392749e-01	k: 6298	n:10000
Cons ci ratio: 1.274153e-02	ci left: 8.985712e-01	ci right 9.101920e-01	k: 9045	n:10000
KS ci ratio: 6.875699e-02	ci left: 2.367933e-01	ci right 2.537553e-01	k: 2452	n:10000
RNF17   10000 perm   2 sec   (5240 perm/sec)   p_kst 2.452000e-01   p_cons 9.045000e-01   p_joint 6.298000e-01

Outputting figure to mutsig2_images.part000000000148/RNF17.2_5012_10000_0.2452_0.9045_0.6298.png
                gene_name: RNF17
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 62 percent done.
RNF32
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.242548e-02	ci left: 2.738884e-01	ci right 2.916384e-01	k: 2827	n:10000
Cons ci ratio: 1.158000e-02	ci left: 9.143035e-01	ci right 9.250505e-01	k: 9198	n:10000
KS ci ratio: 1.969557e-01	ci left: 3.433772e-02	ci right 4.193438e-02	k: 380	n:10000
RNF32   10000 perm   1 sec   (6795 perm/sec)   p_kst 3.800000e-02   p_cons 9.198000e-01   p_joint 2.827000e-01

Joint ci ratio: 2.574400e-02	ci left: 5.299094e-01	ci right 5.437799e-01	k: 10737	n:20000
Cons ci ratio: 7.682208e-03	ci left: 9.250460e-01	ci right 9.322288e-01	k: 18574	n:20000
KS ci ratio: 1.387052e-01	ci left: 3.573081e-02	ci right 4.110445e-02	k: 767	n:20000
RNF32   20000 perm   4 sec   (5375 perm/sec)   p_kst 3.835000e-02   p_cons 9.287000e-01   p_joint 5.368500e-01

Joint ci ratio: 6.287581e-02	ci left: 1.110820e-01	ci right 1.183262e-01	k: 3440	n:30000
Cons ci ratio: 6.294041e-03	ci left: 9.252544e-01	ci right 9.311291e-01	k: 27847	n:30000
KS ci ratio: 1.158942e-01	ci left: 3.460064e-02	ci right 3.888967e-02	k: 1101	n:30000
RNF32   30000 perm   6 sec   (5306 perm/sec)   p_kst 3.670000e-02   p_cons 9.282333e-01   p_joint 1.146667e-01

Joint ci ratio: 1.495023e-02	ci left: 6.274274e-01	ci right 6.369034e-01	k: 25287	n:40000
Cons ci ratio: 5.434541e-03	ci left: 9.260583e-01	ci right 9.311293e-01	k: 37145	n:40000
KS ci ratio: 1.008078e-01	ci left: 3.458588e-02	ci right 3.828181e-02	k: 1456	n:40000
RNF32   40000 perm   8 sec   (5025 perm/sec)   p_kst 3.640000e-02   p_cons 9.286250e-01   p_joint 6.321750e-01

Joint ci ratio: 3.348776e-02	ci left: 2.114852e-01	ci right 2.187079e-01	k: 10754	n:50000
Cons ci ratio: 4.849858e-03	ci left: 9.266327e-01	ci right 9.311574e-01	k: 46446	n:50000
KS ci ratio: 9.095222e-02	ci left: 3.418849e-02	ci right 3.746568e-02	k: 1790	n:50000
RNF32   50000 perm   10 sec   (4899 perm/sec)   p_kst 3.580000e-02   p_cons 9.289200e-01   p_joint 2.150800e-01

Outputting figure to mutsig2_images.part000000000148/RNF32.2_1121_50000_0.0358_0.92892_0.21508.png
                gene_name: RNF32
               theta_stop: 0.091 
                    nperm: 50000 
                     p_ks: 0.036 
        ci_ks_bounds_left: 0.034 
       ci_ks_bounds_right: 0.037 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 75 percent done.
RNF40
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.430567e-02	ci left: 4.292423e-01	ci right 4.487932e-01	k: 4390	n:10000
KS ci ratio: 4.361983e-02	ci left: 4.369227e-01	ci right 4.565083e-01	k: 4467	n:10000
RNF40   10000 perm   2 sec   (5687 perm/sec)   p_kst 4.467000e-01   p_cons 4.390000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000148/RNF40.2_3082_10000_0.4467_0.439_1.png
                gene_name: RNF40
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 88 percent done.
ROCK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.284443e-02	ci left: 8.971340e-01	ci right 9.088300e-01	k: 9031	n:10000
Cons ci ratio: 1.003866e-01	ci left: 1.256193e-01	ci right 1.389957e-01	k: 1322	n:10000
KS ci ratio: 4.008997e-02	ci left: 4.788572e-01	ci right 4.985494e-01	k: 4887	n:10000
ROCK2   10000 perm   3 sec   (3682 perm/sec)   p_kst 4.887000e-01   p_cons 1.322000e-01   p_joint 9.031000e-01

Joint ci ratio: 9.052424e-03	ci left: 8.994767e-01	ci right 9.077055e-01	k: 18073	n:20000
Cons ci ratio: 7.233016e-02	ci left: 1.233991e-01	ci right 1.327093e-01	k: 2560	n:20000
KS ci ratio: 2.811288e-02	ci left: 4.859476e-01	ci right 4.998544e-01	k: 9858	n:20000
ROCK2   20000 perm   6 sec   (3552 perm/sec)   p_kst 4.929000e-01   p_cons 1.280000e-01   p_joint 9.036500e-01

Outputting figure to mutsig2_images.part000000000148/ROCK2.2_4299_20000_0.4929_0.128_0.90365.png
                gene_name: ROCK2
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.91 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000148
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 148 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4398295: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000149> was used as the working directory.
Started at Wed Oct 24 16:16:18 2012
Results reported at Wed Oct 24 16:17:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000149.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000149.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 149  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000149.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     80.23 sec.
    Max Memory :      1034 MB
    Max Swap   :      3844 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
149
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 149
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 149: processing genes 13278 - 13367
Calculating significance of each gene.
Using projection method.
13278	ROM1	1
13279	ROMO1	1
13280	ROPN1	1
13281	ROPN1B	9.014258e-02
13282	ROPN1L	1
13283	ROR1	1
13284	ROR2	1.429483e-01
13285	RORA	1
13286	RORB	1
13287	RORC	2.031536e-01
13288	ROS1	2.153209e-01
13289	RP1	6.807375e-01
13290	RP1L1	5.456864e-01
13291	RP2	1
13292	RP9	1
13293	RPA1	1
13294	RPA2	1
13295	RPA3	1
13296	RPA4	1
13297	RPAIN	1
13298	RPAP1	2.974985e-01
13299	RPAP2	5.979193e-02
13300	RPAP3	1
13301	RPE	1
13302	RPE65	1
13303	RPF1	1
13304	RPF2	1.270152e-01
13305	RPGR	9.459088e-02
13306	RPGRIP1	1.930370e-01
13307	RPGRIP1L	1
13308	RPH3A	1.676718e-01
13309	RPH3AL	1
13310	RPIA	1
13311	RPL10	2.412598e-02
13312	RPL10A	1
13313	RPL10L	1
13314	RPL11	1
13315	RPL12	1
13316	RPL13	1
13317	RPL13A	1.769712e-03
13318	RPL14	1
13319	RPL15	1
13320	RPL17	1
13321	RPL18	9.688912e-02
13322	RPL18A	1
13323	RPL19	1
13324	RPL21	1
13325	RPL22	1
13326	RPL22L1	1
13327	RPL23	1
13328	RPL23A	1
13329	RPL24	1
13330	RPL26	1
13331	RPL26L1	1
13332	RPL27	7.471413e-02
13333	RPL27A	1
13334	RPL28	1
13335	RPL29	1
13336	RPL3	1
13337	RPL30	1
13338	RPL31	1
13339	RPL32	1
13340	RPL34	1
13341	RPL35	1
13342	RPL35A	1
13343	RPL36	1
13344	RPL36A	1
13345	RPL36AL	1.261988e-02
13346	RPL37	1
13347	RPL37A	1
13348	RPL38	1
13349	RPL39	1
13350	RPL39L	1
13351	RPL3L	1
13352	RPL4	1
13353	RPL41	1
13354	RPL5	1
13355	RPL6	1.060535e-01
13356	RPL7	1
13357	RPL7A	1.004735e-01
13358	RPL7L1	1
13359	RPL8	1
13360	RPL9	1
13361	RPLP0	1
13362	RPLP1	1
13363	RPLP2	1
13364	RPN1	1
13365	RPN2	1
13366	RPP14	1
13367	RPP21	1
Done

Running MutSig 2:
Scatter job 149: processing genes 13278 - 13367
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ROS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.897772e-02	ci left: 6.371392e-01	ci right 6.559753e-01	k: 6466	n:10000
KS ci ratio: 3.957213e-02	ci left: 4.853532e-01	ci right 5.050496e-01	k: 4952	n:10000
ROS1   10000 perm   2 sec   (4500 perm/sec)   p_kst 4.952000e-01   p_cons 6.466000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000149/ROS1.2_7216_10000_0.4952_0.6466_1.png
                gene_name: ROS1
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
RPAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.092516e-02	ci left: 4.685668e-01	ci right 4.882458e-01	k: 4784	n:10000
KS ci ratio: 2.666089e-02	ci left: 6.744830e-01	ci right 6.928099e-01	k: 6837	n:10000
RPAP1   10000 perm   2 sec   (5852 perm/sec)   p_kst 6.837000e-01   p_cons 4.784000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000149/RPAP1.2_4278_10000_0.6837_0.4784_1.png
                gene_name: RPAP1
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
RPGR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.665833e-02	ci left: 5.235635e-01	ci right 5.432170e-01	k: 5334	n:10000
Cons ci ratio: 2.844091e-02	ci left: 6.456895e-01	ci right 6.644201e-01	k: 6551	n:10000
KS ci ratio: 1.002121e-01	ci left: 1.260106e-01	ci right 1.394041e-01	k: 1326	n:10000
RPGR   10000 perm   2 sec   (6023 perm/sec)   p_kst 1.326000e-01   p_cons 6.551000e-01   p_joint 5.334000e-01

Joint ci ratio: 2.251793e-02	ci left: 5.955779e-01	ci right 6.091923e-01	k: 12048	n:20000
Cons ci ratio: 1.998934e-02	ci left: 6.512273e-01	ci right 6.644268e-01	k: 13157	n:20000
KS ci ratio: 7.129614e-02	ci left: 1.265990e-01	ci right 1.360085e-01	k: 2625	n:20000
RPGR   20000 perm   4 sec   (5375 perm/sec)   p_kst 1.312500e-01   p_cons 6.578500e-01   p_joint 6.024000e-01

Outputting figure to mutsig2_images.part000000000149/RPGR.2_4078_20000_0.13125_0.65785_0.6024.png
                gene_name: RPGR
               theta_stop: 0.071 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.61 

Current progress: 75 percent done.
RPL13A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.946119e-02	ci left: 6.294971e-01	ci right 6.484219e-01	k: 6390	n:10000
Cons ci ratio: 2.484493e-02	ci left: 7.044263e-01	ci right 7.222493e-01	k: 7134	n:10000
KS ci ratio: 6.081832e-02	ci left: 2.844871e-01	ci right 3.024334e-01	k: 2934	n:10000
RPL13A   10000 perm   1 sec   (7372 perm/sec)   p_kst 2.934000e-01   p_cons 7.134000e-01   p_joint 6.390000e-01

Outputting figure to mutsig2_images.part000000000149/RPL13A.2_644_10000_0.2934_0.7134_0.639.png
                gene_name: RPL13A
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000149
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 149 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 4398297: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000150> was used as the working directory.
Started at Wed Oct 24 16:16:20 2012
Results reported at Wed Oct 24 16:18:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000150.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000150.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 150  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000150.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    188.32 sec.
    Max Memory :      1248 MB
    Max Swap   :      4051 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
150
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 150
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 150: processing genes 13368 - 13456
Calculating significance of each gene.
Using projection method.
13368	RPP25	1
13369	RPP30	1
13370	RPP38	1
13371	RPP40	1
13372	RPRD1A	1
13373	RPRD1B	1
13374	RPRD2	1
13375	RPRM	1
13376	RPRML	1
13377	RPS10	9.127831e-02
13378	RPS11	1
13379	RPS12	1
13380	RPS13	1
13381	RPS14	1
13382	RPS15	1
13383	RPS15A	1
13384	RPS16	1
13385	RPS18	1
13386	RPS19	1
13387	RPS19BP1	1
13388	RPS2	1
13389	RPS20	4.121341e-02
13390	RPS21	1
13391	RPS23	5.388932e-02
13392	RPS24	1
13393	RPS25	1
13394	RPS26	1
13395	RPS27	1
13396	RPS27A	1
13397	RPS27L	1
13398	RPS28	1
13399	RPS29	1
13400	RPS3	1
13401	RPS3A	1
13402	RPS4X	8.792650e-02
13403	RPS5	1
13404	RPS6	1
13405	RPS6KA1	3.388142e-01
13406	RPS6KA2	1
13407	RPS6KA3	1
13408	RPS6KA4	1
13409	RPS6KA5	1
13410	RPS6KA6	1
13411	RPS6KB1	1
13412	RPS6KB2	1
13413	RPS6KC1	1
13414	RPS6KL1	1
13415	RPS7	1
13416	RPS8	1
13417	RPS9	1
13418	RPSA	1
13419	RPTN	1
13420	RPTOR	1
13421	RPUSD1	1
13422	RPUSD2	1
13423	RPUSD3	1
13424	RPUSD4	1
13425	RQCD1	1
13426	RRAD	1
13427	RRAGA	1
13428	RRAGB	1
13429	RRAGC	1
13430	RRAGD	1
13431	RRAS	1
13432	RRAS2	1
13433	RRBP1	1
13434	RREB1	1
13435	RRH	1
13436	RRM1	1
13437	RRM2	1
13438	RRM2B	1
13439	RRN3	1.198648e-01
13440	RRP1	1
13441	RRP12	9.773502e-02
13442	RRP15	1
13443	RRP1B	7.118792e-02
13444	RRP7A	1
13445	RRP8	1
13446	RRP9	1.163939e-01
13447	RRS1	1
13448	RS1	5.034212e-02
13449	RSAD1	1
13450	RSAD2	1
13451	RSBN1	1
13452	RSBN1L	1
13453	RSC1A1	1
13454	RSF1	4.565828e-01
13455	RSL1D1	1
13456	RSL24D1	1
Done

Running MutSig 2:
Scatter job 150: processing genes 13368 - 13456
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RRP12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.019158e-03	ci left: 9.453375e-01	ci right 9.539982e-01	k: 9498	n:10000
Cons ci ratio: 4.361100e-02	ci left: 4.370225e-01	ci right 4.566085e-01	k: 4468	n:10000
KS ci ratio: 1.062743e-02	ci left: 9.264756e-01	ci right 9.364713e-01	k: 9316	n:10000
RRP12   10000 perm   2 sec   (4683 perm/sec)   p_kst 9.316000e-01   p_cons 4.468000e-01   p_joint 9.498000e-01

Outputting figure to mutsig2_images.part000000000150/RRP12.2_4030_10000_0.9316_0.4468_0.9498.png
                gene_name: RRP12
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.95 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000150
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 150 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1535>
Subject: Job 4398302: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1535>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000151> was used as the working directory.
Started at Wed Oct 24 16:16:23 2012
Results reported at Wed Oct 24 16:19:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000151.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000151.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 151  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000151.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    222.08 sec.
    Max Memory :      1304 MB
    Max Swap   :      4060 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
151
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 151
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 151: processing genes 13457 - 13546
Calculating significance of each gene.
Using projection method.
13457	RSPH1	1
13458	RSPH10B	1
13459	RSPH10B2	1
13460	RSPH3	1
13461	RSPH4A	1
13462	RSPH6A	5.689706e-02
13463	RSPH9	1
13464	RSPO1	1
13465	RSPO2	1
13466	RSPO3	1.253242e-01
13467	RSPO4	1
13468	RSPRY1	1
13469	RSRC1	1.342756e-01
13470	RSRC2	1
13471	RSU1	1
13472	RTBDN	1
13473	RTCD1	1
13474	RTDR1	1
13475	RTEL1	1
13476	RTF1	1
13477	RTKN	1
13478	RTKN2	1
13479	RTN1	6.530126e-02
13480	RTN2	7.338710e-02
13481	RTN3	1.509488e-01
13482	RTN4	1.206003e-01
13483	RTN4IP1	1
13484	RTN4R	1
13485	RTN4RL1	1
13486	RTN4RL2	1
13487	RTP1	1
13488	RTP2	1
13489	RTP3	1
13490	RTP4	1
13491	RTTN	1
13492	RUFY1	1.353873e-01
13493	RUFY2	1
13494	RUFY3	1
13495	RUFY4	1
13496	RUNDC1	1
13497	RUNDC2A	1
13498	RUNDC3A	1
13499	RUNDC3B	1
13500	RUNX1	1
13501	RUNX1T1	7.894197e-02
13502	RUNX2	3.504680e-02
13503	RUNX3	1
13504	RUSC1	1
13505	RUSC2	4.674989e-02
13506	RUVBL1	1
13507	RUVBL2	1
13508	RWDD1	1
13509	RWDD2A	2.500492e-02
13510	RWDD2B	1
13511	RWDD3	1
13512	RWDD4A	1
13513	RXFP1	1
13514	RXFP2	3.302229e-01
13515	RXFP3	1
13516	RXFP4	1
13517	RXRA	1
13518	RXRB	1
13519	RXRG	1
13520	RYBP	1
13521	RYK	1
13522	RYR1	7.804386e-01
13523	RYR2	1.589980e-03
13524	RYR3	9.220671e-01
13525	S100A1	1.139952e-02
13526	S100A10	1
13527	S100A11	1
13528	S100A12	1
13529	S100A13	1
13530	S100A14	1
13531	S100A16	1
13532	S100A2	1
13533	S100A3	1
13534	S100A4	1
13535	S100A5	1
13536	S100A6	1
13537	S100A7	1
13538	S100A7A	6.071627e-02
13539	S100A7L2	1
13540	S100A8	1
13541	S100A9	1
13542	S100B	1
13543	S100G	1
13544	S100P	1
13545	S100PBP	1
13546	S100Z	4.531944e-02
Done

Running MutSig 2:
Scatter job 151: processing genes 13457 - 13546
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RYR2
Processing conservation and coverage...
65% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.265054e-01	ci left: 8.203252e-02	ci right 9.320908e-02	k: 875	n:10000
Cons ci ratio: 4.091696e-02	ci left: 4.686667e-01	ci right 4.883458e-01	k: 4785	n:10000
KS ci ratio: 1.943197e-01	ci left: 3.529041e-02	ci right 4.298104e-02	k: 390	n:10000
RYR2   10000 perm   5 sec   (2086 perm/sec)   p_kst 3.900000e-02   p_cons 4.785000e-01   p_joint 8.750000e-02

Joint ci ratio: 9.859149e-02	ci left: 6.962745e-02	ci right 7.689721e-02	k: 1464	n:20000
Cons ci ratio: 2.889441e-02	ci left: 4.722549e-01	ci right 4.861511e-01	k: 9584	n:20000
KS ci ratio: 1.371344e-01	ci left: 3.655254e-02	ci right 4.198245e-02	k: 784	n:20000
RYR2   20000 perm   13 sec   (1546 perm/sec)   p_kst 3.920000e-02   p_cons 4.792000e-01   p_joint 7.320000e-02

Joint ci ratio: 7.953766e-02	ci left: 7.191321e-02	ci right 7.790276e-02	k: 2246	n:30000
Cons ci ratio: 2.367805e-02	ci left: 4.717336e-01	ci right 4.830708e-01	k: 14322	n:30000
KS ci ratio: 1.140274e-01	ci left: 3.573495e-02	ci right 4.008846e-02	k: 1136	n:30000
RYR2   30000 perm   18 sec   (1627 perm/sec)   p_kst 3.786667e-02   p_cons 4.774000e-01   p_joint 7.486667e-02

Joint ci ratio: 7.759539e-02	ci left: 5.764309e-02	ci right 6.232104e-02	k: 2398	n:40000
Cons ci ratio: 2.094471e-02	ci left: 4.619509e-01	ci right 4.717539e-01	k: 18674	n:40000
KS ci ratio: 9.844768e-02	ci left: 3.624504e-02	ci right 4.002239e-02	k: 1524	n:40000
RYR2   40000 perm   24 sec   (1661 perm/sec)   p_kst 3.810000e-02   p_cons 4.668500e-01   p_joint 5.995000e-02

Outputting figure to mutsig2_images.part000000000151/RYR2.8_15324_40000_0.0381_0.46685_0.05995.png
                gene_name: RYR2
               theta_stop: 0.098 
                    nperm: 40000 
                     p_ks: 0.038 
        ci_ks_bounds_left: 0.036 
       ci_ks_bounds_right: 0.040 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.060 
     ci_joint_bounds_left: 0.058 
    ci_joint_bounds_right: 0.062 

Current progress: 20 percent done.
RTN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.117628e-02	ci left: 6.028698e-01	ci right 6.220646e-01	k: 6125	n:10000
Cons ci ratio: 3.204321e-02	ci left: 5.897180e-01	ci right 6.090241e-01	k: 5994	n:10000
KS ci ratio: 4.710281e-02	ci left: 3.994411e-01	ci right 4.188118e-01	k: 4091	n:10000
RTN3   10000 perm   2 sec   (5403 perm/sec)   p_kst 4.091000e-01   p_cons 5.994000e-01   p_joint 6.125000e-01

Outputting figure to mutsig2_images.part000000000151/RTN3.3_3209_10000_0.4091_0.5994_0.6125.png
                gene_name: RTN3
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 40 percent done.
RTN4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.615328e-02	ci left: 5.304715e-01	ci right 5.501050e-01	k: 5403	n:10000
Cons ci ratio: 5.144913e-02	ci left: 3.577420e-01	ci right 3.767354e-01	k: 3672	n:10000
KS ci ratio: 4.276542e-02	ci left: 4.467012e-01	ci right 4.663241e-01	k: 4565	n:10000
RTN4   10000 perm   2 sec   (5289 perm/sec)   p_kst 4.565000e-01   p_cons 3.672000e-01   p_joint 5.403000e-01

Outputting figure to mutsig2_images.part000000000151/RTN4.3_3653_10000_0.4565_0.3672_0.5403.png
                gene_name: RTN4
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 60 percent done.
RSPH6A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.292156e-02	ci left: 2.707198e-01	ci right 2.884088e-01	k: 2795	n:10000
Cons ci ratio: 6.427613e-02	ci left: 2.623061e-01	ci right 2.798274e-01	k: 2710	n:10000
KS ci ratio: 1.007820e-01	ci left: 1.247387e-01	ci right 1.380768e-01	k: 1313	n:10000
RSPH6A   10000 perm   2 sec   (6195 perm/sec)   p_kst 1.313000e-01   p_cons 2.710000e-01   p_joint 2.795000e-01

Joint ci ratio: 4.195079e-02	ci left: 2.974799e-01	ci right 3.102772e-01	k: 6077	n:20000
Cons ci ratio: 4.704972e-02	ci left: 2.515498e-01	ci right 2.637207e-01	k: 5152	n:20000
KS ci ratio: 7.154726e-02	ci left: 1.258113e-01	ci right 1.351964e-01	k: 2609	n:20000
RSPH6A   20000 perm   4 sec   (5430 perm/sec)   p_kst 1.304500e-01   p_cons 2.576000e-01   p_joint 3.038500e-01

Outputting figure to mutsig2_images.part000000000151/RSPH6A.2_2178_20000_0.13045_0.2576_0.30385.png
                gene_name: RSPH6A
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.31 

Current progress: 80 percent done.
RUSC2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.769573e-02	ci left: 6.576653e-01	ci right 6.762373e-01	k: 6670	n:10000
KS ci ratio: 1.546220e-02	ci left: 8.585543e-01	ci right 8.720322e-01	k: 8654	n:10000
RUSC2   10000 perm   2 sec   (4767 perm/sec)   p_kst 8.654000e-01   p_cons 6.670000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000151/RUSC2.2_4595_10000_0.8654_0.667_1.png
                gene_name: RUSC2
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000151
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 151 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4398304: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000152> was used as the working directory.
Started at Wed Oct 24 16:16:23 2012
Results reported at Wed Oct 24 16:18:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000152.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000152.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 152  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000152.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     75.60 sec.
    Max Memory :      1159 MB
    Max Swap   :      3892 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
152
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 152
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 152: processing genes 13547 - 13636
Calculating significance of each gene.
Using projection method.
13547	S1PR1	1
13548	S1PR2	1
13549	S1PR3	1
13550	S1PR4	1
13551	S1PR5	1
13552	SAA1	1
13553	SAA2	1
13554	SAA4	1
13555	SAAL1	1
13556	SAC3D1	1
13557	SACM1L	1
13558	SACS	1
13559	SAE1	1
13560	SAFB	1
13561	SAFB2	1
13562	SAG	1.741991e-01
13563	SAGE1	1
13564	SALL1	1
13565	SALL2	1.071696e-01
13566	SALL3	1
13567	SALL4	1.492660e-01
13568	SAMD1	1
13569	SAMD10	1
13570	SAMD11	1
13571	SAMD12	1
13572	SAMD13	1
13573	SAMD14	1
13574	SAMD3	1
13575	SAMD4A	5.366710e-02
13576	SAMD4B	1
13577	SAMD5	1
13578	SAMD7	1
13579	SAMD8	1
13580	SAMD9	1
13581	SAMD9L	1
13582	SAMHD1	1
13583	SAMM50	1
13584	SAMSN1	1
13585	SAP130	2.852675e-01
13586	SAP18	1
13587	SAP30	1
13588	SAP30BP	1
13589	SAP30L	1
13590	SAPS1	1
13591	SAPS2	2.437358e-01
13592	SAPS3	1
13593	SAR1A	1
13594	SAR1B	1
13595	SARDH	1
13596	SARM1	1.308440e-02
13597	SARNP	1
13598	SARS	1
13599	SARS2	1.456162e-01
13600	SART1	1
13601	SART3	1
13602	SASH1	1
13603	SASH3	1
13604	SASS6	1
13605	SAT1	1
13606	SAT2	1
13607	SATB1	1
13608	SATB2	1
13609	SATL1	1
13610	SAV1	1
13611	SBDS	1.304378e-02
13612	SBF1	1
13613	SBF2	4.607743e-01
13614	SBK1	1
13615	SBK2	1
13616	SBNO1	5.238005e-01
13617	SBNO2	1
13618	SBSN	1
13619	SC4MOL	1.054686e-01
13620	SC5DL	1
13621	SC65	1
13622	SCAF1	1
13623	SCAI	1
13624	SCAMP1	1
13625	SCAMP2	1
13626	SCAMP3	1
13627	SCAMP4	1
13628	SCAMP5	1
13629	SCAND1	1
13630	SCAND3	1
13631	SCAP	1
13632	SCAPER	1.156088e-01
13633	SCARA3	1
13634	SCARA5	1
13635	SCARB1	1
13636	SCARB2	1
Done

Running MutSig 2:
Scatter job 152: processing genes 13547 - 13636
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SAMD4A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.337433e-03	ci left: 9.910526e-01	ci right 9.944508e-01	k: 9929	n:10000
Cons ci ratio: 3.192992e-02	ci left: 5.914243e-01	ci right 6.107168e-01	k: 6011	n:10000
KS ci ratio: 4.269655e-02	ci left: 4.474996e-01	ci right 4.671253e-01	k: 4573	n:10000
SAMD4A   10000 perm   2 sec   (4518 perm/sec)   p_kst 4.573000e-01   p_cons 6.011000e-01   p_joint 9.929000e-01

Outputting figure to mutsig2_images.part000000000152/SAMD4A.2_2314_10000_0.4573_0.6011_0.9929.png
                gene_name: SAMD4A
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 50 percent done.
SBNO1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.080668e-02	ci left: 7.719526e-01	ci right 7.882839e-01	k: 7802	n:10000
KS ci ratio: 8.051572e-03	ci left: 9.555548e-01	ci right 9.633747e-01	k: 9596	n:10000
SBNO1   10000 perm   2 sec   (5474 perm/sec)   p_kst 9.596000e-01   p_cons 7.802000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000152/SBNO1.2_4306_10000_0.9596_0.7802_1.png
                gene_name: SBNO1
               theta_stop: 0.021 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000152
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 152 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1553>
Subject: Job 4398310: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1553>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000153> was used as the working directory.
Started at Wed Oct 24 16:16:29 2012
Results reported at Wed Oct 24 16:20:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000153.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000153.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 153  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000153.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    323.96 sec.
    Max Memory :      1583 MB
    Max Swap   :      3995 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
153
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 153
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 153: processing genes 13637 - 13726
Calculating significance of each gene.
Using projection method.
13637	SCARF1	1.359806e-01
13638	SCARF2	1
13639	SCCPDH	3.353144e-02
13640	SCD	1
13641	SCD5	1
13642	SCEL	1
13643	SCFD1	1
13644	SCFD2	1.156200e-01
13645	SCG2	1
13646	SCG3	1
13647	SCG5	1
13648	SCGB1A1	1
13649	SCGB1C1	1
13650	SCGB1D1	1
13651	SCGB1D2	1
13652	SCGB1D4	1
13653	SCGB2A1	1
13654	SCGB2A2	1
13655	SCGB3A2	1
13656	SCGBL	1
13657	SCGN	1
13658	SCHIP1	1
13659	SCIN	1
13660	SCLT1	1
13661	SCLY	1
13662	SCMH1	1
13663	SCML1	1
13664	SCML2	2.056004e-01
13665	SCML4	1
13666	SCN10A	6.836305e-01
13667	SCN11A	9.953095e-02
13668	SCN1A	1
13669	SCN1B	1
13670	SCN2A	5.832902e-01
13671	SCN2B	1
13672	SCN3A	1
13673	SCN3B	1
13674	SCN4A	4.034018e-01
13675	SCN4B	1
13676	SCN5A	2.223747e-02
13677	SCN7A	1
13678	SCN8A	1
13679	SCN9A	1
13680	SCNM1	4.025004e-02
13681	SCNN1A	1
13682	SCNN1B	1
13683	SCNN1D	1.251137e-01
13684	SCNN1G	7.197252e-02
13685	SCO1	6.391230e-02
13686	SCO2	1
13687	SCOC	1
13688	SCP2	1
13689	SCPEP1	1
13690	SCRG1	1
13691	SCRIB	1
13692	SCRN1	1
13693	SCRN2	1
13694	SCRN3	1
13695	SCRT1	1
13696	SCRT2	1
13697	SCTR	1
13698	SCUBE1	1
13699	SCUBE2	1
13700	SCUBE3	3.989242e-01
13701	SCYL1	1
13702	SCYL2	1
13703	SCYL3	1
13704	SDAD1	1
13705	SDC1	1
13706	SDC2	1.604402e-02
13707	SDC3	1
13708	SDC4	1
13709	SDCBP	6.906661e-03
13710	SDCBP2	1
13711	SDCCAG1	1
13712	SDCCAG3	1
13713	SDCCAG8	1.735385e-01
13714	SDF2	1
13715	SDF2L1	1
13716	SDF4	1
13717	SDHA	1
13718	SDHAF2	1
13719	SDHB	1.454901e-01
13720	SDHC	1
13721	SDHD	1
13722	SDK1	4.582099e-01
13723	SDK2	1.885667e-01
13724	SDPR	2.322169e-01
13725	SDR16C5	1
13726	SDR39U1	1
Done

Running MutSig 2:
Scatter job 153: processing genes 13637 - 13726
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SCN5A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.901577e-02	ci left: 6.365358e-01	ci right 6.553791e-01	k: 6460	n:10000
Cons ci ratio: 4.355812e-02	ci left: 4.376211e-01	ci right 4.572096e-01	k: 4474	n:10000
KS ci ratio: 4.150350e-02	ci left: 4.615758e-01	ci right 4.812409e-01	k: 4714	n:10000
SCN5A   10000 perm   3 sec   (3683 perm/sec)   p_kst 4.714000e-01   p_cons 4.474000e-01   p_joint 6.460000e-01

Outputting figure to mutsig2_images.part000000000153/SCN5A.4_6255_10000_0.4714_0.4474_0.646.png
                gene_name: SCN5A
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 14 percent done.
SCN11A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.268795e-02	ci left: 4.475994e-01	ci right 4.672254e-01	k: 4574	n:10000
Cons ci ratio: 9.939328e-02	ci left: 1.278700e-01	ci right 1.413437e-01	k: 1345	n:10000
KS ci ratio: 2.883207e-02	ci left: 6.394525e-01	ci right 6.582607e-01	k: 6489	n:10000
SCN11A   10000 perm   3 sec   (3992 perm/sec)   p_kst 6.489000e-01   p_cons 1.345000e-01   p_joint 4.574000e-01

Outputting figure to mutsig2_images.part000000000153/SCN11A.3_5480_10000_0.6489_0.1345_0.4574.png
                gene_name: SCN11A
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 29 percent done.
SDHA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.005619e-01	ci left: 1.252279e-01	ci right 1.385873e-01	k: 1318	n:10000
Cons ci ratio: 1.673668e-01	ci left: 4.763334e-02	ci right 5.642994e-02	k: 519	n:10000
KS ci ratio: 1.023114e-01	ci left: 1.214132e-01	ci right 1.346043e-01	k: 1279	n:10000
SDHA   10000 perm   2 sec   (5178 perm/sec)   p_kst 1.279000e-01   p_cons 5.190000e-02   p_joint 1.318000e-01

Joint ci ratio: 7.156303e-02	ci left: 1.257620e-01	ci right 1.351457e-01	k: 2608	n:20000
Cons ci ratio: 1.159572e-01	ci left: 5.090763e-02	ci right 5.722281e-02	k: 1080	n:20000
KS ci ratio: 7.252515e-02	ci left: 1.228085e-01	ci right 1.321001e-01	k: 2548	n:20000
SDHA   20000 perm   4 sec   (4859 perm/sec)   p_kst 1.274000e-01   p_cons 5.400000e-02   p_joint 1.304000e-01

Joint ci ratio: 5.842702e-02	ci left: 1.266416e-01	ci right 1.342968e-01	k: 3913	n:30000
Cons ci ratio: 9.312609e-02	ci left: 5.316386e-02	ci right 5.838925e-02	k: 1672	n:30000
KS ci ratio: 5.856476e-02	ci left: 1.261150e-01	ci right 1.337568e-01	k: 3897	n:30000
SDHA   30000 perm   6 sec   (4698 perm/sec)   p_kst 1.299000e-01   p_cons 5.573333e-02   p_joint 1.304333e-01

Outputting figure to mutsig2_images.part000000000153/SDHA.3_2055_30000_0.1299_0.055733_0.13043.png
                gene_name: SDHA
               theta_stop: 0.093 
                    nperm: 30000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.056 
      ci_cons_bounds_left: 0.053 
     ci_cons_bounds_right: 0.058 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.13 

Current progress: 43 percent done.
SCN4A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.228785e-02	ci left: 7.471549e-01	ci right 7.640960e-01	k: 7557	n:10000
Cons ci ratio: 3.668042e-02	ci left: 5.232632e-01	ci right 5.429175e-01	k: 5331	n:10000
KS ci ratio: 5.168237e-02	ci left: 3.556540e-01	ci right 3.746246e-01	k: 3651	n:10000
SCN4A   10000 perm   2 sec   (4516 perm/sec)   p_kst 3.651000e-01   p_cons 5.331000e-01   p_joint 7.557000e-01

Outputting figure to mutsig2_images.part000000000153/SCN4A.2_5607_10000_0.3651_0.5331_0.7557.png
                gene_name: SCN4A
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.76 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.76 

Current progress: 57 percent done.
SCN8A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.811095e-02	ci left: 3.892832e-01	ci right 4.085757e-01	k: 3989	n:10000
KS ci ratio: 7.134047e-02	ci left: 2.235583e-01	ci right 2.401981e-01	k: 2318	n:10000
SCN8A   10000 perm   2 sec   (4384 perm/sec)   p_kst 2.318000e-01   p_cons 3.989000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000153/SCN8A.2_6047_10000_0.2318_0.3989_1.png
                gene_name: SCN8A
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
SCNN1G
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.344190e-01	ci left: 2.400584e-02	ci right 3.047352e-02	k: 271	n:10000
Cons ci ratio: 6.658135e-02	ci left: 2.487538e-01	ci right 2.659878e-01	k: 2573	n:10000
KS ci ratio: 6.109146e-01	ci left: 2.859150e-03	ci right 5.442922e-03	k: 40	n:10000
SCNN1G   10000 perm   2 sec   (6407 perm/sec)   p_kst 4.000000e-03   p_cons 2.573000e-01   p_joint 2.710000e-02

Joint ci ratio: 3.613336e-01	ci left: 4.794950e-03	ci right 6.952521e-03	k: 116	n:20000
Cons ci ratio: 4.643656e-02	ci left: 2.565608e-01	ci right 2.688082e-01	k: 5253	n:20000
KS ci ratio: 4.517819e-01	ci left: 2.906379e-03	ci right 4.642815e-03	k: 74	n:20000
SCNN1G   20000 perm   4 sec   (5608 perm/sec)   p_kst 3.700000e-03   p_cons 2.626500e-01   p_joint 5.800000e-03

Joint ci ratio: 2.904862e-01	ci left: 5.157558e-03	ci right 6.940142e-03	k: 180	n:30000
Cons ci ratio: 3.806933e-02	ci left: 2.561363e-01	ci right 2.661100e-01	k: 7833	n:30000
KS ci ratio: 3.527233e-01	ci left: 3.378230e-03	ci right 4.853689e-03	k: 122	n:30000
SCNN1G   30000 perm   6 sec   (5309 perm/sec)   p_kst 4.066667e-03   p_cons 2.611000e-01   p_joint 6.000000e-03

Joint ci ratio: 2.456646e-01	ci left: 5.548131e-03	ci right 7.124827e-03	k: 252	n:40000
Cons ci ratio: 3.300397e-02	ci left: 2.564027e-01	ci right 2.650321e-01	k: 10428	n:40000
KS ci ratio: 2.923346e-01	ci left: 3.821418e-03	ci right 5.152096e-03	k: 178	n:40000
SCNN1G   40000 perm   8 sec   (5100 perm/sec)   p_kst 4.450000e-03   p_cons 2.607000e-01   p_joint 6.300000e-03

Joint ci ratio: 2.180875e-01	ci left: 5.719809e-03	ci right 7.138410e-03	k: 320	n:50000
Cons ci ratio: 2.958451e-02	ci left: 2.560200e-01	ci right 2.637279e-01	k: 12993	n:50000
KS ci ratio: 2.584444e-01	ci left: 3.988372e-03	ci right 5.190261e-03	k: 228	n:50000
SCNN1G   50000 perm   10 sec   (4946 perm/sec)   p_kst 4.560000e-03   p_cons 2.598600e-01   p_joint 6.400000e-03

Joint ci ratio: 1.968356e-01	ci left: 5.920171e-03	ci right 7.228244e-03	k: 393	n:60000
Cons ci ratio: 2.711115e-02	ci left: 2.548841e-01	ci right 2.619059e-01	k: 15503	n:60000
KS ci ratio: 2.320561e-01	ci left: 4.184173e-03	ci right 5.297898e-03	k: 283	n:60000
SCNN1G   60000 perm   12 sec   (4820 perm/sec)   p_kst 4.716667e-03   p_cons 2.583833e-01   p_joint 6.550000e-03

Joint ci ratio: 1.825681e-01	ci left: 5.945353e-03	ci right 7.153240e-03	k: 457	n:70000
Cons ci ratio: 2.515914e-02	ci left: 2.542495e-01	ci right 2.607420e-01	k: 18024	n:70000
KS ci ratio: 2.149511e-01	ci left: 4.220328e-03	ci right 5.249959e-03	k: 330	n:70000
SCNN1G   70000 perm   15 sec   (4703 perm/sec)   p_kst 4.714286e-03   p_cons 2.574857e-01   p_joint 6.528571e-03

Joint ci ratio: 7.157594e-02	ci left: 3.484254e-02	ci right 3.744124e-02	k: 2890	n:80000
Cons ci ratio: 2.352192e-02	ci left: 2.546594e-01	ci right 2.607332e-01	k: 20615	n:80000
KS ci ratio: 1.998214e-01	ci left: 4.309088e-03	ci right 5.277362e-03	k: 382	n:80000
SCNN1G   80000 perm   17 sec   (4599 perm/sec)   p_kst 4.775000e-03   p_cons 2.576875e-01   p_joint 3.612500e-02

Joint ci ratio: 6.750806e-02	ci left: 3.489072e-02	ci right 3.733930e-02	k: 3249	n:90000
Cons ci ratio: 2.210670e-02	ci left: 2.560405e-01	ci right 2.617750e-01	k: 23301	n:90000
KS ci ratio: 1.879284e-01	ci left: 4.358920e-03	ci right 5.273446e-03	k: 432	n:90000
SCNN1G   90000 perm   20 sec   (4486 perm/sec)   p_kst 4.800000e-03   p_cons 2.589000e-01   p_joint 3.610000e-02

Joint ci ratio: 6.373418e-02	ci left: 3.528708e-02	ci right 3.761991e-02	k: 3644	n:100000
Cons ci ratio: 2.094830e-02	ci left: 2.566256e-01	ci right 2.620683e-01	k: 25934	n:100000
KS ci ratio: 1.766523e-01	ci left: 4.467060e-03	ci right 5.342037e-03	k: 489	n:100000
SCNN1G   100000 perm   23 sec   (4397 perm/sec)   p_kst 4.890000e-03   p_cons 2.593400e-01   p_joint 3.644000e-02

Joint ci ratio: 1.431299e-01	ci left: 6.287772e-03	ci right 7.265778e-03	k: 744	n:110000
Cons ci ratio: 1.995477e-02	ci left: 2.571107e-01	ci right 2.623020e-01	k: 28567	n:110000
KS ci ratio: 1.684314e-01	ci left: 4.487192e-03	ci right 5.321059e-03	k: 538	n:110000
SCNN1G   110000 perm   26 sec   (4288 perm/sec)   p_kst 4.890909e-03   p_cons 2.597000e-01   p_joint 6.763636e-03

Joint ci ratio: 1.355933e-01	ci left: 6.447475e-03	ci right 7.393257e-03	k: 829	n:120000
Cons ci ratio: 1.912891e-02	ci left: 2.567473e-01	ci right 2.617143e-01	k: 31107	n:120000
KS ci ratio: 1.600347e-01	ci left: 4.576753e-03	ci right 5.380789e-03	k: 596	n:120000
SCNN1G   120000 perm   29 sec   (4204 perm/sec)   p_kst 4.966667e-03   p_cons 2.592250e-01   p_joint 6.908333e-03

Joint ci ratio: 1.294906e-01	ci left: 6.546523e-03	ci right 7.460291e-03	k: 909	n:130000
Cons ci ratio: 1.836865e-02	ci left: 2.570496e-01	ci right 2.618227e-01	k: 33726	n:130000
KS ci ratio: 1.527801e-01	ci left: 4.653408e-03	ci right 5.430461e-03	k: 654	n:130000
SCNN1G   130000 perm   32 sec   (4116 perm/sec)   p_kst 5.030769e-03   p_cons 2.594308e-01   p_joint 6.992308e-03

Joint ci ratio: 1.242073e-01	ci left: 6.625314e-03	ci right 7.509572e-03	k: 988	n:140000
Cons ci ratio: 1.770126e-02	ci left: 2.571197e-01	ci right 2.617188e-01	k: 36318	n:140000
KS ci ratio: 1.466372e-01	ci left: 4.706051e-03	ci right 5.457530e-03	k: 710	n:140000
SCNN1G   140000 perm   35 sec   (4033 perm/sec)   p_kst 5.071429e-03   p_cons 2.594143e-01   p_joint 7.057143e-03

Joint ci ratio: 5.153470e-02	ci left: 3.618205e-02	ci right 3.810256e-02	k: 5570	n:150000
Cons ci ratio: 1.712904e-02	ci left: 2.565716e-01	ci right 2.610110e-01	k: 38818	n:150000
KS ci ratio: 1.415517e-01	ci left: 4.726488e-03	ci right 5.452845e-03	k: 762	n:150000
SCNN1G   150000 perm   38 sec   (3963 perm/sec)   p_kst 5.080000e-03   p_cons 2.587867e-01   p_joint 3.713333e-02

Joint ci ratio: 5.015921e-02	ci left: 3.584572e-02	ci right 3.769611e-02	k: 5882	n:160000
Cons ci ratio: 1.659214e-02	ci left: 2.564807e-01	ci right 2.607781e-01	k: 41380	n:160000
KS ci ratio: 1.367084e-01	ci left: 4.762875e-03	ci right 5.467741e-03	k: 817	n:160000
SCNN1G   160000 perm   41 sec   (3898 perm/sec)   p_kst 5.106250e-03   p_cons 2.586250e-01   p_joint 3.676250e-02

Joint ci ratio: 1.124304e-01	ci left: 6.700643e-03	ci right 7.504540e-03	k: 1206	n:170000
Cons ci ratio: 1.608966e-02	ci left: 2.567134e-01	ci right 2.608831e-01	k: 43995	n:170000
KS ci ratio: 1.329441e-01	ci left: 4.749849e-03	ci right 5.431903e-03	k: 864	n:170000
SCNN1G   170000 perm   44 sec   (3838 perm/sec)   p_kst 5.082353e-03   p_cons 2.587941e-01   p_joint 7.094118e-03

Joint ci ratio: 4.685634e-02	ci left: 3.655011e-02	ci right 3.830927e-02	k: 6736	n:180000
Cons ci ratio: 1.563702e-02	ci left: 2.567556e-01	ci right 2.608077e-01	k: 46580	n:180000
KS ci ratio: 1.296175e-01	ci left: 4.727755e-03	ci right 5.388341e-03	k: 909	n:180000
SCNN1G   180000 perm   48 sec   (3775 perm/sec)   p_kst 5.050000e-03   p_cons 2.587778e-01   p_joint 3.742222e-02

Joint ci ratio: 4.561421e-02	ci left: 3.656168e-02	ci right 3.827352e-02	k: 7108	n:190000
Cons ci ratio: 1.523058e-02	ci left: 2.565430e-01	ci right 2.604855e-01	k: 49117	n:190000
KS ci ratio: 1.256719e-01	ci left: 4.774449e-03	ci right 5.419740e-03	k: 967	n:190000
SCNN1G   190000 perm   51 sec   (3711 perm/sec)   p_kst 5.089474e-03   p_cons 2.585105e-01   p_joint 3.741053e-02

Joint ci ratio: 4.434901e-02	ci left: 3.676062e-02	ci right 3.843281e-02	k: 7518	n:200000
Cons ci ratio: 1.483123e-02	ci left: 2.569464e-01	ci right 2.607906e-01	k: 51773	n:200000
KS ci ratio: 1.220062e-01	ci left: 4.821596e-03	ci right 5.452878e-03	k: 1026	n:200000
SCNN1G   200000 perm   55 sec   (3654 perm/sec)   p_kst 5.130000e-03   p_cons 2.588650e-01   p_joint 3.759000e-02

Joint ci ratio: 4.331143e-02	ci left: 3.672915e-02	ci right 3.835984e-02	k: 7883	n:210000
Cons ci ratio: 1.447446e-02	ci left: 2.569752e-01	ci right 2.607267e-01	k: 54358	n:210000
KS ci ratio: 1.193639e-01	ci left: 4.804429e-03	ci right 5.418878e-03	k: 1072	n:210000
SCNN1G   210000 perm   58 sec   (3597 perm/sec)   p_kst 5.104762e-03   p_cons 2.588476e-01   p_joint 3.753810e-02

Joint ci ratio: 4.231145e-02	ci left: 3.675494e-02	ci right 3.834818e-02	k: 8260	n:220000
Cons ci ratio: 1.413757e-02	ci left: 2.571295e-01	ci right 2.607950e-01	k: 56971	n:220000
KS ci ratio: 1.166766e-01	ci left: 4.806609e-03	ci right 5.406544e-03	k: 1122	n:220000
SCNN1G   220000 perm   62 sec   (3542 perm/sec)   p_kst 5.100000e-03   p_cons 2.589591e-01   p_joint 3.754545e-02

Joint ci ratio: 4.138764e-02	ci left: 3.676167e-02	ci right 3.831958e-02	k: 8633	n:230000
Cons ci ratio: 1.383569e-02	ci left: 2.569242e-01	ci right 2.605080e-01	k: 59504	n:230000
KS ci ratio: 1.135806e-01	ci left: 4.859437e-03	ci right 5.448792e-03	k: 1184	n:230000
SCNN1G   230000 perm   66 sec   (3487 perm/sec)   p_kst 5.147826e-03   p_cons 2.587130e-01   p_joint 3.753478e-02

Joint ci ratio: 4.057802e-02	ci left: 3.666916e-02	ci right 3.819204e-02	k: 8982	n:240000
Cons ci ratio: 1.354279e-02	ci left: 2.570070e-01	ci right 2.605155e-01	k: 62102	n:240000
KS ci ratio: 1.115307e-01	ci left: 4.835129e-03	ci right 5.410256e-03	k: 1228	n:240000
SCNN1G   240000 perm   70 sec   (3437 perm/sec)   p_kst 5.116667e-03   p_cons 2.587583e-01   p_joint 3.742500e-02

Joint ci ratio: 3.980083e-02	ci left: 3.660810e-02	ci right 3.809865e-02	k: 9337	n:250000
Cons ci ratio: 1.327438e-02	ci left: 2.568924e-01	ci right 2.603292e-01	k: 64652	n:250000
KS ci ratio: 1.093722e-01	ci left: 4.832308e-03	ci right 5.395259e-03	k: 1277	n:250000
SCNN1G   250000 perm   74 sec   (3387 perm/sec)   p_kst 5.108000e-03   p_cons 2.586080e-01   p_joint 3.734800e-02

Joint ci ratio: 3.907082e-02	ci left: 3.654437e-02	ci right 3.800443e-02	k: 9690	n:260000
Cons ci ratio: 1.301022e-02	ci left: 2.571134e-01	ci right 2.604842e-01	k: 67287	n:260000
KS ci ratio: 1.076610e-01	ci left: 4.799858e-03	ci right 5.349725e-03	k: 1318	n:260000
SCNN1G   260000 perm   78 sec   (3340 perm/sec)   p_kst 5.069231e-03   p_cons 2.587962e-01   p_joint 3.726923e-02

Joint ci ratio: 3.837163e-02	ci left: 3.650028e-02	ci right 3.793190e-02	k: 10047	n:270000
Cons ci ratio: 1.275963e-02	ci left: 2.573668e-01	ci right 2.606754e-01	k: 69935	n:270000
KS ci ratio: 1.060669e-01	ci left: 4.766269e-03	ci right 5.303699e-03	k: 1358	n:270000
SCNN1G   270000 perm   82 sec   (3294 perm/sec)   p_kst 5.029630e-03   p_cons 2.590185e-01   p_joint 3.721111e-02

Joint ci ratio: 3.765420e-02	ci left: 3.656219e-02	ci right 3.796884e-02	k: 10433	n:280000
Cons ci ratio: 1.252414e-02	ci left: 2.575670e-01	ci right 2.608166e-01	k: 72573	n:280000
KS ci ratio: 1.042796e-01	ci left: 4.759486e-03	ci right 5.286554e-03	k: 1405	n:280000
SCNN1G   280000 perm   86 sec   (3249 perm/sec)   p_kst 5.017857e-03   p_cons 2.591893e-01   p_joint 3.726071e-02

Joint ci ratio: 3.734461e-02	ci left: 3.591948e-02	ci right 3.728980e-02	k: 10614	n:290000
Cons ci ratio: 1.230354e-02	ci left: 2.576816e-01	ci right 2.608750e-01	k: 75190	n:290000
KS ci ratio: 1.030441e-01	ci left: 4.709561e-03	ci right 5.224546e-03	k: 1439	n:290000
SCNN1G   290000 perm   90 sec   (3205 perm/sec)   p_kst 4.962069e-03   p_cons 2.592759e-01   p_joint 3.660000e-02

Joint ci ratio: 3.696933e-02	ci left: 3.545513e-02	ci right 3.679385e-02	k: 10836	n:300000
Cons ci ratio: 1.209788e-02	ci left: 2.576726e-01	ci right 2.608121e-01	k: 77772	n:300000
KS ci ratio: 1.011300e-01	ci left: 4.731231e-03	ci right 5.238404e-03	k: 1494	n:300000
SCNN1G   300000 perm   95 sec   (3164 perm/sec)   p_kst 4.980000e-03   p_cons 2.592400e-01   p_joint 3.612000e-02

Joint ci ratio: 3.639385e-02	ci left: 3.541729e-02	ci right 3.673333e-02	k: 11182	n:310000
Cons ci ratio: 1.190409e-02	ci left: 2.576034e-01	ci right 2.606915e-01	k: 80335	n:310000
KS ci ratio: 9.922225e-02	ci left: 4.761023e-03	ci right 5.261202e-03	k: 1552	n:310000
SCNN1G   310000 perm   99 sec   (3124 perm/sec)   p_kst 5.006452e-03   p_cons 2.591452e-01   p_joint 3.607097e-02

Outputting figure to mutsig2_images.part000000000153/SCNN1G.2_1998_310000_0.0050065_0.25915_0.036071.png
                gene_name: SCNN1G
               theta_stop: 0.099 
                    nperm: 310000 
                     p_ks: 0.0050 
        ci_ks_bounds_left: 0.0048 
       ci_ks_bounds_right: 0.0053 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.036 
     ci_joint_bounds_left: 0.035 
    ci_joint_bounds_right: 0.037 

Current progress: 86 percent done.
SDCBP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.409374e-01	ci left: 6.671876e-02	ci right 7.693236e-02	k: 717	n:10000
KS ci ratio: 3.390452e-02	ci left: 5.622325e-01	ci right 5.817255e-01	k: 5720	n:10000
SDCBP   10000 perm   1 sec   (6908 perm/sec)   p_kst 5.720000e-01   p_cons 7.170000e-02   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 9.823020e-02	ci left: 7.011604e-02	ci right 7.740846e-02	k: 1474	n:20000
KS ci ratio: 2.391441e-02	ci left: 5.663600e-01	ci right 5.801187e-01	k: 11465	n:20000
SDCBP   20000 perm   3 sec   (6010 perm/sec)   p_kst 5.732500e-01   p_cons 7.370000e-02   p_joint 1

Outputting figure to mutsig2_images.part000000000153/SDCBP.2_929_20000_0.57325_0.0737_1.png
                gene_name: SDCBP
               theta_stop: 0.098 
                    nperm: 20000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.074 
      ci_cons_bounds_left: 0.070 
     ci_cons_bounds_right: 0.077 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000153
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 153 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1416>
Subject: Job 4398315: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1416>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000154> was used as the working directory.
Started at Wed Oct 24 16:16:35 2012
Results reported at Wed Oct 24 16:19:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000154.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000154.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 154  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000154.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    246.00 sec.
    Max Memory :      1440 MB
    Max Swap   :      4046 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
154
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 154
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 154: processing genes 13727 - 13815
Calculating significance of each gene.
Using projection method.
13727	SDR42E1	1
13728	SDR9C7	1
13729	SDS	1
13730	SDSL	1
13731	SEBOX	1
13732	SEC11A	1
13733	SEC11C	1
13734	SEC13	1
13735	SEC14L1	1
13736	SEC14L2	1
13737	SEC14L3	1
13738	SEC14L4	9.480255e-02
13739	SEC14L5	2.682589e-01
13740	SEC16A	1
13741	SEC16B	1
13742	SEC22A	1
13743	SEC22B	1.106071e-01
13744	SEC22C	1
13745	SEC23A	1
13746	SEC23B	1
13747	SEC23IP	3.585340e-01
13748	SEC24A	1
13749	SEC24B	1
13750	SEC24C	1
13751	SEC24D	1.229032e-01
13752	SEC31A	1
13753	SEC31B	2.270593e-01
13754	SEC61A1	1
13755	SEC61A2	4.372711e-03
13756	SEC61B	1
13757	SEC61G	1
13758	SEC62	1.084653e-01
13759	SEC63	1
13760	SECISBP2	1
13761	SECISBP2L	1
13762	SECTM1	1
13763	SEH1L	1
13764	SEL1L	1
13765	SEL1L2	2.912042e-01
13766	SEL1L3	1
13767	SELE	1
13768	SELENBP1	1
13769	SELK	1
13770	SELL	1
13771	SELM	1
13772	SELO	1
13773	SELP	1
13774	SELPLG	1
13775	SELS	1
13776	SELT	1
13777	SELV	1
13778	SEMA3A	1.025644e-02
13779	SEMA3B	1
13780	SEMA3C	1
13781	SEMA3D	1
13782	SEMA3E	1
13783	SEMA3F	1
13784	SEMA3G	2.688102e-01
13785	SEMA4A	6.461837e-02
13786	SEMA4B	9.442187e-02
13787	SEMA4C	1
13788	SEMA4D	1
13789	SEMA4F	1
13790	SEMA4G	3.488313e-01
13791	SEMA5A	1
13792	SEMA5B	1
13793	SEMA6A	1.064408e-01
13794	SEMA6B	1
13795	SEMA6C	1
13796	SEMA6D	9.819007e-02
13797	SEMA7A	1
13798	SEMG1	9.095468e-02
13799	SEMG2	1
13800	SENP1	1
13801	SENP2	2.933663e-01
13802	SENP3	1
13803	SENP5	1.893792e-01
13804	SENP6	3.343343e-01
13805	SENP7	1
13806	SENP8	1
13807	SEP15	1
13808	SEPHS1	9.548163e-02
13809	SEPHS2	6.290060e-02
13810	SEPN1	1
13811	SEPP1	1
13812	SEPSECS	1
13813	SEPT1	1
13814	SEPT10	1
13815	SEPT11	1
Done

Running MutSig 2:
Scatter job 154: processing genes 13727 - 13815
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SEC61A2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.752814e-02	ci left: 8.259500e-01	ci right 8.406553e-01	k: 8334	n:10000
Cons ci ratio: 9.353182e-02	ci left: 1.423679e-01	ci right 1.564370e-01	k: 1493	n:10000
KS ci ratio: 3.884302e-02	ci left: 4.946505e-01	ci right 5.143469e-01	k: 5045	n:10000
SEC61A2   10000 perm   2 sec   (6204 perm/sec)   p_kst 5.045000e-01   p_cons 1.493000e-01   p_joint 8.334000e-01

Outputting figure to mutsig2_images.part000000000154/SEC61A2.2_1553_10000_0.5045_0.1493_0.8334.png
                gene_name: SEC61A2
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.84 

Current progress: 33 percent done.
SEMA3A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.155130e-01	ci left: 1.280183e-02	ci right 1.768651e-02	k: 151	n:10000
Cons ci ratio: 3.254388e-01	ci left: 1.197339e-02	ci right 1.671572e-02	k: 142	n:10000
KS ci ratio: 3.690201e-02	ci left: 5.202604e-01	ci right 5.399221e-01	k: 5301	n:10000
SEMA3A   10000 perm   2 sec   (5763 perm/sec)   p_kst 5.301000e-01   p_cons 1.420000e-02   p_joint 1.510000e-02

Joint ci ratio: 1.300529e-01	ci left: 4.061770e-02	ci right 4.631599e-02	k: 868	n:20000
Cons ci ratio: 2.238557e-01	ci left: 1.340842e-02	ci right 1.683467e-02	k: 301	n:20000
KS ci ratio: 2.623721e-02	ci left: 5.204523e-01	ci right 5.343397e-01	k: 10548	n:20000
SEMA3A   20000 perm   4 sec   (5053 perm/sec)   p_kst 5.274000e-01   p_cons 1.505000e-02   p_joint 4.340000e-02

Joint ci ratio: 4.741320e-02	ci left: 1.811485e-01	ci right 1.899792e-01	k: 5566	n:30000
Cons ci ratio: 1.813614e-01	ci left: 1.394148e-02	ci right 1.675352e-02	k: 459	n:30000
KS ci ratio: 2.147041e-02	ci left: 5.206309e-01	ci right 5.319640e-01	k: 15789	n:30000
SEMA3A   30000 perm   6 sec   (4741 perm/sec)   p_kst 5.263000e-01   p_cons 1.530000e-02   p_joint 1.855333e-01

Joint ci ratio: 1.519060e-01	ci left: 1.512992e-02	ci right 1.764100e-02	k: 654	n:40000
Cons ci ratio: 1.556949e-01	ci left: 1.438431e-02	ci right 1.683674e-02	k: 623	n:40000
KS ci ratio: 1.852155e-02	ci left: 5.233435e-01	ci right 5.331524e-01	k: 21130	n:40000
SEMA3A   40000 perm   9 sec   (4590 perm/sec)   p_kst 5.282500e-01   p_cons 1.557500e-02   p_joint 1.635000e-02

Joint ci ratio: 6.000541e-02	ci left: 7.627540e-02	ci right 8.101366e-02	k: 3931	n:50000
Cons ci ratio: 1.376534e-01	ci left: 1.486038e-02	ci right 1.707633e-02	k: 797	n:50000
KS ci ratio: 1.656130e-02	ci left: 5.240129e-01	ci right 5.327838e-01	k: 26420	n:50000
SEMA3A   50000 perm   11 sec   (4468 perm/sec)   p_kst 5.284000e-01   p_cons 1.594000e-02   p_joint 7.862000e-02

Joint ci ratio: 7.689324e-02	ci left: 3.991803e-02	ci right 4.312651e-02	k: 2490	n:60000
Cons ci ratio: 1.262372e-01	ci left: 1.481734e-02	ci right 1.682989e-02	k: 948	n:60000
KS ci ratio: 1.509819e-02	ci left: 5.250630e-01	ci right 5.330675e-01	k: 31744	n:60000
SEMA3A   60000 perm   14 sec   (4353 perm/sec)   p_kst 5.290667e-01   p_cons 1.580000e-02   p_joint 4.150000e-02

Joint ci ratio: 3.676948e-02	ci left: 1.371113e-01	ci right 1.422614e-01	k: 9777	n:70000
Cons ci ratio: 1.165615e-01	ci left: 1.497244e-02	ci right 1.683943e-02	k: 1112	n:70000
KS ci ratio: 1.400820e-02	ci left: 5.242936e-01	ci right 5.317041e-01	k: 36960	n:70000
SEMA3A   70000 perm   16 sec   (4251 perm/sec)   p_kst 5.280000e-01   p_cons 1.588571e-02   p_joint 1.396714e-01

Joint ci ratio: 3.651799e-02	ci left: 1.235962e-01	ci right 1.282060e-01	k: 10071	n:80000
Cons ci ratio: 1.087298e-01	ci left: 1.511752e-02	ci right 1.686783e-02	k: 1278	n:80000
KS ci ratio: 1.309891e-02	ci left: 5.247085e-01	ci right 5.316394e-01	k: 42254	n:80000
SEMA3A   80000 perm   19 sec   (4162 perm/sec)   p_kst 5.281750e-01   p_cons 1.597500e-02   p_joint 1.258875e-01

Joint ci ratio: 2.770364e-02	ci left: 1.794508e-01	ci right 1.845031e-01	k: 16377	n:90000
Cons ci ratio: 1.020396e-01	ci left: 1.530946e-02	ci right 1.696638e-02	k: 1451	n:90000
KS ci ratio: 1.237259e-02	ci left: 5.239874e-01	ci right 5.305219e-01	k: 47453	n:90000
SEMA3A   90000 perm   22 sec   (4081 perm/sec)   p_kst 5.272556e-01   p_cons 1.612222e-02   p_joint 1.819667e-01

Joint ci ratio: 2.627738e-02	ci left: 1.796327e-01	ci right 1.844258e-01	k: 18202	n:100000
Cons ci ratio: 9.666128e-02	ci left: 1.539732e-02	ci right 1.697093e-02	k: 1617	n:100000
KS ci ratio: 1.172652e-02	ci left: 5.246300e-01	ci right 5.308284e-01	k: 52773	n:100000
SEMA3A   100000 perm   25 sec   (4006 perm/sec)   p_kst 5.277300e-01   p_cons 1.617000e-02   p_joint 1.820200e-01

Outputting figure to mutsig2_images.part000000000154/SEMA3A.2_2384_100000_0.52773_0.01617_0.18202.png
                gene_name: SEMA3A
               theta_stop: 0.097 
                    nperm: 100000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.016 
      ci_cons_bounds_left: 0.015 
     ci_cons_bounds_right: 0.017 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.18 

Current progress: 67 percent done.
SEMA4A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.912852e-01	ci left: 3.643453e-02	ci right 4.423614e-02	k: 402	n:10000
Cons ci ratio: 1.151171e-01	ci left: 9.788810e-02	ci right 1.099437e-01	k: 1038	n:10000
KS ci ratio: 1.159281e-01	ci left: 9.662172e-02	ci right 1.086109e-01	k: 1025	n:10000
SEMA4A   10000 perm   2 sec   (6128 perm/sec)   p_kst 1.025000e-01   p_cons 1.038000e-01   p_joint 4.020000e-02

Joint ci ratio: 7.241124e-02	ci left: 1.231530e-01	ci right 1.324555e-01	k: 2555	n:20000
Cons ci ratio: 7.955555e-02	ci left: 1.039271e-01	ci right 1.125872e-01	k: 2164	n:20000
KS ci ratio: 8.186402e-02	ci left: 9.862400e-02	ci right 1.070919e-01	k: 2056	n:20000
SEMA4A   20000 perm   4 sec   (5372 perm/sec)   p_kst 1.028000e-01   p_cons 1.082000e-01   p_joint 1.277500e-01

Outputting figure to mutsig2_images.part000000000154/SEMA4A.2_2342_20000_0.1028_0.1082_0.12775.png
                gene_name: SEMA4A
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.099 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000154
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 154 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4398318: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000155> was used as the working directory.
Started at Wed Oct 24 16:16:35 2012
Results reported at Wed Oct 24 16:18:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000155.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000155.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 155  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000155.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     81.24 sec.
    Max Memory :      1019 MB
    Max Swap   :      3974 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
155
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 155
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 155: processing genes 13816 - 13905
Calculating significance of each gene.
Using projection method.
13816	SEPT12	1.334167e-02
13817	SEPT14	1
13818	SEPT2	2.640647e-02
13819	SEPT3	1
13820	SEPT4	1
13821	SEPT5	1
13822	SEPT6	1.593849e-01
13823	SEPT7	1
13824	SEPT8	1
13825	SEPT9	2.814557e-01
13826	SEPW1	1
13827	SEPX1	1
13828	SERAC1	1
13829	SERBP1	1
13830	SERF2	1
13831	SERGEF	1
13832	SERHL2	1
13833	SERINC1	1
13834	SERINC2	1
13835	SERINC3	1
13836	SERINC4	1
13837	SERINC5	1
13838	SERP1	1
13839	SERP2	1
13840	SERPINA1	1
13841	SERPINA10	1
13842	SERPINA11	1
13843	SERPINA12	1
13844	SERPINA3	1
13845	SERPINA4	1
13846	SERPINA5	1
13847	SERPINA6	1
13848	SERPINA7	1
13849	SERPINA9	1
13850	SERPINB1	1
13851	SERPINB10	1
13852	SERPINB11	8.723421e-02
13853	SERPINB12	1
13854	SERPINB13	1
13855	SERPINB2	1
13856	SERPINB3	1
13857	SERPINB4	1
13858	SERPINB5	1
13859	SERPINB6	1.362054e-02
13860	SERPINB7	1
13861	SERPINB8	1
13862	SERPINB9	1
13863	SERPINC1	1
13864	SERPIND1	1
13865	SERPINE1	1
13866	SERPINE2	1.024242e-01
13867	SERPINE3	1
13868	SERPINF1	1
13869	SERPINF2	1
13870	SERPING1	1.549420e-01
13871	SERPINH1	1
13872	SERPINI1	7.641283e-02
13873	SERPINI2	1
13874	SERTAD1	1
13875	SERTAD2	1
13876	SERTAD3	1
13877	SERTAD4	1
13878	SESN1	1
13879	SESN2	1.684217e-01
13880	SESN3	1
13881	SESTD1	1
13882	SET	1
13883	SETBP1	1
13884	SETD1A	1
13885	SETD2	1.437453e-01
13886	SETD3	1
13887	SETD4	1
13888	SETD5	1
13889	SETD6	1
13890	SETD7	1
13891	SETD8	1
13892	SETDB1	1.259891e-01
13893	SETDB2	1.807397e-01
13894	SETMAR	1
13895	SETX	5.870730e-01
13896	SEZ6	1
13897	SEZ6L	1
13898	SEZ6L2	3.144640e-02
13899	SF1	1
13900	SF3A1	1
13901	SF3A2	1
13902	SF3A3	1
13903	SF3B1	1
13904	SF3B14	1
13905	SF3B2	2.666965e-01
Done

Running MutSig 2:
Scatter job 155: processing genes 13816 - 13905
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SEPT12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.537640e-02	ci left: 1.666153e-01	ci right 1.815750e-01	k: 1740	n:10000
Cons ci ratio: 5.339733e-02	ci left: 3.407457e-01	ci right 3.595416e-01	k: 3501	n:10000
KS ci ratio: 1.037097e-01	ci left: 1.184802e-01	ci right 1.315391e-01	k: 1249	n:10000
SEPT12   10000 perm   1 sec   (7479 perm/sec)   p_kst 1.249000e-01   p_cons 3.501000e-01   p_joint 1.740000e-01

Joint ci ratio: 6.438674e-02	ci left: 1.512925e-01	ci right 1.614077e-01	k: 3126	n:20000
Cons ci ratio: 3.661190e-02	ci left: 3.576257e-01	ci right 3.710138e-01	k: 7286	n:20000
KS ci ratio: 7.336872e-02	ci left: 1.202987e-01	ci right 1.295107e-01	k: 2497	n:20000
SEPT12   20000 perm   5 sec   (4325 perm/sec)   p_kst 1.248500e-01   p_cons 3.643000e-01   p_joint 1.563000e-01

Outputting figure to mutsig2_images.part000000000155/SEPT12.2_1113_20000_0.12485_0.3643_0.1563.png
                gene_name: SEPT12
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.16 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.16 

Current progress: 25 percent done.
SERPINB6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.225082e-01	ci left: 2.674401e-02	ci right 3.353336e-02	k: 300	n:10000
Cons ci ratio: 9.416248e-02	ci left: 1.407013e-01	ci right 1.547046e-01	k: 1476	n:10000
KS ci ratio: 1.227782e-01	ci left: 8.679344e-02	ci right 9.824521e-02	k: 924	n:10000
SERPINB6   10000 perm   1 sec   (7945 perm/sec)   p_kst 9.240000e-02   p_cons 1.476000e-01   p_joint 3.000000e-02

Joint ci ratio: 7.228161e-02	ci left: 1.235468e-01	ci right 1.328616e-01	k: 2563	n:20000
Cons ci ratio: 6.615107e-02	ci left: 1.443871e-01	ci right 1.543151e-01	k: 2986	n:20000
KS ci ratio: 8.532785e-02	ci left: 9.136270e-02	ci right 9.955535e-02	k: 1908	n:20000
SERPINB6   20000 perm   3 sec   (6945 perm/sec)   p_kst 9.540000e-02   p_cons 1.493000e-01   p_joint 1.281500e-01

Outputting figure to mutsig2_images.part000000000155/SERPINB6.2_1155_20000_0.0954_0.1493_0.12815.png
                gene_name: SERPINB6
               theta_stop: 0.085 
                    nperm: 20000 
                     p_ks: 0.095 
        ci_ks_bounds_left: 0.091 
       ci_ks_bounds_right: 0.100 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 50 percent done.
SETD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.886917e-02	ci left: 8.041002e-01	ci right 8.195177e-01	k: 8119	n:10000
KS ci ratio: 2.538644e-02	ci left: 6.954487e-01	ci right 7.134321e-01	k: 7045	n:10000
SETD2   10000 perm   2 sec   (5115 perm/sec)   p_kst 7.045000e-01   p_cons 8.119000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000155/SETD2.2_7779_10000_0.7045_0.8119_1.png
                gene_name: SETD2
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.82 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
SEZ6L2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.125513e-02	ci left: 6.016648e-01	ci right 6.208704e-01	k: 6113	n:10000
Cons ci ratio: 3.204988e-02	ci left: 5.896176e-01	ci right 6.089245e-01	k: 5993	n:10000
KS ci ratio: 3.714711e-02	ci left: 5.169577e-01	ci right 5.366267e-01	k: 5268	n:10000
SEZ6L2   10000 perm   1 sec   (6792 perm/sec)   p_kst 5.268000e-01   p_cons 5.993000e-01   p_joint 6.113000e-01

Outputting figure to mutsig2_images.part000000000155/SEZ6L2.2_2844_10000_0.5268_0.5993_0.6113.png
                gene_name: SEZ6L2
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000155
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 155 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4398324: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000156> was used as the working directory.
Started at Wed Oct 24 16:16:37 2012
Results reported at Wed Oct 24 16:18:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000156.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000156.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 156  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000156.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    135.91 sec.
    Max Memory :      1273 MB
    Max Swap   :      4058 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
156
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 156
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 156: processing genes 13906 - 13995
Calculating significance of each gene.
Using projection method.
13906	SF3B3	1
13907	SF3B4	1
13908	SF3B5	1
13909	SF4	1
13910	SFI1	1
13911	SFMBT1	1
13912	SFMBT2	1.026739e-01
13913	SFN	1.408907e-02
13914	SFPQ	1
13915	SFRP1	1.022429e-01
13916	SFRP2	1
13917	SFRP4	1
13918	SFRP5	1
13919	SFRS1	6.121835e-02
13920	SFRS11	1
13921	SFRS12	1
13922	SFRS12IP1	1
13923	SFRS13B	1
13924	SFRS14	1
13925	SFRS15	1
13926	SFRS16	1.064579e-01
13927	SFRS17A	1.648913e-01
13928	SFRS18	2.535268e-01
13929	SFRS2	1
13930	SFRS2B	1
13931	SFRS2IP	1
13932	SFRS3	1
13933	SFRS4	1
13934	SFRS5	3.720268e-02
13935	SFRS6	1
13936	SFRS7	1
13937	SFRS8	1
13938	SFRS9	1
13939	SFT2D1	1
13940	SFT2D2	1
13941	SFTA2	1
13942	SFTA3	1
13943	SFTPA1	1
13944	SFTPA2	1
13945	SFTPB	1
13946	SFTPC	1
13947	SFTPD	1
13948	SFXN1	1
13949	SFXN2	1
13950	SFXN3	1
13951	SFXN4	1
13952	SFXN5	5.297526e-02
13953	SGCA	1
13954	SGCB	1
13955	SGCD	1.778091e-02
13956	SGCE	1
13957	SGCG	1
13958	SGCZ	1
13959	SGEF	1
13960	SGIP1	1.390789e-01
13961	SGK1	1
13962	SGK196	1
13963	SGK2	1
13964	SGK223	2.834636e-01
13965	SGK269	1
13966	SGK3	1
13967	SGK494	1
13968	SGMS1	1
13969	SGMS2	1
13970	SGOL1	1
13971	SGOL2	2.161312e-02
13972	SGPL1	1.425595e-02
13973	SGPP1	1
13974	SGPP2	1
13975	SGSH	1
13976	SGSM1	4.561905e-02
13977	SGSM2	1
13978	SGSM3	8.856905e-03
13979	SGTA	1
13980	SGTB	1
13981	SH2B1	1
13982	SH2B2	1
13983	SH2B3	1
13984	SH2D1A	1
13985	SH2D1B	1
13986	SH2D2A	1
13987	SH2D3A	1.320833e-01
13988	SH2D3C	1
13989	SH2D4A	1
13990	SH2D4B	1
13991	SH2D5	1
13992	SH2D6	1
13993	SH2D7	1
13994	SH3BGR	1
13995	SH3BGRL	1
Done

Running MutSig 2:
Scatter job 156: processing genes 13906 - 13995
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SGOL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.007820e-01	ci left: 1.247387e-01	ci right 1.380768e-01	k: 1313	n:10000
Cons ci ratio: 1.634260e-01	ci left: 4.993888e-02	ci right 5.892291e-02	k: 543	n:10000
KS ci ratio: 3.110410e-02	ci left: 6.039745e-01	ci right 6.231593e-01	k: 6136	n:10000
SGOL2   10000 perm   2 sec   (5167 perm/sec)   p_kst 6.136000e-01   p_cons 5.430000e-02   p_joint 1.313000e-01

Joint ci ratio: 7.305160e-02	ci left: 1.212336e-01	ci right 1.304754e-01	k: 2516	n:20000
Cons ci ratio: 1.235762e-01	ci left: 4.493272e-02	ci right 5.089960e-02	k: 957	n:20000
KS ci ratio: 2.190470e-02	ci left: 6.087667e-01	ci right 6.222997e-01	k: 12311	n:20000
SGOL2   20000 perm   7 sec   (3031 perm/sec)   p_kst 6.155500e-01   p_cons 4.785000e-02   p_joint 1.258000e-01

Joint ci ratio: 5.483868e-02	ci left: 1.415278e-01	ci right 1.495410e-01	k: 4365	n:30000
Cons ci ratio: 9.466392e-02	ci left: 5.150162e-02	ci right 5.665183e-02	k: 1621	n:30000
KS ci ratio: 1.786842e-02	ci left: 6.104688e-01	ci right 6.215088e-01	k: 18480	n:30000
SGOL2   30000 perm   9 sec   (3355 perm/sec)   p_kst 6.160000e-01   p_cons 5.403333e-02   p_joint 1.455000e-01

Outputting figure to mutsig2_images.part000000000156/SGOL2.3_3838_30000_0.616_0.054033_0.1455.png
                gene_name: SGOL2
               theta_stop: 0.095 
                    nperm: 30000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.054 
      ci_cons_bounds_left: 0.052 
     ci_cons_bounds_right: 0.057 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.15 

Current progress: 20 percent done.
SFN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 9.079719e-02	ci left: 1.499203e-01	ci right 1.642801e-01	k: 1570	n:10000
KS ci ratio: 5.045670e-02	ci left: 3.667920e-01	ci right 3.858801e-01	k: 3763	n:10000
SFN   10000 perm   1 sec   (6687 perm/sec)   p_kst 3.763000e-01   p_cons 1.570000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000156/SFN.2_751_10000_0.3763_0.157_1.png
                gene_name: SFN
               theta_stop: 0.091 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.16 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 40 percent done.
SGPL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.613156e-02	ci left: 2.513249e-01	ci right 2.686151e-01	k: 2599	n:10000
KS ci ratio: 4.620859e-02	ci left: 4.087065e-01	ci right 4.281410e-01	k: 4184	n:10000
SGPL1   10000 perm   2 sec   (6030 perm/sec)   p_kst 4.184000e-01   p_cons 2.599000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000156/SGPL1.2_1763_10000_0.4184_0.2599_1.png
                gene_name: SGPL1
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
SGSM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.682125e-02	ci left: 6.718638e-01	ci right 6.902306e-01	k: 6811	n:10000
Cons ci ratio: 1.772336e-02	ci left: 8.227970e-01	ci right 8.376101e-01	k: 8303	n:10000
KS ci ratio: 4.094976e-02	ci left: 4.682672e-01	ci right 4.879456e-01	k: 4781	n:10000
SGSM1   10000 perm   2 sec   (5078 perm/sec)   p_kst 4.781000e-01   p_cons 8.303000e-01   p_joint 6.811000e-01

Outputting figure to mutsig2_images.part000000000156/SGSM1.2_3551_10000_0.4781_0.8303_0.6811.png
                gene_name: SGSM1
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.69 

Current progress: 80 percent done.
SGSM3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.416833e-02	ci left: 5.584231e-01	ci right 5.779372e-01	k: 5682	n:10000
Cons ci ratio: 6.596015e-02	ci left: 2.523139e-01	ci right 2.696255e-01	k: 2609	n:10000
KS ci ratio: 3.931972e-02	ci left: 4.885519e-01	ci right 5.082490e-01	k: 4984	n:10000
SGSM3   10000 perm   2 sec   (6045 perm/sec)   p_kst 4.984000e-01   p_cons 2.609000e-01   p_joint 5.682000e-01

Outputting figure to mutsig2_images.part000000000156/SGSM3.2_2334_10000_0.4984_0.2609_0.5682.png
                gene_name: SGSM3
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000156
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 156 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1650>
Subject: Job 4398326: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1650>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000157> was used as the working directory.
Started at Wed Oct 24 16:16:37 2012
Results reported at Wed Oct 24 16:19:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000157.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000157.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 157  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000157.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    164.90 sec.
    Max Memory :      1550 MB
    Max Swap   :      3995 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
157
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 157
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 157: processing genes 13996 - 14084
Calculating significance of each gene.
Using projection method.
13996	SH3BGRL2	1
13997	SH3BGRL3	1
13998	SH3BP1	1
13999	SH3BP2	1
14000/17942 14000	SH3BP4	1
14001	SH3BP5	1
14002	SH3BP5L	1
14003	SH3D19	1
14004	SH3GL1	9.226603e-02
14005	SH3GL2	1
14006	SH3GL3	1
14007	SH3GLB1	1
14008	SH3GLB2	1
14009	SH3KBP1	1
14010	SH3PXD2A	1
14011	SH3PXD2B	1
14012	SH3RF1	1
14013	SH3RF2	1
14014	SH3RF3	1
14015	SH3TC1	1
14016	SH3TC2	1
14017	SH3YL1	1
14018	SHANK1	2.012118e-01
14019	SHANK2	1
14020	SHANK3	1
14021	SHARPIN	1
14022	SHB	1
14023	SHBG	1.196692e-01
14024	SHC1	1
14025	SHC2	1
14026	SHC3	1
14027	SHC4	1
14028	SHCBP1	1
14029	SHD	1
14030	SHE	1
14031	SHF	1
14032	SHFM1	1
14033	SHH	1
14034	SHISA2	1
14035	SHISA3	1
14036	SHISA4	1
14037	SHISA5	1
14038	SHKBP1	1
14039	SHMT1	2.305630e-01
14040	SHMT2	1
14041	SHOC2	1
14042	SHOX	1
14043	SHOX2	1
14044	SHPK	1
14045	SHPRH	9.057047e-02
14046	SHQ1	1
14047	SHROOM1	1
14048	SHROOM2	6.481461e-02
14049	SHROOM3	1
14050	SHROOM4	2.913833e-01
14051	SI	3.401331e-01
14052	SIAE	1
14053	SIAH1	5.979415e-02
14054	SIAH2	1
14055	SIAH3	1
14056	SIDT1	1.962536e-01
14057	SIDT2	1
14058	SIGIRR	1.579801e-01
14059	SIGLEC1	1.982915e-01
14060	SIGLEC10	3.684652e-03
14061	SIGLEC11	9.770437e-02
14062	SIGLEC12	9.894067e-02
14063	SIGLEC14	1
14064	SIGLEC15	1
14065	SIGLEC5	1
14066	SIGLEC6	1
14067	SIGLEC7	1
14068	SIGLEC8	1
14069	SIGLEC9	1
14070	SIGMAR1	5.094337e-02
14071	SIK1	1
14072	SIK2	6.144870e-02
14073	SIK3	1
14074	SIKE1	1
14075	SIL1	1
14076	SILV	1
14077	SIM1	1
14078	SIM2	1
14079	SIN3A	2.387112e-01
14080	SIN3B	1
14081	SIP1	1
14082	SIPA1	2.641806e-01
14083	SIPA1L1	6.478500e-01
14084	SIPA1L2	5.012919e-01
Done

Running MutSig 2:
Scatter job 157: processing genes 13996 - 14084
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SHROOM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.350465e-02	ci left: 5.680480e-01	ci right 5.875066e-01	k: 5778	n:10000
KS ci ratio: 1.905420e-02	ci left: 8.010545e-01	ci right 8.165651e-01	k: 8089	n:10000
SHROOM2   10000 perm   2 sec   (4678 perm/sec)   p_kst 8.089000e-01   p_cons 5.778000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000157/SHROOM2.3_4891_10000_0.8089_0.5778_1.png
                gene_name: SHROOM2
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 12 percent done.
SIGLEC10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.093572e-02	ci left: 1.822537e-01	ci right 1.977273e-01	k: 1899	n:10000
Cons ci ratio: 2.118569e-01	ci left: 2.958536e-02	ci right 3.669001e-02	k: 330	n:10000
KS ci ratio: 1.864034e-02	ci left: 8.078575e-01	ci right 8.231582e-01	k: 8156	n:10000
SIGLEC10   10000 perm   2 sec   (6311 perm/sec)   p_kst 8.156000e-01   p_cons 3.300000e-02   p_joint 1.899000e-01

Joint ci ratio: 7.146855e-02	ci left: 1.260574e-01	ci right 1.354502e-01	k: 2614	n:20000
Cons ci ratio: 1.519588e-01	ci left: 2.974850e-02	ci right 3.468873e-02	k: 643	n:20000
KS ci ratio: 1.287488e-02	ci left: 8.171834e-01	ci right 8.278227e-01	k: 16451	n:20000
SIGLEC10   20000 perm   4 sec   (5557 perm/sec)   p_kst 8.225500e-01   p_cons 3.215000e-02   p_joint 1.307000e-01

Joint ci ratio: 4.029233e-02	ci left: 2.349773e-01	ci right 2.446732e-01	k: 7194	n:30000
Cons ci ratio: 1.355170e-01	ci left: 2.529183e-02	ci right 2.900051e-02	k: 813	n:30000
KS ci ratio: 1.061464e-02	ci left: 8.153022e-01	ci right 8.240358e-01	k: 24591	n:30000
SIGLEC10   30000 perm   6 sec   (5303 perm/sec)   p_kst 8.197000e-01   p_cons 2.710000e-02   p_joint 2.398000e-01

Joint ci ratio: 4.140972e-02	ci left: 1.792213e-01	ci right 1.868247e-01	k: 7320	n:40000
Cons ci ratio: 1.102704e-01	ci left: 2.893381e-02	ci right 3.233478e-02	k: 1224	n:40000
KS ci ratio: 9.236006e-03	ci left: 8.144857e-01	ci right 8.220681e-01	k: 32732	n:40000
SIGLEC10   40000 perm   8 sec   (5110 perm/sec)   p_kst 8.183000e-01   p_cons 3.060000e-02   p_joint 1.830000e-01

Joint ci ratio: 4.627181e-02	ci left: 1.226080e-01	ci right 1.284355e-01	k: 6275	n:50000
Cons ci ratio: 9.863736e-02	ci left: 2.910765e-02	ci right 3.214716e-02	k: 1530	n:50000
KS ci ratio: 8.259242e-03	ci left: 8.149521e-01	ci right 8.217309e-01	k: 40918	n:50000
SIGLEC10   50000 perm   10 sec   (4968 perm/sec)   p_kst 8.183600e-01   p_cons 3.060000e-02   p_joint 1.255000e-01

Outputting figure to mutsig2_images.part000000000157/SIGLEC10.3_2138_50000_0.81836_0.0306_0.1255.png
                gene_name: SIGLEC10
               theta_stop: 0.099 
                    nperm: 50000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.031 
      ci_cons_bounds_left: 0.029 
     ci_cons_bounds_right: 0.032 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 25 percent done.
SHPRH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.922919e-02	ci left: 2.954883e-01	ci right 3.136257e-01	k: 3045	n:10000
KS ci ratio: 1.224866e-01	ci left: 8.718231e-02	ci right 9.865611e-02	k: 928	n:10000
SHPRH   10000 perm   2 sec   (5057 perm/sec)   p_kst 9.280000e-02   p_cons 3.045000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 4.205513e-02	ci left: 2.964362e-01	ci right 3.092211e-01	k: 6056	n:20000
KS ci ratio: 8.821853e-02	ci left: 8.587260e-02	ci right 9.384710e-02	k: 1796	n:20000
SHPRH   20000 perm   4 sec   (4546 perm/sec)   p_kst 8.980000e-02   p_cons 3.028000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000157/SHPRH.2_5212_20000_0.0898_0.3028_1.png
                gene_name: SHPRH
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.090 
        ci_ks_bounds_left: 0.086 
       ci_ks_bounds_right: 0.094 
                   p_cons: 0.30 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 38 percent done.
SIDT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.836201e-03	ci left: 9.825290e-01	ci right 9.873825e-01	k: 9851	n:10000
Cons ci ratio: 2.223957e-02	ci left: 7.479640e-01	ci right 7.648864e-01	k: 7565	n:10000
KS ci ratio: 1.060242e-02	ci left: 9.267855e-01	ci right 9.367612e-01	k: 9319	n:10000
SIDT1   10000 perm   2 sec   (6004 perm/sec)   p_kst 9.319000e-01   p_cons 7.565000e-01   p_joint 9.851000e-01

Outputting figure to mutsig2_images.part000000000157/SIDT1.2_2584_10000_0.9319_0.7565_0.9851.png
                gene_name: SIDT1
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 50 percent done.
SIGIRR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.962739e-02	ci left: 6.268832e-01	ci right 6.458373e-01	k: 6364	n:10000
Cons ci ratio: 6.905540e-02	ci left: 2.352124e-01	ci right 2.521372e-01	k: 2436	n:10000
KS ci ratio: 2.547181e-02	ci left: 6.940369e-01	ci right 7.120447e-01	k: 7031	n:10000
SIGIRR   10000 perm   1 sec   (6704 perm/sec)   p_kst 7.031000e-01   p_cons 2.436000e-01   p_joint 6.364000e-01

Outputting figure to mutsig2_images.part000000000157/SIGIRR.2_1269_10000_0.7031_0.2436_0.6364.png
                gene_name: SIGIRR
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 62 percent done.
SIGLEC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.244472e-02	ci left: 7.445255e-01	ci right 7.615269e-01	k: 7531	n:10000
Cons ci ratio: 1.388992e-02	ci left: 8.821675e-01	ci right 8.946052e-01	k: 8885	n:10000
KS ci ratio: 3.386992e-02	ci left: 5.627338e-01	ci right 5.822240e-01	k: 5725	n:10000
SIGLEC1   10000 perm   2 sec   (4954 perm/sec)   p_kst 5.725000e-01   p_cons 8.885000e-01   p_joint 7.531000e-01

Outputting figure to mutsig2_images.part000000000157/SIGLEC1.2_5214_10000_0.5725_0.8885_0.7531.png
                gene_name: SIGLEC1
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.74 
    ci_joint_bounds_right: 0.76 

Current progress: 75 percent done.
SIK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.558138e-02	ci left: 8.567172e-01	ci right 8.702703e-01	k: 8636	n:10000
Cons ci ratio: 1.892472e-02	ci left: 8.031864e-01	ci right 8.186320e-01	k: 8110	n:10000
KS ci ratio: 2.067928e-02	ci left: 7.740800e-01	ci right 7.903553e-01	k: 7823	n:10000
SIK2   10000 perm   2 sec   (5689 perm/sec)   p_kst 7.823000e-01   p_cons 8.110000e-01   p_joint 8.636000e-01

Outputting figure to mutsig2_images.part000000000157/SIK2.2_2841_10000_0.7823_0.811_0.8636.png
                gene_name: SIK2
               theta_stop: 0.021 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.82 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 88 percent done.
SIN3A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.010768e-02	ci left: 7.836063e-01	ci right 7.996234e-01	k: 7917	n:10000
KS ci ratio: 7.499060e-02	ci left: 2.064889e-01	ci right 2.226777e-01	k: 2145	n:10000
SIN3A   10000 perm   2 sec   (5660 perm/sec)   p_kst 2.145000e-01   p_cons 7.917000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000157/SIN3A.2_3902_10000_0.2145_0.7917_1.png
                gene_name: SIN3A
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000157
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 157 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4398330: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000158> was used as the working directory.
Started at Wed Oct 24 16:16:39 2012
Results reported at Wed Oct 24 16:17:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000158.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000158.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 158  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000158.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     77.39 sec.
    Max Memory :      1103 MB
    Max Swap   :      4068 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
158
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 158
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 158: processing genes 14085 - 14174
Calculating significance of each gene.
Using projection method.
14085	SIPA1L3	1.918415e-01
14086	SIRPA	1.625934e-01
14087	SIRPB1	1
14088	SIRPB2	1
14089	SIRPD	5.298735e-02
14090	SIRPG	1
14091	SIRT1	1
14092	SIRT2	1
14093	SIRT3	1
14094	SIRT4	1
14095	SIRT5	1
14096	SIRT6	5.143876e-03
14097	SIRT7	1
14098	SIT1	1
14099	SIVA1	1
14100	SIX1	1
14101	SIX2	1
14102	SIX3	1
14103	SIX4	1
14104	SIX5	1
14105	SIX6	1
14106	SKA1	1
14107	SKA2	1
14108	SKA3	1
14109	SKAP1	1.191639e-01
14110	SKAP2	1
14111	SKI	1
14112	SKIL	2.109299e-01
14113	SKIV2L	2.631141e-01
14114	SKIV2L2	1
14115	SKP1	1
14116	SKP2	1
14117	SLA	7.147610e-02
14118	SLA2	1
14119	SLAIN1	1
14120	SLAIN2	1
14121	SLAMF1	1
14122	SLAMF6	1
14123	SLAMF7	1
14124	SLAMF8	1
14125	SLAMF9	1
14126	SLBP	1
14127	SLC10A1	1
14128	SLC10A2	1
14129	SLC10A3	1
14130	SLC10A4	1
14131	SLC10A5	1
14132	SLC10A6	1
14133	SLC10A7	1
14134	SLC11A1	1
14135	SLC11A2	2.639645e-01
14136	SLC12A1	1
14137	SLC12A2	1
14138	SLC12A3	1
14139	SLC12A4	3.471044e-01
14140	SLC12A5	1
14141	SLC12A6	4.748828e-01
14142	SLC12A7	1
14143	SLC12A8	1
14144	SLC12A9	1
14145	SLC13A1	3.870591e-02
14146	SLC13A2	1
14147	SLC13A3	1
14148	SLC13A4	1
14149	SLC13A5	2.613733e-01
14150	SLC14A1	1
14151	SLC14A2	1
14152	SLC15A1	1
14153	SLC15A2	1
14154	SLC15A3	1
14155	SLC15A4	1
14156	SLC16A1	1
14157	SLC16A10	1
14158	SLC16A11	1
14159	SLC16A12	8.138897e-02
14160	SLC16A13	1
14161	SLC16A14	1
14162	SLC16A2	1
14163	SLC16A3	1
14164	SLC16A4	1
14165	SLC16A5	1.028699e-01
14166	SLC16A6	1
14167	SLC16A7	1
14168	SLC16A9	1
14169	SLC17A1	1
14170	SLC17A2	1
14171	SLC17A3	1
14172	SLC17A4	1.133915e-01
14173	SLC17A5	1
14174	SLC17A6	1
Done

Running MutSig 2:
Scatter job 158: processing genes 14085 - 14174
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC16A5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.654491e-03	ci left: 9.492931e-01	ci right 9.576401e-01	k: 9536	n:10000
Cons ci ratio: 1.737651e-02	ci left: 8.283916e-01	ci right 8.430123e-01	k: 8358	n:10000
KS ci ratio: 1.073223e-01	ci left: 1.113483e-01	ci right 1.240753e-01	k: 1176	n:10000
SLC16A5   10000 perm   2 sec   (6396 perm/sec)   p_kst 1.176000e-01   p_cons 8.358000e-01   p_joint 9.536000e-01

Joint ci ratio: 9.906965e-03	ci left: 8.822768e-01	ci right 8.911105e-01	k: 17735	n:20000
Cons ci ratio: 1.298278e-02	ci left: 8.147053e-01	ci right 8.254015e-01	k: 16402	n:20000
KS ci ratio: 7.698740e-02	ci left: 1.103149e-01	ci right 1.191974e-01	k: 2294	n:20000
SLC16A5   20000 perm   5 sec   (3786 perm/sec)   p_kst 1.147000e-01   p_cons 8.201000e-01   p_joint 8.867500e-01

Outputting figure to mutsig2_images.part000000000158/SLC16A5.2_1538_20000_0.1147_0.8201_0.88675.png
                gene_name: SLC16A5
               theta_stop: 0.077 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000158
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 158 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4398333: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000159> was used as the working directory.
Started at Wed Oct 24 16:16:55 2012
Results reported at Wed Oct 24 16:18:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000159.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000159.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 159  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000159.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     82.36 sec.
    Max Memory :      1023 MB
    Max Swap   :      3870 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
159
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 159
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 159: processing genes 14175 - 14264
Calculating significance of each gene.
Using projection method.
14175	SLC17A7	1
14176	SLC17A8	1
14177	SLC17A9	1
14178	SLC18A1	1
14179	SLC18A2	9.062237e-02
14180	SLC18A3	1
14181	SLC19A1	1
14182	SLC19A2	1
14183	SLC19A3	7.820448e-02
14184	SLC1A1	1
14185	SLC1A2	9.986409e-03
14186	SLC1A3	1
14187	SLC1A4	1.519610e-01
14188	SLC1A5	1.389408e-01
14189	SLC1A6	1
14190	SLC1A7	1
14191	SLC20A1	3.058749e-01
14192	SLC20A2	1
14193	SLC22A1	7.291359e-02
14194	SLC22A10	1
14195	SLC22A11	1
14196	SLC22A12	1
14197	SLC22A13	1
14198	SLC22A14	1
14199	SLC22A15	1
14200	SLC22A16	1
14201	SLC22A17	1.932217e-01
14202	SLC22A18	1
14203	SLC22A2	1
14204	SLC22A20	1
14205	SLC22A23	1
14206	SLC22A25	1
14207	SLC22A3	1
14208	SLC22A4	1
14209	SLC22A5	1
14210	SLC22A6	1
14211	SLC22A7	1
14212	SLC22A8	6.348812e-02
14213	SLC22A9	2.651549e-01
14214	SLC23A1	1
14215	SLC23A2	1
14216	SLC23A3	1
14217	SLC24A1	1
14218	SLC24A2	1
14219	SLC24A3	1
14220	SLC24A4	1.771031e-01
14221	SLC24A5	5.224713e-02
14222	SLC24A6	1
14223	SLC25A1	1.343391e-02
14224	SLC25A10	1
14225	SLC25A11	1
14226	SLC25A12	1
14227	SLC25A13	1
14228	SLC25A14	1
14229	SLC25A15	1
14230	SLC25A16	1
14231	SLC25A17	1
14232	SLC25A18	1
14233	SLC25A19	1
14234	SLC25A2	1
14235	SLC25A20	1
14236	SLC25A21	8.940278e-02
14237	SLC25A22	1
14238	SLC25A23	1.705999e-01
14239	SLC25A24	1
14240	SLC25A25	1
14241	SLC25A26	1
14242	SLC25A27	1
14243	SLC25A28	1
14244	SLC25A29	1
14245	SLC25A3	1.012217e-01
14246	SLC25A30	1
14247	SLC25A31	1
14248	SLC25A32	1
14249	SLC25A33	1
14250	SLC25A34	1
14251	SLC25A35	1
14252	SLC25A36	1
14253	SLC25A37	1
14254	SLC25A38	1
14255	SLC25A39	1
14256	SLC25A4	1
14257	SLC25A40	3.622518e-02
14258	SLC25A41	1
14259	SLC25A42	1.357395e-01
14260	SLC25A43	1
14261	SLC25A44	1
14262	SLC25A45	1
14263	SLC25A46	1
14264	SLC25A5	1
Done

Running MutSig 2:
Scatter job 159: processing genes 14175 - 14264
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC1A2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.620383e-02	ci left: 8.470282e-01	ci right 8.609649e-01	k: 8541	n:10000
Cons ci ratio: 5.815626e-02	ci left: 3.032226e-01	ci right 3.214868e-01	k: 3123	n:10000
KS ci ratio: 2.385131e-02	ci left: 7.209804e-01	ci right 7.384856e-01	k: 7298	n:10000
SLC1A2   10000 perm   2 sec   (6172 perm/sec)   p_kst 7.298000e-01   p_cons 3.123000e-01   p_joint 8.541000e-01

Outputting figure to mutsig2_images.part000000000159/SLC1A2.2_1769_10000_0.7298_0.3123_0.8541.png
                gene_name: SLC1A2
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.85 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.86 

Current progress: 50 percent done.
SLC25A3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.447022e-02	ci left: 3.318056e-01	ci right 3.504870e-01	k: 3411	n:10000
Cons ci ratio: 8.310267e-02	ci left: 1.743827e-01	ci right 1.896031e-01	k: 1819	n:10000
KS ci ratio: 1.146865e-01	ci left: 9.857012e-02	ci right 1.106613e-01	k: 1045	n:10000
SLC25A3   10000 perm   1 sec   (6933 perm/sec)   p_kst 1.045000e-01   p_cons 1.819000e-01   p_joint 3.411000e-01

Joint ci ratio: 3.165163e-02	ci left: 4.271161e-01	ci right 4.409031e-01	k: 8680	n:20000
Cons ci ratio: 5.952428e-02	ci left: 1.728691e-01	ci right 1.835247e-01	k: 3563	n:20000
KS ci ratio: 8.088140e-02	ci left: 1.008332e-01	ci right 1.093820e-01	k: 2101	n:20000
SLC25A3   20000 perm   3 sec   (6131 perm/sec)   p_kst 1.050500e-01   p_cons 1.781500e-01   p_joint 4.340000e-01

Outputting figure to mutsig2_images.part000000000159/SLC25A3.2_1243_20000_0.10505_0.17815_0.434.png
                gene_name: SLC25A3
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.44 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000159
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 159 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1428>
Subject: Job 4398338: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000160> was used as the working directory.
Started at Wed Oct 24 16:16:55 2012
Results reported at Wed Oct 24 16:19:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000160.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000160.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 160  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000160.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    154.50 sec.
    Max Memory :      1250 MB
    Max Swap   :      3937 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
160
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 160
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 160: processing genes 14265 - 14354
Calculating significance of each gene.
Using projection method.
14265	SLC25A6	1
14266	SLC26A1	1
14267	SLC26A10	1
14268	SLC26A11	1
14269	SLC26A2	1
14270	SLC26A3	1
14271	SLC26A4	1
14272	SLC26A5	1.519091e-01
14273	SLC26A6	1
14274	SLC26A7	2.773620e-01
14275	SLC26A8	3.858589e-02
14276	SLC26A9	1
14277	SLC27A1	1
14278	SLC27A2	1.386600e-01
14279	SLC27A3	1
14280	SLC27A4	1
14281	SLC27A5	1
14282	SLC27A6	1
14283	SLC28A1	1.936341e-01
14284	SLC28A2	1
14285	SLC28A3	1
14286	SLC29A1	1
14287	SLC29A2	1
14288	SLC29A3	1
14289	SLC29A4	1.355320e-01
14290	SLC2A1	2.017793e-01
14291	SLC2A10	1
14292	SLC2A11	1
14293	SLC2A12	1.252896e-01
14294	SLC2A13	1
14295	SLC2A14	1
14296	SLC2A2	1
14297	SLC2A3	2.405930e-01
14298	SLC2A4	1
14299	SLC2A4RG	1
14300	SLC2A5	1
14301	SLC2A6	1
14302	SLC2A7	1
14303	SLC2A8	1.102535e-01
14304	SLC2A9	1
14305	SLC30A1	1
14306	SLC30A10	1
14307	SLC30A2	1
14308	SLC30A3	1
14309	SLC30A4	1
14310	SLC30A5	1
14311	SLC30A6	9.527942e-02
14312	SLC30A7	1
14313	SLC30A8	1
14314	SLC30A9	1
14315	SLC31A1	1
14316	SLC31A2	1
14317	SLC32A1	1
14318	SLC33A1	1.939562e-02
14319	SLC34A1	2.950871e-01
14320	SLC34A2	2.135802e-01
14321	SLC34A3	5.921206e-02
14322	SLC35A1	1
14323	SLC35A2	1
14324	SLC35A3	1
14325	SLC35A4	1
14326	SLC35A5	1
14327	SLC35B1	1
14328	SLC35B2	1
14329	SLC35B3	1
14330	SLC35B4	1
14331	SLC35C1	1
14332	SLC35C2	1.999096e-01
14333	SLC35D1	1
14334	SLC35D2	1
14335	SLC35D3	1
14336	SLC35E1	1
14337	SLC35E3	1.427753e-01
14338	SLC35E4	1
14339	SLC35F1	1
14340	SLC35F2	1
14341	SLC35F3	7.201288e-02
14342	SLC35F4	1
14343	SLC35F5	1
14344	SLC36A1	1
14345	SLC36A2	1.252549e-01
14346	SLC36A3	1
14347	SLC36A4	1
14348	SLC37A1	1
14349	SLC37A2	1.018270e-01
14350	SLC37A3	1
14351	SLC37A4	1
14352	SLC38A1	1
14353	SLC38A10	1
14354	SLC38A11	1
Done

Running MutSig 2:
Scatter job 160: processing genes 14265 - 14354
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC26A8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.630636e-02	ci left: 5.283689e-01	ci right 5.480089e-01	k: 5382	n:10000
Cons ci ratio: 2.517934e-02	ci left: 6.988779e-01	ci right 7.168009e-01	k: 7079	n:10000
KS ci ratio: 9.671176e-02	ci left: 1.342342e-01	ci right 1.479756e-01	k: 1410	n:10000
SLC26A8   10000 perm   2 sec   (5218 perm/sec)   p_kst 1.410000e-01   p_cons 7.079000e-01   p_joint 5.382000e-01

Outputting figure to mutsig2_images.part000000000160/SLC26A8.2_2989_10000_0.141_0.7079_0.5382.png
                gene_name: SLC26A8
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 33 percent done.
SLC2A3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.595455e-02	ci left: 6.860719e-01	ci right 7.042143e-01	k: 6952	n:10000
KS ci ratio: 1.710368e-02	ci left: 8.327676e-01	ci right 8.472337e-01	k: 8401	n:10000
SLC2A3   10000 perm   2 sec   (6542 perm/sec)   p_kst 8.401000e-01   p_cons 6.952000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000160/SLC2A3.2_1531_10000_0.8401_0.6952_1.png
                gene_name: SLC2A3
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.70 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
SLC33A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.775073e-02	ci left: 2.422288e-01	ci right 2.593166e-01	k: 2507	n:10000
KS ci ratio: 6.601149e-02	ci left: 2.520172e-01	ci right 2.693224e-01	k: 2606	n:10000
SLC33A1   10000 perm   2 sec   (6543 perm/sec)   p_kst 2.606000e-01   p_cons 2.507000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000160/SLC33A1.2_1674_10000_0.2606_0.2507_1.png
                gene_name: SLC33A1
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000160
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 160 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4398340: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000161> was used as the working directory.
Started at Wed Oct 24 16:16:58 2012
Results reported at Wed Oct 24 16:19:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000161.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000161.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 161  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000161.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    219.29 sec.
    Max Memory :      1204 MB
    Max Swap   :      3968 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
161
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 161
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 161: processing genes 14355 - 14443
Calculating significance of each gene.
Using projection method.
14355	SLC38A2	2.338891e-01
14356	SLC38A3	1
14357	SLC38A4	1
14358	SLC38A5	1
14359	SLC38A6	1
14360	SLC38A7	1
14361	SLC38A8	1
14362	SLC38A9	1
14363	SLC39A1	1
14364	SLC39A10	3.650742e-02
14365	SLC39A11	1
14366	SLC39A12	1
14367	SLC39A13	1
14368	SLC39A14	1
14369	SLC39A2	1
14370	SLC39A3	1
14371	SLC39A4	1
14372	SLC39A5	3.420315e-02
14373	SLC39A6	1
14374	SLC39A7	1
14375	SLC39A8	1
14376	SLC39A9	1
14377	SLC3A1	1
14378	SLC3A2	1
14379	SLC40A1	1
14380	SLC41A1	1
14381	SLC41A2	1.765670e-01
14382	SLC41A3	1
14383	SLC43A1	1
14384	SLC43A2	1
14385	SLC43A3	1
14386	SLC44A1	1
14387	SLC44A2	1
14388	SLC44A3	1
14389	SLC44A4	1.729988e-01
14390	SLC44A5	1
14391	SLC45A1	5.902567e-02
14392	SLC45A2	1.374903e-01
14393	SLC45A3	1.911287e-01
14394	SLC45A4	2.298886e-01
14395	SLC46A1	1
14396	SLC46A2	1
14397	SLC46A3	1.413468e-01
14398	SLC47A1	6.671799e-02
14399	SLC47A2	1
14400	SLC4A1	1.821251e-01
14401	SLC4A10	1.792519e-01
14402	SLC4A11	2.255551e-01
14403	SLC4A1AP	5.499536e-02
14404	SLC4A2	1
14405	SLC4A3	4.893013e-01
14406	SLC4A4	1.511386e-01
14407	SLC4A5	1
14408	SLC4A7	1
14409	SLC4A8	1
14410	SLC4A9	1
14411	SLC5A1	1.857549e-01
14412	SLC5A10	1
14413	SLC5A11	1
14414	SLC5A12	1
14415	SLC5A2	1
14416	SLC5A3	1
14417	SLC5A4	1
14418	SLC5A5	2.558592e-01
14419	SLC5A6	1
14420	SLC5A7	1
14421	SLC5A8	1
14422	SLC5A9	1
14423	SLC6A1	1
14424	SLC6A11	1.484868e-01
14425	SLC6A12	1
14426	SLC6A13	1
14427	SLC6A14	1
14428	SLC6A15	1
14429	SLC6A16	1
14430	SLC6A17	1
14431	SLC6A18	1
14432	SLC6A19	1.985170e-01
14433	SLC6A2	1
14434	SLC6A20	1
14435	SLC6A3	1
14436	SLC6A4	1
14437	SLC6A5	2.196916e-01
14438	SLC6A6	1
14439	SLC6A7	1
14440	SLC6A8	1
14441	SLC6A9	1
14442	SLC7A1	1
14443	SLC7A10	1
Done

Running MutSig 2:
Scatter job 161: processing genes 14355 - 14443
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC39A5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.408775e-02	ci left: 1.408974e-01	ci right 1.549084e-01	k: 1478	n:10000
Cons ci ratio: 8.991607e-02	ci left: 1.524718e-01	ci right 1.669270e-01	k: 1596	n:10000
KS ci ratio: 1.013601e-01	ci left: 1.234670e-01	ci right 1.367493e-01	k: 1300	n:10000
SLC39A5   10000 perm   2 sec   (4808 perm/sec)   p_kst 1.300000e-01   p_cons 1.596000e-01   p_joint 1.478000e-01

Joint ci ratio: 7.092353e-02	ci left: 1.277807e-01	ci right 1.372264e-01	k: 2649	n:20000
Cons ci ratio: 6.214010e-02	ci left: 1.607684e-01	ci right 1.711289e-01	k: 3318	n:20000
KS ci ratio: 7.075435e-02	ci left: 1.283224e-01	ci right 1.377845e-01	k: 2660	n:20000
SLC39A5   20000 perm   7 sec   (2790 perm/sec)   p_kst 1.330000e-01   p_cons 1.659000e-01   p_joint 1.324500e-01

Outputting figure to mutsig2_images.part000000000161/SLC39A5.3_1663_20000_0.133_0.1659_0.13245.png
                gene_name: SLC39A5
               theta_stop: 0.071 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 33 percent done.
SLC39A10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.634954e-03	ci left: 9.495015e-01	ci right 9.578316e-01	k: 9538	n:10000
Cons ci ratio: 2.423853e-02	ci left: 7.145185e-01	ci right 7.321512e-01	k: 7234	n:10000
KS ci ratio: 3.476387e-02	ci left: 5.499041e-01	ci right 5.694611e-01	k: 5597	n:10000
SLC39A10   10000 perm   2 sec   (4496 perm/sec)   p_kst 5.597000e-01   p_cons 7.234000e-01   p_joint 9.538000e-01

Outputting figure to mutsig2_images.part000000000161/SLC39A10.2_2532_10000_0.5597_0.7234_0.9538.png
                gene_name: SLC39A10
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 67 percent done.
SLC4A1AP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.988650e-03	ci left: 9.342335e-01	ci right 9.437088e-01	k: 9391	n:10000
Cons ci ratio: 4.990243e-02	ci left: 3.719650e-01	ci right 3.911040e-01	k: 3815	n:10000
KS ci ratio: 2.485100e-02	ci left: 7.043254e-01	ci right 7.221502e-01	k: 7133	n:10000
SLC4A1AP   10000 perm   2 sec   (5461 perm/sec)   p_kst 7.133000e-01   p_cons 3.815000e-01   p_joint 9.391000e-01

Outputting figure to mutsig2_images.part000000000161/SLC4A1AP.2_2447_10000_0.7133_0.3815_0.9391.png
                gene_name: SLC4A1AP
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000161
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 161 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 4398343: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000162> was used as the working directory.
Started at Wed Oct 24 16:17:04 2012
Results reported at Wed Oct 24 16:19:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000162.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000162.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 162  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000162.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    262.36 sec.
    Max Memory :      1619 MB
    Max Swap   :      3925 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
162
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 162
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 162: processing genes 14444 - 14533
Calculating significance of each gene.
Using projection method.
14444	SLC7A11	1
14445	SLC7A13	1
14446	SLC7A14	1.574915e-02
14447	SLC7A2	1
14448	SLC7A3	1
14449	SLC7A4	1
14450	SLC7A5	1
14451	SLC7A6	1
14452	SLC7A6OS	1
14453	SLC7A7	1
14454	SLC7A8	1
14455	SLC7A9	1
14456	SLC8A1	1.800460e-01
14457	SLC8A2	1
14458	SLC8A3	1
14459	SLC9A1	3.519212e-02
14460	SLC9A10	2.581027e-01
14461	SLC9A11	1
14462	SLC9A2	1
14463	SLC9A3	1
14464	SLC9A3R1	1
14465	SLC9A3R2	1
14466	SLC9A4	1.609996e-01
14467	SLC9A5	2.869999e-01
14468	SLC9A6	1
14469	SLC9A7	2.541181e-02
14470	SLC9A8	1
14471	SLC9A9	1
14472	SLCO1A2	1
14473	SLCO1B1	1
14474	SLCO1B3	1
14475	SLCO1C1	3.106233e-01
14476	SLCO2A1	1.911477e-01
14477	SLCO2B1	1
14478	SLCO3A1	1
14479	SLCO4A1	1
14480	SLCO4C1	1
14481	SLCO5A1	1
14482	SLCO6A1	1
14483	SLFN11	8.248495e-02
14484	SLFN12	1
14485	SLFN13	1
14486	SLFN5	3.965770e-01
14487	SLFNL1	1
14488	SLIT1	1
14489	SLIT2	4.483714e-01
14490	SLIT3	1
14491	SLITRK1	1.627504e-01
14492	SLITRK2	1
14493	SLITRK3	1.366325e-01
14494	SLITRK4	1
14495	SLITRK5	4.688627e-02
14496	SLITRK6	1
14497	SLK	1
14498	SLMAP	1.557551e-01
14499	SLMO1	1
14500	SLMO2	1
14501	SLN	1
14502	SLPI	1
14503	SLTM	1
14504	SLU7	1
14505	SLURP1	1
14506	SMAD1	1
14507	SMAD2	1
14508	SMAD3	1
14509	SMAD4	4.898197e-02
14510	SMAD5	5.070670e-02
14511	SMAD6	1
14512	SMAD7	1
14513	SMAD9	1
14514	SMAGP	1
14515	SMAP1	1
14516	SMAP2	1
14517	SMARCA1	1
14518	SMARCA2	1
14519	SMARCA4	2.514975e-01
14520	SMARCA5	1
14521	SMARCAD1	7.523214e-02
14522	SMARCAL1	3.310459e-01
14523	SMARCB1	1
14524	SMARCC1	2.898711e-02
14525	SMARCC2	1.195430e-01
14526	SMARCD1	1
14527	SMARCD2	1
14528	SMARCD3	1.778035e-01
14529	SMARCE1	2.030517e-02
14530	SMC1A	1
14531	SMC1B	3.441550e-01
14532	SMC2	3.751940e-01
14533	SMC3	2.513990e-01
Done

Running MutSig 2:
Scatter job 162: processing genes 14444 - 14533
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC7A14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.543566e-02	ci left: 8.589625e-01	ci right 8.724236e-01	k: 8658	n:10000
KS ci ratio: 1.705912e-02	ci left: 8.334802e-01	ci right 8.479208e-01	k: 8408	n:10000
SLC7A14   10000 perm   2 sec   (5698 perm/sec)   p_kst 8.408000e-01   p_cons 8.658000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SLC7A14.2_2344_10000_0.8408_0.8658_1.png
                gene_name: SLC7A14
               theta_stop: 0.017 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 11 percent done.
SLC9A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.540473e-02	ci left: 6.951461e-01	ci right 7.131348e-01	k: 7042	n:10000
KS ci ratio: 8.693458e-03	ci left: 9.488764e-01	ci right 9.572571e-01	k: 9532	n:10000
SLC9A1   10000 perm   2 sec   (5236 perm/sec)   p_kst 9.532000e-01   p_cons 7.042000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SLC9A1.2_2496_10000_0.9532_0.7042_1.png
                gene_name: SLC9A1
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.71 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 22 percent done.
SLC9A7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.988391e-02	ci left: 6.228625e-01	ci right 6.418603e-01	k: 6324	n:10000
Cons ci ratio: 8.051746e-02	ci left: 1.838286e-01	ci right 1.993515e-01	k: 1915	n:10000
KS ci ratio: 5.297765e-02	ci left: 3.443228e-01	ci right 3.631625e-01	k: 3537	n:10000
SLC9A7   10000 perm   2 sec   (6011 perm/sec)   p_kst 3.537000e-01   p_cons 1.915000e-01   p_joint 6.324000e-01

Outputting figure to mutsig2_images.part000000000162/SLC9A7.2_2246_10000_0.3537_0.1915_0.6324.png
                gene_name: SLC9A7
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 33 percent done.
SLFN11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.366397e-02	ci left: 4.364239e-01	ci right 4.560074e-01	k: 4462	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
SLFN11   10000 perm   2 sec   (4853 perm/sec)   p_kst 1   p_cons 4.462000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SLFN11.2_2722_10000_1_0.4462_1.png
                gene_name: SLFN11
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 44 percent done.
SLITRK5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.768563e-02	ci left: 8.234072e-01	ci right 8.381996e-01	k: 8309	n:10000
KS ci ratio: 2.756493e-02	ci left: 6.597794e-01	ci right 6.783220e-01	k: 6691	n:10000
SLITRK5   10000 perm   2 sec   (5409 perm/sec)   p_kst 6.691000e-01   p_cons 8.309000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SLITRK5.2_2881_10000_0.6691_0.8309_1.png
                gene_name: SLITRK5
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.84 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 56 percent done.
SMAD5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.478410e-02	ci left: 2.592386e-01	ci right 2.766968e-01	k: 2679	n:10000
Cons ci ratio: 3.752127e-02	ci left: 5.119543e-01	ci right 5.316330e-01	k: 5218	n:10000
KS ci ratio: 1.342088e-01	ci left: 7.330186e-02	ci right 8.394515e-02	k: 785	n:10000
SMAD5   10000 perm   2 sec   (6525 perm/sec)   p_kst 7.850000e-02   p_cons 5.218000e-01   p_joint 2.679000e-01

Joint ci ratio: 8.049680e-02	ci left: 1.017171e-01	ci right 1.102979e-01	k: 2119	n:20000
Cons ci ratio: 2.636908e-02	ci left: 5.179509e-01	ci right 5.318419e-01	k: 10498	n:20000
KS ci ratio: 9.549654e-02	ci left: 7.397763e-02	ci right 8.144569e-02	k: 1553	n:20000
SMAD5   20000 perm   4 sec   (5663 perm/sec)   p_kst 7.765000e-02   p_cons 5.249000e-01   p_joint 1.059500e-01

Outputting figure to mutsig2_images.part000000000162/SMAD5.2_1421_20000_0.07765_0.5249_0.10595.png
                gene_name: SMAD5
               theta_stop: 0.095 
                    nperm: 20000 
                     p_ks: 0.078 
        ci_ks_bounds_left: 0.074 
       ci_ks_bounds_right: 0.081 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 67 percent done.
SMARCAD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.183513e-02	ci left: 7.547419e-01	ci right 7.715046e-01	k: 7632	n:10000
Cons ci ratio: 6.231794e-02	ci left: 2.745815e-01	ci right 2.923448e-01	k: 2834	n:10000
KS ci ratio: 4.594381e-02	ci left: 4.114968e-01	ci right 4.309491e-01	k: 4212	n:10000
SMARCAD1   10000 perm   2 sec   (5619 perm/sec)   p_kst 4.212000e-01   p_cons 2.834000e-01   p_joint 7.632000e-01

Outputting figure to mutsig2_images.part000000000162/SMARCAD1.2_3179_10000_0.4212_0.2834_0.7632.png
                gene_name: SMARCAD1
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.76 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.77 

Current progress: 78 percent done.
SMARCC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.296607e-02	ci left: 3.444222e-01	ci right 3.632630e-01	k: 3538	n:10000
KS ci ratio: 3.023188e-02	ci left: 6.174357e-01	ci right 6.364903e-01	k: 6270	n:10000
SMARCC1   10000 perm   2 sec   (5235 perm/sec)   p_kst 6.270000e-01   p_cons 3.538000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SMARCC1.2_3430_10000_0.627_0.3538_1.png
                gene_name: SMARCC1
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 89 percent done.
SMARCE1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.017843e-02	ci left: 3.693784e-01	ci right 3.884922e-01	k: 3789	n:10000
KS ci ratio: 2.448693e-02	ci left: 7.103801e-01	ci right 7.280920e-01	k: 7193	n:10000
SMARCE1   10000 perm   2 sec   (6664 perm/sec)   p_kst 7.193000e-01   p_cons 3.789000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SMARCE1.2_1276_10000_0.7193_0.3789_1.png
                gene_name: SMARCE1
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000162
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 162 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4398394: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000163> was used as the working directory.
Started at Wed Oct 24 16:17:09 2012
Results reported at Wed Oct 24 16:19:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000163.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000163.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 163  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000163.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    152.84 sec.
    Max Memory :      1178 MB
    Max Swap   :      3939 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
163
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 163
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 163: processing genes 14534 - 14623
Calculating significance of each gene.
Using projection method.
14534	SMC4	3.824435e-01
14535	SMC5	1
14536	SMC6	1.589761e-01
14537	SMCHD1	4.544783e-01
14538	SMCP	3.631510e-02
14539	SMCR7	1
14540	SMCR7L	1
14541	SMCR8	1
14542	SMEK1	1
14543	SMEK2	1
14544	SMG1	4.228108e-03
14545	SMG5	1
14546	SMG6	1
14547	SMG7	1
14548	SMNDC1	1
14549	SMO	1
14550	SMOC1	1
14551	SMOC2	5.231240e-02
14552	SMOX	1
14553	SMPD1	1
14554	SMPD2	1
14555	SMPD3	1
14556	SMPD4	1
14557	SMPDL3A	1
14558	SMPDL3B	1
14559	SMPX	1
14560	SMR3A	1
14561	SMR3B	1
14562	SMS	1
14563	SMTN	1
14564	SMTNL1	1
14565	SMTNL2	1
14566	SMU1	1
14567	SMUG1	1
14568	SMURF1	1
14569	SMURF2	1
14570	SMYD1	1
14571	SMYD2	1
14572	SMYD3	1
14573	SMYD4	1.031390e-02
14574	SMYD5	1
14575	SNAI1	1.031309e-01
14576	SNAI2	1
14577	SNAI3	1
14578	SNAP23	1
14579	SNAP25	1
14580	SNAP29	1
14581	SNAP47	1
14582	SNAP91	1
14583	SNAPC1	1
14584	SNAPC2	1
14585	SNAPC3	1
14586	SNAPC4	1
14587	SNAPC5	1
14588	SNAPIN	1
14589	SNCA	1
14590	SNCAIP	1
14591	SNCB	1
14592	SNCG	1
14593	SND1	1
14594	SNED1	1
14595	SNF8	5.659214e-02
14596	SNHG3-RCC1	1
14597	SNIP1	1.996829e-01
14598	SNN	1
14599	SNPH	1.050374e-01
14600	SNRK	1
14601	SNRNP200	1
14602	SNRNP25	1
14603	SNRNP27	2.294613e-02
14604	SNRNP35	1
14605	SNRNP40	1
14606	SNRNP48	1
14607	SNRNP70	1.278997e-01
14608	SNRPA	1
14609	SNRPA1	1
14610	SNRPB	1
14611	SNRPB2	1
14612	SNRPC	1
14613	SNRPD1	1
14614	SNRPD2	1.142027e-02
14615	SNRPD3	1
14616	SNRPE	1
14617	SNRPF	1
14618	SNRPG	1
14619	SNRPN	1
14620	SNTA1	1.187697e-03
14621	SNTB1	1
14622	SNTB2	1
14623	SNTG1	1
Done

Running MutSig 2:
Scatter job 163: processing genes 14534 - 14623
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SMG1
Processing conservation and coverage...
88% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.435169e-02	ci left: 1.700559e-01	ci right 1.851324e-01	k: 1775	n:10000
Cons ci ratio: 2.383922e-02	ci left: 7.211824e-01	ci right 7.386835e-01	k: 7300	n:10000
KS ci ratio: 1.023114e-01	ci left: 1.214132e-01	ci right 1.346043e-01	k: 1279	n:10000
SMG1   10000 perm   3 sec   (3611 perm/sec)   p_kst 1.279000e-01   p_cons 7.300000e-01   p_joint 1.775000e-01

Joint ci ratio: 4.502865e-02	ci left: 2.685716e-01	ci right 2.809940e-01	k: 5495	n:20000
Cons ci ratio: 1.696407e-02	ci left: 7.212716e-01	ci right 7.336623e-01	k: 14550	n:20000
KS ci ratio: 7.139006e-02	ci left: 1.263036e-01	ci right 1.357040e-01	k: 2619	n:20000
SMG1   20000 perm   9 sec   (2175 perm/sec)   p_kst 1.309500e-01   p_cons 7.275000e-01   p_joint 2.747500e-01

Outputting figure to mutsig2_images.part000000000163/SMG1.5_11238_20000_0.13095_0.7275_0.27475.png
                gene_name: SMG1
               theta_stop: 0.071 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.28 

Current progress: 33 percent done.
SMYD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.472863e-02	ci left: 5.504051e-01	ci right 5.699598e-01	k: 5602	n:10000
Cons ci ratio: 6.336175e-02	ci left: 2.679478e-01	ci right 2.855824e-01	k: 2767	n:10000
KS ci ratio: 2.803927e-02	ci left: 6.521295e-01	ci right 6.707764e-01	k: 6615	n:10000
SMYD4   10000 perm   2 sec   (5085 perm/sec)   p_kst 6.615000e-01   p_cons 2.767000e-01   p_joint 5.602000e-01

Outputting figure to mutsig2_images.part000000000163/SMYD4.3_2455_10000_0.6615_0.2767_0.5602.png
                gene_name: SMYD4
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.57 

Current progress: 67 percent done.
SNTA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.209756e-02	ci left: 9.074079e-01	ci right 9.185501e-01	k: 9131	n:10000
Cons ci ratio: 4.580278e-02	ci left: 4.129917e-01	ci right 4.324533e-01	k: 4227	n:10000
KS ci ratio: 2.268605e-02	ci left: 7.404812e-01	ci right 7.575735e-01	k: 7491	n:10000
SNTA1   10000 perm   2 sec   (6609 perm/sec)   p_kst 7.491000e-01   p_cons 4.227000e-01   p_joint 9.131000e-01

Outputting figure to mutsig2_images.part000000000163/SNTA1.2_1550_10000_0.7491_0.4227_0.9131.png
                gene_name: SNTA1
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000163
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 163 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1549>
Subject: Job 4398399: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1549>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000164> was used as the working directory.
Started at Wed Oct 24 16:17:12 2012
Results reported at Wed Oct 24 16:20:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000164.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000164.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 164  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000164.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    245.69 sec.
    Max Memory :      1466 MB
    Max Swap   :      3977 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
164
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 164
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 164: processing genes 14624 - 14712
Calculating significance of each gene.
Using projection method.
14624	SNTG2	2.566828e-03
14625	SNTN	1
14626	SNUPN	1
14627	SNURF	2.568305e-02
14628	SNW1	1.271776e-01
14629	SNX1	1
14630	SNX10	1
14631	SNX11	8.365268e-02
14632	SNX12	1
14633	SNX13	1
14634	SNX14	1
14635	SNX15	1
14636	SNX16	1
14637	SNX17	7.368027e-02
14638	SNX18	1
14639	SNX19	1
14640	SNX2	1
14641	SNX20	1
14642	SNX21	1
14643	SNX22	1
14644	SNX24	1
14645	SNX25	1
14646	SNX27	1.780641e-01
14647	SNX29	6.255209e-03
14648	SNX3	1
14649	SNX30	1
14650	SNX31	1
14651	SNX32	1
14652	SNX33	1
14653	SNX4	1
14654	SNX5	1
14655	SNX6	1
14656	SNX7	1
14657	SNX8	1
14658	SNX9	1
14659	SOAT1	1
14660	SOAT2	1
14661	SOBP	1.608714e-01
14662	SOCS1	1
14663	SOCS2	8.097658e-02
14664	SOCS3	1
14665	SOCS4	1.101509e-01
14666	SOCS5	1
14667	SOCS6	8.190215e-02
14668	SOCS7	1
14669	SOD1	1
14670	SOD2	1
14671	SOHLH1	1
14672	SOHLH2	1
14673	SOLH	1.253866e-01
14674	SON	8.367346e-02
14675	SORBS1	2.265944e-01
14676	SORBS2	1
14677	SORBS3	1
14678	SORCS1	4.821314e-01
14679	SORCS2	1
14680	SORCS3	1.689942e-01
14681	SORD	1
14682	SORL1	1
14683	SORT1	1
14684	SOS1	5.018191e-01
14685	SOS2	1.940973e-01
14686	SOST	1
14687	SOSTDC1	1
14688	SOX1	1
14689	SOX10	1
14690	SOX11	8.355560e-02
14691	SOX12	1
14692	SOX13	1
14693	SOX14	1
14694	SOX15	1
14695	SOX17	1
14696	SOX2	9.071907e-02
14697	SOX21	1
14698	SOX3	1
14699	SOX30	1
14700	SOX4	1
14701	SOX5	1
14702	SOX6	1
14703	SOX7	1
14704	SOX8	1
14705	SOX9	1
14706	SP1	1
14707	SP100	1
14708	SP110	1
14709	SP140	1
14710	SP140L	1
14711	SP2	1
14712	SP3	1.775439e-01
Done

Running MutSig 2:
Scatter job 164: processing genes 14624 - 14712
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SON
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.092186e-02	ci left: 7.700281e-01	ci right 7.864095e-01	k: 7783	n:10000
Cons ci ratio: 9.472717e-03	ci left: 9.402467e-01	ci right 9.492921e-01	k: 9449	n:10000
KS ci ratio: 4.110596e-02	ci left: 4.663694e-01	ci right 4.860444e-01	k: 4762	n:10000
SON   10000 perm   3 sec   (3467 perm/sec)   p_kst 4.762000e-01   p_cons 9.449000e-01   p_joint 7.783000e-01

Outputting figure to mutsig2_images.part000000000164/SON.4_7588_10000_0.4762_0.9449_0.7783.png
                gene_name: SON
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 25 percent done.
SNTG2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.372648e-01	ci left: 7.020239e-02	ci right 8.064655e-02	k: 753	n:10000
Cons ci ratio: 2.742813e-02	ci left: 6.619944e-01	ci right 6.805058e-01	k: 6713	n:10000
KS ci ratio: 3.428867e-01	ci left: 1.068957e-02	ci right 1.520079e-02	k: 128	n:10000
SNTG2   10000 perm   1 sec   (6669 perm/sec)   p_kst 1.280000e-02   p_cons 6.713000e-01   p_joint 7.530000e-02

Joint ci ratio: 4.760968e-02	ci left: 2.470855e-01	ci right 2.591864e-01	k: 5062	n:20000
Cons ci ratio: 1.969709e-02	ci left: 6.578575e-01	ci right 6.709947e-01	k: 13289	n:20000
KS ci ratio: 2.410476e-01	ci left: 1.147624e-02	ci right 1.466766e-02	k: 260	n:20000
SNTG2   20000 perm   3 sec   (5742 perm/sec)   p_kst 1.300000e-02   p_cons 6.644500e-01   p_joint 2.531000e-01

Joint ci ratio: 7.607835e-02	ci left: 7.819866e-02	ci right 8.441604e-02	k: 2438	n:30000
Cons ci ratio: 1.616764e-02	ci left: 6.567155e-01	ci right 6.674531e-01	k: 19863	n:30000
KS ci ratio: 1.915552e-01	ci left: 1.244696e-02	ci right 1.511510e-02	k: 412	n:30000
SNTG2   30000 perm   6 sec   (5444 perm/sec)   p_kst 1.373333e-02   p_cons 6.621000e-01   p_joint 8.126667e-02

Joint ci ratio: 1.008797e-01	ci left: 3.453709e-02	ci right 3.823061e-02	k: 1454	n:40000
Cons ci ratio: 1.445019e-02	ci left: 6.431461e-01	ci right 6.525324e-01	k: 25914	n:40000
KS ci ratio: 1.644846e-01	ci left: 1.284752e-02	ci right 1.517383e-02	k: 559	n:40000
SNTG2   40000 perm   8 sec   (5238 perm/sec)   p_kst 1.397500e-02   p_cons 6.478500e-01   p_joint 3.635000e-02

Joint ci ratio: 9.613937e-02	ci left: 3.063081e-02	ci right 3.374382e-02	k: 1608	n:50000
Cons ci ratio: 1.295161e-02	ci left: 6.426924e-01	ci right 6.510906e-01	k: 32345	n:50000
KS ci ratio: 1.488548e-01	ci left: 1.266089e-02	ci right 1.471615e-02	k: 683	n:50000
SNTG2   50000 perm   10 sec   (5080 perm/sec)   p_kst 1.366000e-02   p_cons 6.469000e-01   p_joint 3.216000e-02

Joint ci ratio: 8.837490e-02	ci left: 3.034511e-02	ci right 3.316709e-02	k: 1904	n:60000
Cons ci ratio: 1.182189e-02	ci left: 6.431106e-01	ci right 6.507752e-01	k: 38817	n:60000
KS ci ratio: 1.369723e-01	ci left: 1.254355e-02	ci right 1.440395e-02	k: 807	n:60000
SNTG2   60000 perm   12 sec   (4933 perm/sec)   p_kst 1.345000e-02   p_cons 6.469500e-01   p_joint 3.173333e-02

Joint ci ratio: 6.655722e-02	ci left: 4.564067e-02	ci right 4.879700e-02	k: 3304	n:70000
Cons ci ratio: 1.096089e-02	ci left: 6.427307e-01	ci right 6.498286e-01	k: 45240	n:70000
KS ci ratio: 1.251841e-01	ci left: 1.294884e-02	ci right 1.469180e-02	k: 966	n:70000
SNTG2   70000 perm   15 sec   (4792 perm/sec)   p_kst 1.380000e-02   p_cons 6.462857e-01   p_joint 4.720000e-02

Joint ci ratio: 5.675494e-02	ci left: 5.467561e-02	ci right 5.788167e-02	k: 4501	n:80000
Cons ci ratio: 1.024734e-02	ci left: 6.432134e-01	ci right 6.498510e-01	k: 51723	n:80000
KS ci ratio: 1.159942e-01	ci left: 1.325797e-02	ci right 1.490255e-02	k: 1125	n:80000
SNTG2   80000 perm   17 sec   (4684 perm/sec)   p_kst 1.406250e-02   p_cons 6.465375e-01   p_joint 5.626250e-02

Joint ci ratio: 5.537425e-02	ci left: 5.128203e-02	ci right 5.421354e-02	k: 4746	n:90000
Cons ci ratio: 9.661151e-03	ci left: 6.434111e-01	ci right 6.496684e-01	k: 58189	n:90000
KS ci ratio: 1.092184e-01	ci left: 1.333985e-02	ci right 1.489170e-02	k: 1269	n:90000
SNTG2   90000 perm   20 sec   (4579 perm/sec)   p_kst 1.410000e-02   p_cons 6.465444e-01   p_joint 5.273333e-02

Joint ci ratio: 5.554051e-02	ci left: 4.613059e-02	ci right 4.877574e-02	k: 4744	n:100000
Cons ci ratio: 9.166273e-03	ci left: 6.435278e-01	ci right 6.494637e-01	k: 64650	n:100000
KS ci ratio: 1.048302e-01	ci left: 1.306659e-02	ci right 1.452181e-02	k: 1378	n:100000
SNTG2   100000 perm   22 sec   (4484 perm/sec)   p_kst 1.378000e-02   p_cons 6.465000e-01   p_joint 4.744000e-02

Joint ci ratio: 5.051161e-02	ci left: 5.059640e-02	ci right 5.322729e-02	k: 5709	n:110000
Cons ci ratio: 8.749094e-03	ci left: 6.431748e-01	ci right 6.488357e-01	k: 71061	n:110000
KS ci ratio: 1.007597e-01	ci left: 1.288838e-02	ci right 1.426471e-02	k: 1492	n:110000
SNTG2   110000 perm   25 sec   (4398 perm/sec)   p_kst 1.356364e-02   p_cons 6.460091e-01   p_joint 5.190000e-02

Joint ci ratio: 4.908475e-02	ci left: 4.922658e-02	ci right 5.171186e-02	k: 6055	n:120000
Cons ci ratio: 8.377402e-03	ci left: 6.432533e-01	ci right 6.486730e-01	k: 77516	n:120000
KS ci ratio: 9.670290e-02	ci left: 1.285467e-02	ci right 1.416900e-02	k: 1620	n:120000
SNTG2   120000 perm   28 sec   (4304 perm/sec)   p_kst 1.350000e-02   p_cons 6.459667e-01   p_joint 5.045833e-02

Outputting figure to mutsig2_images.part000000000164/SNTG2.2_1688_120000_0.0135_0.64597_0.050458.png
                gene_name: SNTG2
               theta_stop: 0.097 
                    nperm: 120000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.013 
       ci_ks_bounds_right: 0.014 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.050 
     ci_joint_bounds_left: 0.049 
    ci_joint_bounds_right: 0.052 

Current progress: 50 percent done.
SNX29
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.510603e-02	ci left: 4.204677e-01	ci right 4.399730e-01	k: 4302	n:10000
Cons ci ratio: 2.149680e-02	ci left: 7.604092e-01	ci right 7.770340e-01	k: 7688	n:10000
KS ci ratio: 7.776672e-02	ci left: 1.946611e-01	ci right 2.105125e-01	k: 2025	n:10000
SNX29   10000 perm   2 sec   (6396 perm/sec)   p_kst 2.025000e-01   p_cons 7.688000e-01   p_joint 4.302000e-01

Outputting figure to mutsig2_images.part000000000164/SNX29.2_1339_10000_0.2025_0.7688_0.4302.png
                gene_name: SNX29
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 75 percent done.
SORBS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.786852e-02	ci left: 5.073522e-01	ci right 5.270378e-01	k: 5172	n:10000
Cons ci ratio: 1.179891e-01	ci left: 9.350575e-02	ci right 1.053288e-01	k: 993	n:10000
KS ci ratio: 4.187168e-02	ci left: 4.571824e-01	ci right 4.768369e-01	k: 4670	n:10000
SORBS1   10000 perm   2 sec   (5110 perm/sec)   p_kst 4.670000e-01   p_cons 9.930000e-02   p_joint 5.172000e-01

Joint ci ratio: 5.186701e-02	ci left: 2.163551e-01	ci right 2.279258e-01	k: 4442	n:20000
Cons ci ratio: 7.432380e-02	ci left: 1.175435e-01	ci right 1.266667e-01	k: 2441	n:20000
KS ci ratio: 2.958341e-02	ci left: 4.605153e-01	ci right 4.743941e-01	k: 9349	n:20000
SORBS1   20000 perm   4 sec   (4592 perm/sec)   p_kst 4.674500e-01   p_cons 1.220500e-01   p_joint 2.221000e-01

Outputting figure to mutsig2_images.part000000000164/SORBS1.2_4200_20000_0.46745_0.12205_0.2221.png
                gene_name: SORBS1
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000164
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 164 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1705>
Subject: Job 4398403: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000165> was used as the working directory.
Started at Wed Oct 24 16:17:12 2012
Results reported at Wed Oct 24 16:19:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000165.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000165.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 165  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000165.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    177.76 sec.
    Max Memory :      1488 MB
    Max Swap   :      4046 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
165
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 165
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 165: processing genes 14713 - 14802
Calculating significance of each gene.
Using projection method.
14713	SP4	1
14714	SP5	1
14715	SP6	1
14716	SP7	6.784821e-02
14717	SP8	1
14718	SPA17	1
14719	SPACA1	1
14720	SPACA3	1
14721	SPACA4	1
14722	SPAG1	4.537635e-02
14723	SPAG11A	1
14724	SPAG11B	1
14725	SPAG16	1
14726	SPAG17	8.584636e-02
14727	SPAG4	2.138703e-02
14728	SPAG5	1
14729	SPAG6	1
14730	SPAG7	1
14731	SPAG8	1
14732	SPAG9	8.020671e-02
14733	SPAM1	6.950539e-02
14734	SPANXC	1
14735	SPANXD	1
14736	SPANXE	1
14737	SPANXN1	1
14738	SPANXN2	1.319574e-02
14739	SPANXN3	1
14740	SPANXN4	1
14741	SPANXN5	2.092949e-03
14742	SPARC	1
14743	SPARCL1	1.276814e-01
14744	SPAST	1
14745	SPATA1	1
14746	SPATA12	5.472951e-02
14747	SPATA13	1
14748	SPATA16	9.521711e-02
14749	SPATA17	7.106507e-02
14750	SPATA18	1
14751	SPATA19	1.048197e-01
14752	SPATA2	1
14753	SPATA20	1
14754	SPATA21	1
14755	SPATA22	1
14756	SPATA2L	1.318526e-01
14757	SPATA4	5.736893e-02
14758	SPATA5	1
14759	SPATA5L1	1
14760	SPATA6	1
14761	SPATA7	9.564374e-03
14762	SPATA8	1
14763	SPATA9	1
14764	SPATC1	1
14765	SPATS1	1
14766	SPATS2	1
14767	SPATS2L	1
14768	SPC24	1
14769	SPC25	1
14770	SPCS1	1
14771	SPCS2	1
14772	SPCS3	1
14773	SPDEF	1
14774	SPDYA	1.038080e-01
14775	SPDYC	1
14776	SPDYE1	1
14777	SPDYE3	1
14778	SPDYE5	6.717837e-02
14779	SPEF1	1.164221e-02
14780	SPEF2	8.196209e-02
14781	SPEG	4.666844e-01
14782	SPEM1	1
14783	SPEN	3.513275e-02
14784	SPERT	1
14785	SPESP1	1
14786	SPG11	1.767947e-01
14787	SPG20	1
14788	SPG21	1
14789	SPG7	1
14790	SPHAR	1
14791	SPHK1	9.667317e-02
14792	SPHK2	1
14793	SPHKAP	2.402193e-01
14794	SPI1	1
14795	SPIB	1
14796	SPIC	1.282840e-01
14797	SPIN1	1
14798	SPIN2A	1
14799	SPIN2B	1
14800	SPIN3	1
14801	SPIN4	1
14802	SPINK1	1
Done

Running MutSig 2:
Scatter job 165: processing genes 14713 - 14802
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SPEN
Processing conservation and coverage...
90% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.557379e-02	ci left: 2.039253e-01	ci right 2.200428e-01	k: 2119	n:10000
Cons ci ratio: 1.561441e-02	ci left: 8.562070e-01	ci right 8.697808e-01	k: 8631	n:10000
KS ci ratio: 1.645486e-01	ci left: 4.926618e-02	ci right 5.819605e-02	k: 536	n:10000
SPEN   10000 perm   3 sec   (3450 perm/sec)   p_kst 5.360000e-02   p_cons 8.631000e-01   p_joint 2.119000e-01

Joint ci ratio: 5.361592e-02	ci left: 2.052141e-01	ci right 2.165701e-01	k: 4217	n:20000
Cons ci ratio: 1.113109e-02	ci left: 8.562802e-01	ci right 8.659146e-01	k: 17223	n:20000
KS ci ratio: 1.161276e-01	ci left: 5.076176e-02	ci right 5.706873e-02	k: 1077	n:20000
SPEN   20000 perm   9 sec   (2329 perm/sec)   p_kst 5.385000e-02   p_cons 8.611500e-01   p_joint 2.108500e-01

Joint ci ratio: 4.375985e-02	ci left: 2.063944e-01	ci right 2.156616e-01	k: 6330	n:30000
Cons ci ratio: 9.026746e-03	ci left: 8.588212e-01	ci right 8.666418e-01	k: 25883	n:30000
KS ci ratio: 9.330341e-02	ci left: 5.296827e-02	ci right 5.818489e-02	k: 1666	n:30000
SPEN   30000 perm   12 sec   (2450 perm/sec)   p_kst 5.553333e-02   p_cons 8.627667e-01   p_joint 2.110000e-01

Outputting figure to mutsig2_images.part000000000165/SPEN.7_11055_30000_0.055533_0.86277_0.211.png
                gene_name: SPEN
               theta_stop: 0.093 
                    nperm: 30000 
                     p_ks: 0.056 
        ci_ks_bounds_left: 0.053 
       ci_ks_bounds_right: 0.058 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 10 percent done.
SPAG4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.249459e-02	ci left: 3.484968e-01	ci right 3.673860e-01	k: 3579	n:10000
Cons ci ratio: 7.530342e-02	ci left: 2.051084e-01	ci right 2.212590e-01	k: 2131	n:10000
KS ci ratio: 6.174011e-02	ci left: 2.783450e-01	ci right 2.961790e-01	k: 2872	n:10000
SPAG4   10000 perm   2 sec   (6203 perm/sec)   p_kst 2.872000e-01   p_cons 2.131000e-01   p_joint 3.579000e-01

Outputting figure to mutsig2_images.part000000000165/SPAG4.3_1362_10000_0.2872_0.2131_0.3579.png
                gene_name: SPAG4
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 20 percent done.
SP7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.574656e-02	ci left: 6.894995e-01	ci right 7.075847e-01	k: 6986	n:10000
Cons ci ratio: 1.268989e-02	ci left: 8.992899e-01	ci right 9.108729e-01	k: 9052	n:10000
KS ci ratio: 9.619643e-02	ci left: 1.355076e-01	ci right 1.493014e-01	k: 1423	n:10000
SP7   10000 perm   2 sec   (6451 perm/sec)   p_kst 1.423000e-01   p_cons 9.052000e-01   p_joint 6.986000e-01

Outputting figure to mutsig2_images.part000000000165/SP7.2_1304_10000_0.1423_0.9052_0.6986.png
                gene_name: SP7
               theta_stop: 0.096 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.69 
    ci_joint_bounds_right: 0.71 

Current progress: 30 percent done.
SPAG17
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.363547e-03	ci left: 9.622595e-01	ci right 9.694658e-01	k: 9660	n:10000
Cons ci ratio: 8.266728e-03	ci left: 9.533608e-01	ci right 9.613700e-01	k: 9575	n:10000
KS ci ratio: 1.966194e-02	ci left: 7.910089e-01	ci right 8.068166e-01	k: 7990	n:10000
SPAG17   10000 perm   2 sec   (4474 perm/sec)   p_kst 7.990000e-01   p_cons 9.575000e-01   p_joint 9.660000e-01

Outputting figure to mutsig2_images.part000000000165/SPAG17.2_6864_10000_0.799_0.9575_0.966.png
                gene_name: SPAG17
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 40 percent done.
SPAG9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.948673e-02	ci left: 6.290949e-01	ci right 6.480243e-01	k: 6386	n:10000
Cons ci ratio: 1.688045e-02	ci left: 8.363308e-01	ci right 8.506684e-01	k: 8436	n:10000
KS ci ratio: 1.317679e-01	ci left: 7.591905e-02	ci right 8.672633e-02	k: 812	n:10000
SPAG9   10000 perm   2 sec   (5423 perm/sec)   p_kst 8.120000e-02   p_cons 8.436000e-01   p_joint 6.386000e-01

Joint ci ratio: 9.330090e-02	ci left: 7.730380e-02	ci right 8.491851e-02	k: 1621	n:20000
Cons ci ratio: 1.193336e-02	ci left: 8.385417e-01	ci right 8.486582e-01	k: 16873	n:20000
KS ci ratio: 9.330090e-02	ci left: 7.730380e-02	ci right 8.491851e-02	k: 1621	n:20000
SPAG9   20000 perm   4 sec   (4528 perm/sec)   p_kst 8.105000e-02   p_cons 8.436500e-01   p_joint 8.105000e-02

Outputting figure to mutsig2_images.part000000000165/SPAG9.2_4086_20000_0.08105_0.84365_0.08105.png
                gene_name: SPAG9
               theta_stop: 0.093 
                    nperm: 20000 
                     p_ks: 0.081 
        ci_ks_bounds_left: 0.077 
       ci_ks_bounds_right: 0.085 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.081 
     ci_joint_bounds_left: 0.077 
    ci_joint_bounds_right: 0.085 

Current progress: 50 percent done.
SPANXN2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.974757e-02	ci left: 7.895889e-01	ci right 8.054374e-01	k: 7976	n:10000
Cons ci ratio: 2.724812e-02	ci left: 6.649144e-01	ci right 6.833840e-01	k: 6742	n:10000
KS ci ratio: 8.876129e-02	ci left: 1.559077e-01	ci right 1.704891e-01	k: 1631	n:10000
SPANXN2   10000 perm   1 sec   (7108 perm/sec)   p_kst 1.631000e-01   p_cons 6.742000e-01   p_joint 7.976000e-01

Outputting figure to mutsig2_images.part000000000165/SPANXN2.2_551_10000_0.1631_0.6742_0.7976.png
                gene_name: SPANXN2
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.80 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.81 

Current progress: 60 percent done.
SPARCL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.054284e-02	ci left: 6.126129e-01	ci right 6.317159e-01	k: 6222	n:10000
Cons ci ratio: 3.957213e-02	ci left: 4.853532e-01	ci right 5.050496e-01	k: 4952	n:10000
KS ci ratio: 3.396687e-02	ci left: 5.613302e-01	ci right 5.808283e-01	k: 5711	n:10000
SPARCL1   10000 perm   2 sec   (6263 perm/sec)   p_kst 5.711000e-01   p_cons 4.952000e-01   p_joint 6.222000e-01

Outputting figure to mutsig2_images.part000000000165/SPARCL1.2_2035_10000_0.5711_0.4952_0.6222.png
                gene_name: SPARCL1
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.63 

Current progress: 70 percent done.
SPATA7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.329191e-02	ci left: 3.416399e-01	ci right 3.604469e-01	k: 3510	n:10000
KS ci ratio: 1.107859e-02	ci left: 9.207974e-01	ci right 9.311528e-01	k: 9261	n:10000
SPATA7   10000 perm   2 sec   (6433 perm/sec)   p_kst 9.261000e-01   p_cons 3.510000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000165/SPATA7.2_1848_10000_0.9261_0.351_1.png
                gene_name: SPATA7
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
SPEF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.239677e-02	ci left: 4.509930e-01	ci right 4.706299e-01	k: 4608	n:10000
Cons ci ratio: 1.934937e-02	ci left: 7.961830e-01	ci right 8.118395e-01	k: 8041	n:10000
KS ci ratio: 1.097680e-01	ci left: 1.068582e-01	ci right 1.193681e-01	k: 1130	n:10000
SPEF2   10000 perm   2 sec   (4952 perm/sec)   p_kst 1.130000e-01   p_cons 8.041000e-01   p_joint 4.608000e-01

Joint ci ratio: 2.902688e-03	ci left: 9.876692e-01	ci right 9.905860e-01	k: 19784	n:20000
Cons ci ratio: 1.436020e-02	ci left: 7.826727e-01	ci right 7.940434e-01	k: 15768	n:20000
KS ci ratio: 7.750332e-02	ci left: 1.089878e-01	ci right 1.178249e-01	k: 2267	n:20000
SPEF2   20000 perm   4 sec   (4500 perm/sec)   p_kst 1.133500e-01   p_cons 7.884000e-01   p_joint 9.892000e-01

Outputting figure to mutsig2_images.part000000000165/SPEF2.2_5638_20000_0.11335_0.7884_0.9892.png
                gene_name: SPEF2
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 90 percent done.
SPG11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.678368e-02	ci left: 5.218619e-01	ci right 5.415197e-01	k: 5317	n:10000
Cons ci ratio: 4.894348e-02	ci left: 3.811202e-01	ci right 4.003435e-01	k: 3907	n:10000
KS ci ratio: 3.259309e-02	ci left: 5.814892e-01	ci right 6.008577e-01	k: 5912	n:10000
SPG11   10000 perm   2 sec   (4367 perm/sec)   p_kst 5.912000e-01   p_cons 3.907000e-01   p_joint 5.317000e-01

Outputting figure to mutsig2_images.part000000000165/SPG11.2_7492_10000_0.5912_0.3907_0.5317.png
                gene_name: SPG11
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.54 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000165
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 165 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1710>
Subject: Job 4398405: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000166> was used as the working directory.
Started at Wed Oct 24 16:17:12 2012
Results reported at Wed Oct 24 16:19:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000166.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000166.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 166  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000166.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    146.28 sec.
    Max Memory :      1554 MB
    Max Swap   :      4016 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
166
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 166
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 166: processing genes 14803 - 14892
Calculating significance of each gene.
Using projection method.
14803	SPINK13	1.471031e-02
14804	SPINK14	1
14805	SPINK2	1
14806	SPINK4	1
14807	SPINK5	2.500074e-01
14808	SPINK6	1
14809	SPINK7	1
14810	SPINK8	1
14811	SPINK9	1
14812	SPINLW1	1
14813	SPINT1	1
14814	SPINT2	1
14815	SPINT4	1
14816	SPIRE1	1
14817	SPIRE2	1
14818	SPN	1
14819	SPNS1	1
14820	SPNS2	1
14821	SPNS3	1
14822	SPO11	1
14823	SPOCD1	1
14824	SPOCK1	1
14825	SPOCK2	1
14826	SPOCK3	1
14827	SPON1	1
14828	SPON2	1
14829	SPOP	1
14830	SPOPL	7.067692e-03
14831	SPP1	1
14832	SPP2	1
14833	SPPL2A	1
14834	SPPL2B	1
14835	SPPL3	1
14836	SPR	1
14837	SPRED1	1
14838	SPRED2	1
14839	SPRED3	1
14840	SPRR1A	1
14841	SPRR1B	1
14842	SPRR2A	1
14843	SPRR2B	1
14844	SPRR2D	1
14845	SPRR2E	1
14846	SPRR2F	1
14847	SPRR2G	1
14848	SPRR3	6.098861e-03
14849	SPRR4	1
14850	SPRY1	1
14851	SPRY2	1
14852	SPRY3	2.279774e-02
14853	SPRY4	1
14854	SPRYD3	1
14855	SPRYD4	1
14856	SPRYD5	1
14857	SPSB1	1
14858	SPSB2	1
14859	SPSB3	1
14860	SPSB4	1
14861	SPTA1	2.937964e-01
14862	SPTAN1	2.280432e-01
14863	SPTB	5.100601e-01
14864	SPTBN1	1
14865	SPTBN2	5.557209e-01
14866	SPTBN4	1
14867	SPTBN5	3.314365e-01
14868	SPTLC1	1
14869	SPTLC2	7.650949e-02
14870	SPTLC3	1
14871	SPTY2D1	3.066136e-02
14872	SPZ1	1
14873	SQLE	1
14874	SQRDL	1
14875	SQSTM1	1
14876	SR140	1.350950e-01
14877	SRA1	1
14878	SRBD1	2.073209e-01
14879	SRC	1
14880	SRCAP	2.293184e-02
14881	SRCIN1	1
14882	SRCRB4D	1
14883	SRD5A1	1
14884	SRD5A2	1
14885	SRD5A3	7.108802e-02
14886	SREBF1	2.305385e-01
14887	SREBF2	1
14888	SRF	1
14889	SRFBP1	1
14890	SRGAP1	2.585530e-01
14891	SRGAP2	1
14892	SRGAP3	1
Done

Running MutSig 2:
Scatter job 166: processing genes 14803 - 14892
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SRCAP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.449635e-02	ci left: 1.695643e-01	ci right 1.846243e-01	k: 1770	n:10000
Cons ci ratio: 2.566102e-02	ci left: 6.909110e-01	ci right 7.089724e-01	k: 7000	n:10000
KS ci ratio: 1.186529e-01	ci left: 9.253239e-02	ci right 1.043027e-01	k: 983	n:10000
SRCAP   10000 perm   3 sec   (3768 perm/sec)   p_kst 9.830000e-02   p_cons 7.000000e-01   p_joint 1.770000e-01

Joint ci ratio: 5.870414e-02	ci left: 1.769212e-01	ci right 1.876713e-01	k: 3645	n:20000
Cons ci ratio: 1.804628e-02	ci left: 6.959089e-01	ci right 7.086322e-01	k: 14046	n:20000
KS ci ratio: 8.068851e-02	ci left: 1.012751e-01	ci right 1.098399e-01	k: 2110	n:20000
SRCAP   20000 perm   8 sec   (2641 perm/sec)   p_kst 1.055000e-01   p_cons 7.023000e-01   p_joint 1.822500e-01

Outputting figure to mutsig2_images.part000000000166/SRCAP.7_9821_20000_0.1055_0.7023_0.18225.png
                gene_name: SRCAP
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 17 percent done.
SPTY2D1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.853352e-02	ci left: 4.986503e-01	ci right 5.183447e-01	k: 5085	n:10000
Cons ci ratio: 1.337314e-02	ci left: 8.896462e-01	ci right 9.017222e-01	k: 8958	n:10000
KS ci ratio: 4.782131e-02	ci left: 3.921708e-01	ci right 4.114864e-01	k: 4018	n:10000
SPTY2D1   10000 perm   2 sec   (6031 perm/sec)   p_kst 4.018000e-01   p_cons 8.958000e-01   p_joint 5.085000e-01

Outputting figure to mutsig2_images.part000000000166/SPTY2D1.3_2082_10000_0.4018_0.8958_0.5085.png
                gene_name: SPTY2D1
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.51 
     ci_joint_bounds_left: 0.50 
    ci_joint_bounds_right: 0.52 

Current progress: 33 percent done.
SPOPL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.028188e-02	ci left: 9.307143e-01	ci right 9.404301e-01	k: 9357	n:10000
Cons ci ratio: 4.463091e-02	ci left: 4.256523e-01	ci right 4.451853e-01	k: 4354	n:10000
KS ci ratio: 3.710988e-02	ci left: 5.174580e-01	ci right 5.371261e-01	k: 5273	n:10000
SPOPL   10000 perm   2 sec   (6664 perm/sec)   p_kst 5.273000e-01   p_cons 4.354000e-01   p_joint 9.357000e-01

Outputting figure to mutsig2_images.part000000000166/SPOPL.2_1219_10000_0.5273_0.4354_0.9357.png
                gene_name: SPOPL
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 50 percent done.
SPTA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.174931e-02	ci left: 3.550575e-01	ci right 3.740215e-01	k: 3645	n:10000
Cons ci ratio: 5.513094e-02	ci left: 3.264433e-01	ci right 3.450525e-01	k: 3357	n:10000
KS ci ratio: 7.596042e-02	ci left: 2.022494e-01	ci right 2.183197e-01	k: 2102	n:10000
SPTA1   10000 perm   2 sec   (4436 perm/sec)   p_kst 2.102000e-01   p_cons 3.357000e-01   p_joint 3.645000e-01

Outputting figure to mutsig2_images.part000000000166/SPTA1.2_7468_10000_0.2102_0.3357_0.3645.png
                gene_name: SPTA1
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 67 percent done.
SPTAN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.073529e-02	ci left: 9.251327e-01	ci right 9.352150e-01	k: 9303	n:10000
Cons ci ratio: 7.589188e-02	ci left: 2.025451e-01	ci right 2.186238e-01	k: 2105	n:10000
KS ci ratio: 5.795385e-02	ci left: 3.047104e-01	ci right 3.229982e-01	k: 3138	n:10000
SPTAN1   10000 perm   2 sec   (4401 perm/sec)   p_kst 3.138000e-01   p_cons 2.105000e-01   p_joint 9.303000e-01

Outputting figure to mutsig2_images.part000000000166/SPTAN1.2_7658_10000_0.3138_0.2105_0.9303.png
                gene_name: SPTAN1
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 83 percent done.
SREBF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.757738e-02	ci left: 6.595781e-01	ci right 6.781235e-01	k: 6689	n:10000
Cons ci ratio: 1.996134e-02	ci left: 7.860396e-01	ci right 8.019887e-01	k: 7941	n:10000
KS ci ratio: 9.723386e-02	ci left: 1.329609e-01	ci right 1.466496e-01	k: 1397	n:10000
SREBF1   10000 perm   2 sec   (5568 perm/sec)   p_kst 1.397000e-01   p_cons 7.941000e-01   p_joint 6.689000e-01

Outputting figure to mutsig2_images.part000000000166/SREBF1.2_3614_10000_0.1397_0.7941_0.6689.png
                gene_name: SREBF1
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    ci_joint_bounds_right: 0.68 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000166
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 166 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1430>
Subject: Job 4398410: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1430>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000167> was used as the working directory.
Started at Wed Oct 24 16:17:20 2012
Results reported at Wed Oct 24 16:19:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000167.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000167.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 167  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000167.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    214.53 sec.
    Max Memory :      1302 MB
    Max Swap   :      4032 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
167
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 167
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 167: processing genes 14893 - 14982
Calculating significance of each gene.
Using projection method.
14893	SRGN	1
14894	SRI	1
14895	SRL	1
14896	SRM	1
14897	SRMS	1
14898	SRP14	1
14899	SRP19	7.488153e-02
14900	SRP54	1
14901	SRP68	1
14902	SRP72	1
14903	SRP9	1
14904	SRPK1	1
14905	SRPK2	1
14906	SRPK3	1
14907	SRPR	1
14908	SRPRB	1
14909	SRPX	3.714390e-02
14910	SRPX2	1
14911	SRR	1
14912	SRRD	1
14913	SRRM1	1
14914	SRRM2	9.885733e-02
14915	SRRM4	1
14916	SRRT	1.956882e-02
14917	SRXN1	1
14918	SS18	1
14919	SS18L1	1
14920	SS18L2	1
14921	SSB	1
14922	SSBP1	1
14923	SSBP2	5.978022e-02
14924	SSBP3	1
14925	SSBP4	1
14926	SSFA2	1
14927	SSH1	1
14928	SSH2	4.782467e-01
14929	SSH3	9.832656e-02
14930	SSNA1	1
14931	SSPN	1
In gene SSPO the following bins exceed PROBCAP:
    CESC-DS-A0VL-TP	categ 6	N = 9728    n = 1	mu =   4.43e-07
14932	SSPO	4.970439e-02
14933	SSR1	1
14934	SSR2	1
14935	SSR3	1.130122e-02
14936	SSR4	1
14937	SSRP1	1.598273e-01
14938	SSSCA1	1
14939	SST	1
14940	SSTR1	1
14941	SSTR2	1
14942	SSTR3	1
14943	SSTR4	1
14944	SSTR5	1
14945	SSU72	1
14946	SSX1	1
14947	SSX2IP	1
14948	SSX3	1
14949	SSX5	1.625614e-02
14950	SSX7	2.609606e-02
14951	ST13	1.939606e-01
14952	ST14	1
14953	ST18	1
14954	ST20	1
14955	ST3GAL1	1
14956	ST3GAL2	1
14957	ST3GAL3	1
14958	ST3GAL4	1
14959	ST3GAL5	1.403791e-01
14960	ST3GAL6	1
14961	ST5	1
14962	ST6GAL1	1
14963	ST6GAL2	1.312173e-01
14964	ST6GALNAC1	1
14965	ST6GALNAC2	1.132550e-01
14966	ST6GALNAC3	1
14967	ST6GALNAC4	1
14968	ST6GALNAC5	1
14969	ST6GALNAC6	1
14970	ST7	1
14971	ST7L	1
14972	ST8SIA1	1
14973	ST8SIA2	1
14974	ST8SIA3	4.725846e-02
14975	ST8SIA4	1
14976	ST8SIA5	1
14977	ST8SIA6	1
14978	STAB1	1
14979	STAB2	5.219158e-01
14980	STAC	1
14981	STAC2	1
14982	STAC3	1.663034e-01
Done

Running MutSig 2:
Scatter job 167: processing genes 14893 - 14982
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SRRM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.257621e-02	ci left: 1.762516e-01	ci right 1.915330e-01	k: 1838	n:10000
Cons ci ratio: 5.781514e-03	ci left: 9.757832e-01	ci right 9.815332e-01	k: 9788	n:10000
KS ci ratio: 1.290236e-01	ci left: 7.902317e-02	ci right 9.002028e-02	k: 844	n:10000
SRRM2   10000 perm   3 sec   (3310 perm/sec)   p_kst 8.440000e-02   p_cons 9.788000e-01   p_joint 1.838000e-01

Joint ci ratio: 5.782345e-02	ci left: 1.814192e-01	ci right 1.922720e-01	k: 3736	n:20000
Cons ci ratio: 4.064079e-03	ci left: 9.769168e-01	ci right 9.809423e-01	k: 19580	n:20000
KS ci ratio: 9.138306e-02	ci left: 8.038716e-02	ci right 8.813421e-02	k: 1684	n:20000
SRRM2   20000 perm   9 sec   (2124 perm/sec)   p_kst 8.420000e-02   p_cons 9.790000e-01   p_joint 1.868000e-01

Outputting figure to mutsig2_images.part000000000167/SRRM2.5_8315_20000_0.0842_0.979_0.1868.png
                gene_name: SRRM2
               theta_stop: 0.091 
                    nperm: 20000 
                     p_ks: 0.084 
        ci_ks_bounds_left: 0.080 
       ci_ks_bounds_right: 0.088 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 25 percent done.
SSPO
Processing conservation and coverage...
62% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.650411e-02	ci left: 4.056177e-01	ci right 4.250317e-01	k: 4153	n:10000
Cons ci ratio: 9.661964e-03	ci left: 9.380680e-01	ci right 9.472720e-01	k: 9428	n:10000
KS ci ratio: 7.277146e-02	ci left: 2.166492e-01	ci right 2.331114e-01	k: 2248	n:10000
SSPO   10000 perm   4 sec   (2245 perm/sec)   p_kst 2.248000e-01   p_cons 9.428000e-01   p_joint 4.153000e-01

Outputting figure to mutsig2_images.part000000000167/SSPO.3_15875_10000_0.2248_0.9428_0.4153.png
                gene_name: SSPO
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 50 percent done.
SRRT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.363681e-02	ci left: 1.725141e-01	ci right 1.876728e-01	k: 1800	n:10000
Cons ci ratio: 7.944208e-02	ci left: 1.879635e-01	ci right 2.036141e-01	k: 1957	n:10000
KS ci ratio: 6.751719e-02	ci left: 2.435138e-01	ci right 2.606309e-01	k: 2520	n:10000
SRRT   10000 perm   2 sec   (5585 perm/sec)   p_kst 2.520000e-01   p_cons 1.957000e-01   p_joint 1.800000e-01

Outputting figure to mutsig2_images.part000000000167/SRRT.2_2707_10000_0.252_0.1957_0.18.png
                gene_name: SRRT
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.19 

Current progress: 75 percent done.
ST6GAL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.740181e-02	ci left: 8.279846e-01	ci right 8.426195e-01	k: 8354	n:10000
Cons ci ratio: 2.143635e-02	ci left: 7.614214e-01	ci right 7.780212e-01	k: 7698	n:10000
KS ci ratio: 5.760589e-02	ci left: 3.072893e-01	ci right 3.256177e-01	k: 3164	n:10000
ST6GAL2   10000 perm   2 sec   (6502 perm/sec)   p_kst 3.164000e-01   p_cons 7.698000e-01   p_joint 8.354000e-01

Outputting figure to mutsig2_images.part000000000167/ST6GAL2.2_1697_10000_0.3164_0.7698_0.8354.png
                gene_name: ST6GAL2
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.84 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000167
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 167 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1559>
Subject: Job 4398413: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1559>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000168> was used as the working directory.
Started at Wed Oct 24 16:17:23 2012
Results reported at Wed Oct 24 16:19:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000168.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000168.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 168  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000168.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    184.90 sec.
    Max Memory :       770 MB
    Max Swap   :      3711 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
168
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 168
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 168: processing genes 14983 - 15071
Calculating significance of each gene.
Using projection method.
14983	STAG1	4.387379e-01
14984	STAG2	3.856723e-01
14985	STAG3	2.577892e-01
14986	STAG3L2	5.426235e-03
14987	STAG3L4	1
14988	STAM	1
14989	STAM2	1
14990	STAMBP	1
14991	STAMBPL1	1
14992	STAP1	1
14993	STAP2	1
14994	STAR	1
14995	STARD10	1
14996	STARD13	1
14997	STARD3	1
14998	STARD3NL	1
14999	STARD4	1.034307e-01
15000/17942 15000	STARD5	1
15001	STARD6	1
15002	STARD7	1
15003	STARD8	1
15004	STAT1	2.767803e-02
15005	STAT2	1
15006	STAT3	2.199607e-01
15007	STAT4	1.801060e-01
15008	STAT5A	1
15009	STAT5B	1
15010	STAT6	1
15011	STATH	1
15012	STAU1	1
15013	STAU2	2.221550e-01
15014	STBD1	1
15015	STC1	5.096759e-02
15016	STC2	1
15017	STEAP1	1
15018	STEAP2	1
15019	STEAP3	1
15020	STEAP4	1
15021	STH	1
15022	STIL	3.531480e-01
15023	STIM1	1
15024	STIM2	1
15025	STIP1	1
15026	STK10	2.157241e-01
15027	STK11	1
15028	STK11IP	1
15029	STK16	7.066870e-02
15030	STK17A	1
15031	STK17B	1
15032	STK19	1
15033	STK24	1
15034	STK25	1
15035	STK3	1
15036	STK31	4.436690e-02
15037	STK32A	1
15038	STK32B	1
15039	STK32C	1
15040	STK33	2.324279e-01
15041	STK35	1
15042	STK36	5.187142e-01
15043	STK38	1
15044	STK38L	1
15045	STK39	1
15046	STK4	1
15047	STK40	1.226931e-01
15048	STMN1	1
15049	STMN2	1
15050	STMN3	1
15051	STMN4	1
15052	STOM	1
15053	STOML1	1
15054	STOML2	1
15055	STOML3	1
15056	STON1	1
15057	STON1-GTF2A1L	1
15058	STON2	1
15059	STOX1	1
15060	STOX2	1
15061	STRA13	1
15062	STRA6	1
15063	STRA8	1
15064	STRADA	1
15065	STRADB	1
15066	STRAP	4.682441e-02
15067	STRBP	1.683706e-01
15068	STRC	1
15069	STRN	1
15070	STRN3	1
15071	STRN4	1
Done

Running MutSig 2:
Scatter job 168: processing genes 14983 - 15071
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
STAT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.545732e-02	ci left: 4.166796e-01	ci right 4.361633e-01	k: 4264	n:10000
Cons ci ratio: 9.280476e-03	ci left: 9.424271e-01	ci right 9.513103e-01	k: 9470	n:10000
KS ci ratio: 5.693376e-02	ci left: 3.123490e-01	ci right 3.307550e-01	k: 3215	n:10000
STAT1   10000 perm   2 sec   (5444 perm/sec)   p_kst 3.215000e-01   p_cons 9.470000e-01   p_joint 4.264000e-01

Outputting figure to mutsig2_images.part000000000168/STAT1.2_2349_10000_0.3215_0.947_0.4264.png
                gene_name: STAT1
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 50 percent done.
STK31
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.598207e-02	ci left: 3.196927e-01	ci right 3.382070e-01	k: 3289	n:10000
Cons ci ratio: 8.513967e-02	ci left: 1.674016e-01	ci right 1.823882e-01	k: 1748	n:10000
KS ci ratio: 3.646732e-02	ci left: 5.261663e-01	ci right 5.458127e-01	k: 5360	n:10000
STK31   10000 perm   2 sec   (5581 perm/sec)   p_kst 5.360000e-01   p_cons 1.748000e-01   p_joint 3.289000e-01

Outputting figure to mutsig2_images.part000000000168/STK31.2_3156_10000_0.536_0.1748_0.3289.png
                gene_name: STK31
               theta_stop: 0.085 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000168
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 168 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1707>
Subject: Job 4398416: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1707>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000169> was used as the working directory.
Started at Wed Oct 24 16:17:23 2012
Results reported at Wed Oct 24 16:19:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000169.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000169.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 169  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000169.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    130.63 sec.
    Max Memory :      1077 MB
    Max Swap   :      3966 MB

    Max Processes  :         7
    Max Threads    :        57

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
169
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 169
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 169: processing genes 15072 - 15161
Calculating significance of each gene.
Using projection method.
15072	STS	1
15073	STT3A	1.772128e-01
15074	STT3B	1
15075	STUB1	1
15076	STX10	1
15077	STX11	1
15078	STX12	1
15079	STX16	8.951911e-02
15080	STX17	1
15081	STX18	2.914352e-02
15082	STX19	1
15083	STX1A	1
15084	STX1B	1
15085	STX2	1
15086	STX3	1
15087	STX4	1
15088	STX5	1
15089	STX6	3.966290e-02
15090	STX7	1
15091	STX8	1
15092	STXBP1	1.948528e-01
15093	STXBP2	1
15094	STXBP3	1
15095	STXBP4	6.258065e-02
15096	STXBP5	1
15097	STXBP5L	2.022239e-01
15098	STXBP6	4.946036e-02
15099	STYK1	1.748949e-01
15100	STYX	1
15101	STYXL1	1
15102	SUB1	1
15103	SUCLA2	1
15104	SUCLG1	1
15105	SUCLG2	1
15106	SUCNR1	1
15107	SUDS3	1
15108	SUFU	1
15109	SUGT1	1.057042e-01
15110	SULF1	1
15111	SULF2	1
15112	SULT1A1	1
15113	SULT1A2	1
15114	SULT1B1	1.528455e-01
15115	SULT1C2	1
15116	SULT1C3	1
15117	SULT1C4	1
15118	SULT1E1	1
15119	SULT2A1	1
15120	SULT2B1	1.638263e-01
15121	SULT4A1	1
15122	SULT6B1	1
15123	SUMF1	7.052989e-02
15124	SUMF2	1
15125	SUMO1	1.498460e-03
15126	SUMO2	1
15127	SUMO3	1
15128	SUMO4	1
15129	SUN1	1
15130	SUN2	1
15131	SUN3	1
15132	SUN5	6.807220e-02
15133	SUOX	1
15134	SUPT16H	1
15135	SUPT3H	1
15136	SUPT4H1	1
15137	SUPT5H	1
15138	SUPT6H	5.166566e-01
15139	SUPT7L	1
15140	SUPV3L1	1
15141	SURF1	1
15142	SURF2	1
15143	SURF4	1
15144	SURF6	1
15145	SUSD1	1
15146	SUSD2	1
15147	SUSD3	1
15148	SUSD4	2.515780e-01
15149	SUSD5	1
15150	SUV39H1	1
15151	SUV39H2	6.318589e-02
15152	SUV420H1	1
15153	SUV420H2	1
15154	SUZ12	1
15155	SV2A	1
15156	SV2B	2.540854e-01
15157	SV2C	1
15158	SVEP1	2.518187e-01
15159	SVIL	1.957273e-01
15160	SVIP	7.851868e-04
15161	SVOP	1
Done

Running MutSig 2:
Scatter job 169: processing genes 15072 - 15161
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SVEP1
Processing conservation and coverage...
91% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.628775e-02	ci left: 3.173107e-01	ci right 3.357904e-01	k: 3265	n:10000
Cons ci ratio: 1.067067e-01	ci left: 1.125202e-01	ci right 1.253028e-01	k: 1188	n:10000
KS ci ratio: 3.002544e-02	ci left: 6.206514e-01	ci right 6.396727e-01	k: 6302	n:10000
SVEP1   10000 perm   3 sec   (3230 perm/sec)   p_kst 6.302000e-01   p_cons 1.188000e-01   p_joint 3.265000e-01

Joint ci ratio: 3.673076e-02	ci left: 3.561318e-01	ci right 3.695081e-01	k: 7256	n:20000
Cons ci ratio: 7.644287e-02	ci left: 1.117405e-01	ci right 1.206714e-01	k: 2323	n:20000
KS ci ratio: 2.125042e-02	ci left: 6.230646e-01	ci right 6.364977e-01	k: 12596	n:20000
SVEP1   20000 perm   9 sec   (2282 perm/sec)   p_kst 6.298000e-01   p_cons 1.161500e-01   p_joint 3.628000e-01

Outputting figure to mutsig2_images.part000000000169/SVEP1.3_10908_20000_0.6298_0.11615_0.3628.png
                gene_name: SVEP1
               theta_stop: 0.076 
                    nperm: 20000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 25 percent done.
SUMO1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.352252e-03	ci left: 9.712187e-01	ci right 9.775008e-01	k: 9745	n:10000
Cons ci ratio: 1.391093e-02	ci left: 8.818604e-01	ci right 8.943125e-01	k: 8882	n:10000
KS ci ratio: 6.632113e-02	ci left: 2.502371e-01	ci right 2.675036e-01	k: 2588	n:10000
SUMO1   10000 perm   1 sec   (7389 perm/sec)   p_kst 2.588000e-01   p_cons 8.882000e-01   p_joint 9.745000e-01

Outputting figure to mutsig2_images.part000000000169/SUMO1.2_326_10000_0.2588_0.8882_0.9745.png
                gene_name: SUMO1
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 50 percent done.
SUSD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.536256e-02	ci left: 8.600854e-01	ci right 8.735001e-01	k: 8669	n:10000
Cons ci ratio: 1.107859e-02	ci left: 9.207974e-01	ci right 9.311528e-01	k: 9261	n:10000
KS ci ratio: 1.885682e-02	ci left: 8.043033e-01	ci right 8.197145e-01	k: 8121	n:10000
SUSD4   10000 perm   1 sec   (6714 perm/sec)   p_kst 8.121000e-01   p_cons 9.261000e-01   p_joint 8.669000e-01

Outputting figure to mutsig2_images.part000000000169/SUSD4.2_1658_10000_0.8121_0.9261_0.8669.png
                gene_name: SUSD4
               theta_stop: 0.019 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 75 percent done.
SVIL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.406444e-02	ci left: 8.796083e-01	ci right 8.921659e-01	k: 8860	n:10000
Cons ci ratio: 5.346779e-02	ci left: 3.401496e-01	ci right 3.589381e-01	k: 3495	n:10000
KS ci ratio: 5.822401e-02	ci left: 3.027268e-01	ci right 3.209830e-01	k: 3118	n:10000
SVIL   10000 perm   2 sec   (4534 perm/sec)   p_kst 3.118000e-01   p_cons 3.495000e-01   p_joint 8.860000e-01

Outputting figure to mutsig2_images.part000000000169/SVIL.2_6785_10000_0.3118_0.3495_0.886.png
                gene_name: SVIL
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000169
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 169 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4398439: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000170> was used as the working directory.
Started at Wed Oct 24 16:17:23 2012
Results reported at Wed Oct 24 16:27:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000170.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000170.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 170  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000170.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    530.61 sec.
    Max Memory :      1585 MB
    Max Swap   :      4063 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
170
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 170
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 170: processing genes 15162 - 15251
Calculating significance of each gene.
Using projection method.
15162	SVOPL	1
15163	SWAP70	1
15164	SYAP1	1
15165	SYBU	3.230079e-01
15166	SYCE1	1
15167	SYCE2	1
15168	SYCN	1
15169	SYCP1	1
15170	SYCP2	1
15171	SYCP2L	1
15172	SYCP3	1
15173	SYDE1	1
15174	SYDE2	1
15175	SYF2	1
15176	SYK	1.477431e-01
15177	SYMPK	3.580352e-01
15178	SYN1	1.327333e-01
15179	SYN2	1
15180	SYN3	1
15181	SYNC	1
15182	SYNCRIP	1
15183	SYNE1	2.652639e-01
15184	SYNE2	1.981555e-01
15185	SYNGAP1	1
15186	SYNGR1	1
15187	SYNGR2	1
15188	SYNGR3	1
15189	SYNGR4	7.514757e-02
15190	SYNJ1	5.720297e-01
15191	SYNJ2	1
15192	SYNJ2BP	1
15193	SYNM	1
15194	SYNPO	1.867880e-01
15195	SYNPO2	1.397786e-01
15196	SYNPO2L	1
15197	SYNPR	1
15198	SYNRG	1
15199	SYP	1
15200	SYPL1	1
15201	SYPL2	1
15202	SYS1	1
15203	SYT1	2.189257e-02
15204	SYT10	1
15205	SYT11	1
15206	SYT12	1.131887e-01
15207	SYT13	1
15208	SYT14	1
15209	SYT15	1
15210	SYT16	1
15211	SYT17	1
15212	SYT2	1
15213	SYT3	1
15214	SYT4	1
15215	SYT5	1
15216	SYT6	1
15217	SYT7	5.694799e-02
15218	SYT8	1
15219	SYT9	1
15220	SYTL1	1
15221	SYTL2	1
15222	SYTL3	1
15223	SYTL4	1
15224	SYTL5	1
15225	SYVN1	1
15226	T	1
15227	TAAR1	1
15228	TAAR2	1
15229	TAAR5	1
15230	TAAR6	1.578009e-01
15231	TAAR8	1
15232	TAAR9	1
15233	TAB1	1
15234	TAB2	2.430356e-01
15235	TAB3	1
15236	TAC1	1
15237	TAC3	2.382328e-03
15238	TAC4	1
15239	TACC1	1
15240	TACC2	8.218820e-01
15241	TACC3	1.989506e-01
15242	TACO1	1
15243	TACR1	1
15244	TACR2	1
15245	TACR3	1
15246	TACSTD2	1
15247	TADA1	1
15248	TADA2A	7.137691e-03
15249	TADA2B	3.278022e-02
15250	TADA3	1
15251	TAF1	2.225488e-01
Done

Running MutSig 2:
Scatter job 170: processing genes 15162 - 15251
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SYNE2
Processing conservation and coverage...
47% 94% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.370683e-01	ci left: 7.039603e-02	ci right 8.085279e-02	k: 755	n:10000
Cons ci ratio: 2.835287e-02	ci left: 6.470981e-01	ci right 6.658107e-01	k: 6565	n:10000
KS ci ratio: 2.560455e-01	ci left: 1.996408e-02	ci right 2.591832e-02	k: 228	n:10000
SYNE2   10000 perm   5 sec   (2032 perm/sec)   p_kst 2.280000e-02   p_cons 6.565000e-01   p_joint 7.550000e-02

Joint ci ratio: 1.461933e-01	ci left: 3.215814e-02	ci right 3.727829e-02	k: 693	n:20000
Cons ci ratio: 2.022741e-02	ci left: 6.458539e-01	ci right 6.591018e-01	k: 13050	n:20000
KS ci ratio: 1.894834e-01	ci left: 1.896235e-02	ci right 2.297861e-02	k: 418	n:20000
SYNE2   20000 perm   13 sec   (1570 perm/sec)   p_kst 2.090000e-02   p_cons 6.525000e-01   p_joint 3.465000e-02

Joint ci ratio: 9.460228e-02	ci left: 5.156679e-02	ci right 5.671998e-02	k: 1623	n:30000
Cons ci ratio: 1.643580e-02	ci left: 6.492882e-01	ci right 6.600818e-01	k: 19641	n:30000
KS ci ratio: 1.514834e-01	ci left: 2.017731e-02	ci right 2.351618e-02	k: 654	n:30000
SYNE2   30000 perm   18 sec   (1687 perm/sec)   p_kst 2.180000e-02   p_cons 6.547000e-01   p_joint 5.410000e-02

Joint ci ratio: 8.543346e-02	ci left: 4.785992e-02	ci right 5.215571e-02	k: 1999	n:40000
Cons ci ratio: 1.428038e-02	ci left: 6.485373e-01	ci right 6.578904e-01	k: 26129	n:40000
KS ci ratio: 1.337423e-01	ci left: 1.961722e-02	ci right 2.245291e-02	k: 840	n:40000
SYNE2   40000 perm   23 sec   (1769 perm/sec)   p_kst 2.100000e-02   p_cons 6.532250e-01   p_joint 4.997500e-02

Joint ci ratio: 8.150171e-02	ci left: 4.241491e-02	ci right 4.603825e-02	k: 2210	n:50000
Cons ci ratio: 1.276562e-02	ci left: 6.492902e-01	ci right 6.576520e-01	k: 32674	n:50000
KS ci ratio: 1.203412e-01	ci left: 1.952814e-02	ci right 2.204793e-02	k: 1038	n:50000
SYNE2   50000 perm   27 sec   (1819 perm/sec)   p_kst 2.076000e-02   p_cons 6.534800e-01   p_joint 4.420000e-02

Joint ci ratio: 7.695773e-02	ci left: 3.985259e-02	ci right 4.305862e-02	k: 2486	n:60000
Cons ci ratio: 1.162673e-02	ci left: 6.506960e-01	ci right 6.583224e-01	k: 39271	n:60000
KS ci ratio: 1.106196e-01	ci left: 1.936485e-02	ci right 2.164853e-02	k: 1229	n:60000
SYNE2   60000 perm   32 sec   (1849 perm/sec)   p_kst 2.048333e-02   p_cons 6.545167e-01   p_joint 4.143333e-02

Joint ci ratio: 7.895667e-02	ci left: 3.266966e-02	ci right 3.536914e-02	k: 2380	n:70000
Cons ci ratio: 1.079904e-02	ci left: 6.495175e-01	ci right 6.565841e-01	k: 45714	n:70000
KS ci ratio: 1.023412e-01	ci left: 1.947696e-02	ci right 2.159161e-02	k: 1436	n:70000
SYNE2   70000 perm   38 sec   (1866 perm/sec)   p_kst 2.051429e-02   p_cons 6.530571e-01   p_joint 3.400000e-02

Joint ci ratio: 6.620094e-02	ci left: 4.059579e-02	ci right 4.338755e-02	k: 3358	n:80000
Cons ci ratio: 1.009479e-02	ci left: 6.500530e-01	ci right 6.566609e-01	k: 52269	n:80000
KS ci ratio: 9.591911e-02	ci left: 1.946820e-02	ci right 2.144179e-02	k: 1635	n:80000
SYNE2   80000 perm   43 sec   (1875 perm/sec)   p_kst 2.043750e-02   p_cons 6.533625e-01   p_joint 4.197500e-02

Outputting figure to mutsig2_images.part000000000170/SYNE2.9_21229_80000_0.020438_0.65336_0.041975.png
                gene_name: SYNE2
               theta_stop: 0.096 
                    nperm: 80000 
                     p_ks: 0.020 
        ci_ks_bounds_left: 0.019 
       ci_ks_bounds_right: 0.021 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.042 
     ci_joint_bounds_left: 0.041 
    ci_joint_bounds_right: 0.043 

Current progress: 25 percent done.
SYNE1
Processing conservation and coverage...
36% 73% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.328022e-02	ci left: 3.417393e-01	ci right 3.605475e-01	k: 3511	n:10000
Cons ci ratio: 4.367280e-02	ci left: 4.363242e-01	ci right 4.559072e-01	k: 4461	n:10000
KS ci ratio: 7.060744e-02	ci left: 2.272116e-01	ci right 2.439427e-01	k: 2355	n:10000
SYNE1   10000 perm   5 sec   (2128 perm/sec)   p_kst 2.355000e-01   p_cons 4.461000e-01   p_joint 3.511000e-01

Outputting figure to mutsig2_images.part000000000170/SYNE1.5_27068_10000_0.2355_0.4461_0.3511.png
                gene_name: SYNE1
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.35 
     ci_joint_bounds_left: 0.34 
    ci_joint_bounds_right: 0.36 

Current progress: 50 percent done.
TADA2A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.752551e+00	ci left: 1.089969e-04	ci right 1.023839e-03	k: 4	n:10000
Cons ci ratio: 1.251787e-01	ci left: 8.368370e-02	ci right 9.495688e-02	k: 892	n:10000
KS ci ratio: 8.163954e-01	ci left: 1.379226e-03	ci right 3.328943e-03	k: 22	n:10000
TADA2A   10000 perm   2 sec   (6176 perm/sec)   p_kst 2.200000e-03   p_cons 8.920000e-02   p_joint 4.000000e-04

Joint ci ratio: 1.600053e+00	ci left: 8.117914e-05	ci right 5.833193e-04	k: 5	n:20000
Cons ci ratio: 9.050606e-02	ci left: 8.185600e-02	ci right 8.966493e-02	k: 1714	n:20000
KS ci ratio: 5.902971e-01	ci left: 1.556389e-03	ci right 2.894955e-03	k: 43	n:20000
TADA2A   20000 perm   4 sec   (5613 perm/sec)   p_kst 2.150000e-03   p_cons 8.570000e-02   p_joint 2.500000e-04

Joint ci ratio: 4.973175e-01	ci left: 1.555685e-03	ci right 2.611146e-03	k: 61	n:30000
Cons ci ratio: 7.368711e-02	ci left: 8.301484e-02	ci right 8.939890e-02	k: 2585	n:30000
KS ci ratio: 4.973175e-01	ci left: 1.555685e-03	ci right 2.611146e-03	k: 61	n:30000
TADA2A   30000 perm   6 sec   (5382 perm/sec)   p_kst 2.033333e-03   p_cons 8.616667e-02   p_joint 2.033333e-03

Joint ci ratio: 4.615547e-01	ci left: 1.386542e-03	ci right 2.238401e-03	k: 71	n:40000
Cons ci ratio: 6.396751e-02	ci left: 8.307302e-02	ci right 8.858728e-02	k: 3432	n:40000
KS ci ratio: 4.615547e-01	ci left: 1.386542e-03	ci right 2.238401e-03	k: 71	n:40000
TADA2A   40000 perm   8 sec   (5210 perm/sec)   p_kst 1.775000e-03   p_cons 8.580000e-02   p_joint 1.775000e-03

Joint ci ratio: 4.151451e-01	ci left: 1.411803e-03	ci right 2.167926e-03	k: 88	n:50000
Cons ci ratio: 5.705637e-02	ci left: 8.379351e-02	ci right 8.873465e-02	k: 4312	n:50000
KS ci ratio: 4.151451e-01	ci left: 1.411803e-03	ci right 2.167926e-03	k: 88	n:50000
TADA2A   50000 perm   10 sec   (5080 perm/sec)   p_kst 1.760000e-03   p_cons 8.624000e-02   p_joint 1.760000e-03

Joint ci ratio: 3.822148e-01	ci left: 1.416472e-03	ci right 2.099838e-03	k: 104	n:60000
Cons ci ratio: 5.210501e-02	ci left: 8.394955e-02	ci right 8.845724e-02	k: 5171	n:60000
KS ci ratio: 3.822148e-01	ci left: 1.416472e-03	ci right 2.099838e-03	k: 104	n:60000
TADA2A   60000 perm   12 sec   (4963 perm/sec)   p_kst 1.733333e-03   p_cons 8.618333e-02   p_joint 1.733333e-03

Joint ci ratio: 3.590377e-01	ci left: 1.395503e-03	ci right 2.018400e-03	k: 118	n:70000
Cons ci ratio: 4.812218e-02	ci left: 8.449829e-02	ci right 8.867891e-02	k: 6060	n:70000
KS ci ratio: 3.590377e-01	ci left: 1.395503e-03	ci right 2.018400e-03	k: 118	n:70000
TADA2A   70000 perm   14 sec   (4851 perm/sec)   p_kst 1.685714e-03   p_cons 8.657143e-02   p_joint 1.685714e-03

Joint ci ratio: 3.298304e-01	ci left: 1.472328e-03	ci right 2.064743e-03	k: 140	n:80000
Cons ci ratio: 4.519969e-02	ci left: 8.399177e-02	ci right 8.788832e-02	k: 6874	n:80000
KS ci ratio: 3.298304e-01	ci left: 1.472328e-03	ci right 2.064743e-03	k: 140	n:80000
TADA2A   80000 perm   17 sec   (4753 perm/sec)   p_kst 1.750000e-03   p_cons 8.592500e-02   p_joint 1.750000e-03

Joint ci ratio: 3.115829e-01	ci left: 1.482432e-03	ci right 2.039359e-03	k: 157	n:90000
Cons ci ratio: 4.260980e-02	ci left: 8.412111e-02	ci right 8.779451e-02	k: 7735	n:90000
KS ci ratio: 3.115829e-01	ci left: 1.482432e-03	ci right 2.039359e-03	k: 157	n:90000
TADA2A   90000 perm   19 sec   (4660 perm/sec)   p_kst 1.744444e-03   p_cons 8.594444e-02   p_joint 1.744444e-03

Joint ci ratio: 2.943829e-01	ci left: 1.509760e-03	ci right 2.039809e-03	k: 176	n:100000
Cons ci ratio: 4.040666e-02	ci left: 8.427925e-02	ci right 8.776481e-02	k: 8601	n:100000
KS ci ratio: 2.943829e-01	ci left: 1.509760e-03	ci right 2.039809e-03	k: 176	n:100000
TADA2A   100000 perm   22 sec   (4571 perm/sec)   p_kst 1.760000e-03   p_cons 8.601000e-02   p_joint 1.760000e-03

Joint ci ratio: 2.811900e-01	ci left: 1.515906e-03	ci right 2.020037e-03	k: 193	n:110000
Cons ci ratio: 3.858920e-02	ci left: 8.410626e-02	ci right 8.742470e-02	k: 9433	n:110000
KS ci ratio: 2.811900e-01	ci left: 1.515906e-03	ci right 2.020037e-03	k: 193	n:110000
TADA2A   110000 perm   25 sec   (4475 perm/sec)   p_kst 1.754545e-03   p_cons 8.575455e-02   p_joint 1.754545e-03

Joint ci ratio: 2.722226e-01	ci left: 1.490396e-03	ci right 1.967535e-03	k: 206	n:120000
Cons ci ratio: 3.694957e-02	ci left: 8.416340e-02	ci right 8.733998e-02	k: 10289	n:120000
KS ci ratio: 2.722226e-01	ci left: 1.490396e-03	ci right 1.967535e-03	k: 206	n:120000
TADA2A   120000 perm   27 sec   (4374 perm/sec)   p_kst 1.716667e-03   p_cons 8.574167e-02   p_joint 1.716667e-03

Joint ci ratio: 2.634625e-01	ci left: 1.476211e-03	ci right 1.931094e-03	k: 220	n:130000
Cons ci ratio: 3.549740e-02	ci left: 8.423718e-02	ci right 8.728902e-02	k: 11148	n:130000
KS ci ratio: 2.634625e-01	ci left: 1.476211e-03	ci right 1.931094e-03	k: 220	n:130000
TADA2A   130000 perm   30 sec   (4291 perm/sec)   p_kst 1.692308e-03   p_cons 8.575385e-02   p_joint 1.692308e-03

Joint ci ratio: 2.517684e-01	ci left: 1.511090e-03	ci right 1.952815e-03	k: 241	n:140000
Cons ci ratio: 3.419621e-02	ci left: 8.433796e-02	ci right 8.727923e-02	k: 12012	n:140000
KS ci ratio: 2.517684e-01	ci left: 1.511090e-03	ci right 1.952815e-03	k: 241	n:140000
TADA2A   140000 perm   33 sec   (4205 perm/sec)   p_kst 1.721429e-03   p_cons 8.580000e-02   p_joint 1.721429e-03

Joint ci ratio: 2.419660e-01	ci left: 1.535441e-03	ci right 1.964187e-03	k: 261	n:150000
Cons ci ratio: 3.306771e-02	ci left: 8.424180e-02	ci right 8.708091e-02	k: 12848	n:150000
KS ci ratio: 2.419660e-01	ci left: 1.535441e-03	ci right 1.964187e-03	k: 261	n:150000
TADA2A   150000 perm   37 sec   (4107 perm/sec)   p_kst 1.740000e-03   p_cons 8.565333e-02   p_joint 1.740000e-03

Joint ci ratio: 2.311819e-01	ci left: 1.586474e-03	ci right 2.006909e-03	k: 286	n:160000
Cons ci ratio: 3.202228e-02	ci left: 8.426455e-02	ci right 8.701298e-02	k: 13701	n:160000
KS ci ratio: 2.311819e-01	ci left: 1.586474e-03	ci right 2.006909e-03	k: 286	n:160000
TADA2A   160000 perm   39 sec   (4069 perm/sec)   p_kst 1.787500e-03   p_cons 8.563125e-02   p_joint 1.787500e-03

Joint ci ratio: 2.231596e-01	ci left: 1.609656e-03	ci right 2.019398e-03	k: 307	n:170000
Cons ci ratio: 3.110050e-02	ci left: 8.413402e-02	ci right 8.679778e-02	k: 14528	n:170000
KS ci ratio: 2.231596e-01	ci left: 1.609656e-03	ci right 2.019398e-03	k: 307	n:170000
TADA2A   170000 perm   42 sec   (4042 perm/sec)   p_kst 1.805882e-03   p_cons 8.545882e-02   p_joint 1.805882e-03

Joint ci ratio: 2.159184e-01	ci left: 1.630485e-03	ci right 2.030277e-03	k: 328	n:180000
Cons ci ratio: 3.026369e-02	ci left: 8.396936e-02	ci right 8.655512e-02	k: 15346	n:180000
KS ci ratio: 2.159184e-01	ci left: 1.630485e-03	ci right 2.030277e-03	k: 328	n:180000
TADA2A   180000 perm   45 sec   (4012 perm/sec)   p_kst 1.822222e-03   p_cons 8.525556e-02   p_joint 1.822222e-03

Joint ci ratio: 2.099410e-01	ci left: 1.639339e-03	ci right 2.028744e-03	k: 347	n:190000
Cons ci ratio: 2.945315e-02	ci left: 8.402158e-02	ci right 8.653846e-02	k: 16202	n:190000
KS ci ratio: 2.099410e-01	ci left: 1.639339e-03	ci right 2.028744e-03	k: 347	n:190000
TADA2A   190000 perm   48 sec   (3979 perm/sec)   p_kst 1.826316e-03   p_cons 8.527368e-02   p_joint 1.826316e-03

Joint ci ratio: 2.019679e-01	ci left: 1.690159e-03	ci right 2.074509e-03	k: 375	n:200000
Cons ci ratio: 2.866129e-02	ci left: 8.430287e-02	ci right 8.675916e-02	k: 17105	n:200000
KS ci ratio: 2.019679e-01	ci left: 1.690159e-03	ci right 2.074509e-03	k: 375	n:200000
TADA2A   200000 perm   51 sec   (3945 perm/sec)   p_kst 1.875000e-03   p_cons 8.552500e-02   p_joint 1.875000e-03

Joint ci ratio: 1.975523e-01	ci left: 1.686578e-03	ci right 2.060719e-03	k: 392	n:210000
Cons ci ratio: 2.795975e-02	ci left: 8.439256e-02	ci right 8.679032e-02	k: 17973	n:210000
KS ci ratio: 1.975523e-01	ci left: 1.686578e-03	ci right 2.060719e-03	k: 392	n:210000
TADA2A   210000 perm   54 sec   (3910 perm/sec)   p_kst 1.866667e-03   p_cons 8.558571e-02   p_joint 1.866667e-03

Joint ci ratio: 1.943663e-01	ci left: 1.666106e-03	ci right 2.029039e-03	k: 405	n:220000
Cons ci ratio: 2.730257e-02	ci left: 8.450188e-02	ci right 8.684542e-02	k: 18847	n:220000
KS ci ratio: 1.943663e-01	ci left: 1.666106e-03	ci right 2.029039e-03	k: 405	n:220000
TADA2A   220000 perm   57 sec   (3871 perm/sec)   p_kst 1.840909e-03   p_cons 8.566818e-02   p_joint 1.840909e-03

Joint ci ratio: 1.906471e-01	ci left: 1.659878e-03	ci right 2.013735e-03	k: 421	n:230000
Cons ci ratio: 2.672078e-02	ci left: 8.442078e-02	ci right 8.671141e-02	k: 19679	n:230000
KS ci ratio: 1.906471e-01	ci left: 1.659878e-03	ci right 2.013735e-03	k: 421	n:230000
TADA2A   230000 perm   60 sec   (3836 perm/sec)   p_kst 1.830435e-03   p_cons 8.556087e-02   p_joint 1.830435e-03

Joint ci ratio: 1.871335e-01	ci left: 1.654231e-03	ci right 1.999645e-03	k: 437	n:240000
Cons ci ratio: 2.617397e-02	ci left: 8.435108e-02	ci right 8.659227e-02	k: 20512	n:240000
KS ci ratio: 1.871335e-01	ci left: 1.654231e-03	ci right 1.999645e-03	k: 437	n:240000
TADA2A   240000 perm   63 sec   (3796 perm/sec)   p_kst 1.820833e-03   p_cons 8.546667e-02   p_joint 1.820833e-03

Joint ci ratio: 1.828015e-01	ci left: 1.668173e-03	ci right 2.007543e-03	k: 458	n:250000
Cons ci ratio: 2.565152e-02	ci left: 8.433512e-02	ci right 8.653050e-02	k: 21357	n:250000
KS ci ratio: 1.828015e-01	ci left: 1.668173e-03	ci right 2.007543e-03	k: 458	n:250000
TADA2A   250000 perm   66 sec   (3760 perm/sec)   p_kst 1.832000e-03   p_cons 8.542800e-02   p_joint 1.832000e-03

Joint ci ratio: 1.785709e-01	ci left: 1.684803e-03	ci right 2.018766e-03	k: 480	n:260000
Cons ci ratio: 2.513070e-02	ci left: 8.449672e-02	ci right 8.665099e-02	k: 22248	n:260000
KS ci ratio: 1.785709e-01	ci left: 1.684803e-03	ci right 2.018766e-03	k: 480	n:260000
TADA2A   260000 perm   70 sec   (3723 perm/sec)   p_kst 1.846154e-03   p_cons 8.556923e-02   p_joint 1.846154e-03

Joint ci ratio: 1.751450e-01	ci left: 1.689658e-03	ci right 2.017479e-03	k: 499	n:270000
Cons ci ratio: 2.462931e-02	ci left: 8.471673e-02	ci right 8.683291e-02	k: 23158	n:270000
KS ci ratio: 1.751450e-01	ci left: 1.689658e-03	ci right 2.017479e-03	k: 499	n:270000
TADA2A   270000 perm   73 sec   (3686 perm/sec)   p_kst 1.848148e-03   p_cons 8.577037e-02   p_joint 1.848148e-03

Joint ci ratio: 1.714134e-01	ci left: 1.704479e-03	ci right 2.027400e-03	k: 521	n:280000
Cons ci ratio: 2.418261e-02	ci left: 8.475448e-02	ci right 8.683267e-02	k: 24021	n:280000
KS ci ratio: 1.714134e-01	ci left: 1.704479e-03	ci right 2.027400e-03	k: 521	n:280000
TADA2A   280000 perm   77 sec   (3646 perm/sec)   p_kst 1.860714e-03   p_cons 8.578929e-02   p_joint 1.860714e-03

Joint ci ratio: 1.691614e-01	ci left: 1.691921e-03	ci right 2.007822e-03	k: 535	n:290000
Cons ci ratio: 2.370833e-02	ci left: 8.512606e-02	ci right 8.717187e-02	k: 24982	n:290000
KS ci ratio: 1.691614e-01	ci left: 1.691921e-03	ci right 2.007822e-03	k: 535	n:290000
TADA2A   290000 perm   80 sec   (3608 perm/sec)   p_kst 1.844828e-03   p_cons 8.614483e-02   p_joint 1.844828e-03

Joint ci ratio: 1.666924e-01	ci left: 1.686615e-03	ci right 1.996468e-03	k: 551	n:300000
Cons ci ratio: 2.332985e-02	ci left: 8.500903e-02	ci right 8.701897e-02	k: 25803	n:300000
KS ci ratio: 1.666924e-01	ci left: 1.686615e-03	ci right 1.996468e-03	k: 551	n:300000
TADA2A   300000 perm   84 sec   (3572 perm/sec)   p_kst 1.836667e-03   p_cons 8.601000e-02   p_joint 1.836667e-03

Joint ci ratio: 1.640394e-01	ci left: 1.687870e-03	ci right 1.992531e-03	k: 569	n:310000
Cons ci ratio: 2.295855e-02	ci left: 8.497040e-02	ci right 8.694703e-02	k: 26646	n:310000
KS ci ratio: 1.640394e-01	ci left: 1.687870e-03	ci right 1.992531e-03	k: 569	n:310000
TADA2A   310000 perm   88 sec   (3537 perm/sec)   p_kst 1.835484e-03   p_cons 8.595484e-02   p_joint 1.835484e-03

Joint ci ratio: 1.617851e-01	ci left: 1.683085e-03	ci right 1.982302e-03	k: 585	n:320000
Cons ci ratio: 2.259589e-02	ci left: 8.499349e-02	ci right 8.693902e-02	k: 27508	n:320000
KS ci ratio: 1.617851e-01	ci left: 1.683085e-03	ci right 1.982302e-03	k: 585	n:320000
TADA2A   320000 perm   91 sec   (3499 perm/sec)   p_kst 1.828125e-03   p_cons 8.596250e-02   p_joint 1.828125e-03

Joint ci ratio: 1.597542e-01	ci left: 1.675708e-03	ci right 1.969515e-03	k: 600	n:330000
Cons ci ratio: 2.224731e-02	ci left: 8.503350e-02	ci right 8.694953e-02	k: 28376	n:330000
KS ci ratio: 1.597542e-01	ci left: 1.675708e-03	ci right 1.969515e-03	k: 600	n:330000
TADA2A   330000 perm   95 sec   (3462 perm/sec)   p_kst 1.818182e-03   p_cons 8.598788e-02   p_joint 1.818182e-03

Joint ci ratio: 1.575419e-01	ci left: 1.674437e-03	ci right 1.963571e-03	k: 617	n:340000
Cons ci ratio: 2.191234e-02	ci left: 8.508601e-02	ci right 8.697400e-02	k: 29249	n:340000
KS ci ratio: 1.575419e-01	ci left: 1.674437e-03	ci right 1.963571e-03	k: 617	n:340000
TADA2A   340000 perm   99 sec   (3425 perm/sec)   p_kst 1.814706e-03   p_cons 8.602647e-02   p_joint 1.814706e-03

Joint ci ratio: 1.551744e-01	ci left: 1.678758e-03	ci right 1.963877e-03	k: 636	n:350000
Cons ci ratio: 2.157951e-02	ci left: 8.522670e-02	ci right 8.708873e-02	k: 30154	n:350000
KS ci ratio: 1.551744e-01	ci left: 1.678758e-03	ci right 1.963877e-03	k: 636	n:350000
TADA2A   350000 perm   103 sec   (3389 perm/sec)   p_kst 1.817143e-03   p_cons 8.615429e-02   p_joint 1.817143e-03

Joint ci ratio: 1.530275e-01	ci left: 1.680198e-03	ci right 1.961251e-03	k: 654	n:360000
Cons ci ratio: 2.127227e-02	ci left: 8.527961e-02	ci right 8.711594e-02	k: 31030	n:360000
KS ci ratio: 1.530275e-01	ci left: 1.680198e-03	ci right 1.961251e-03	k: 654	n:360000
TADA2A   360000 perm   107 sec   (3355 perm/sec)   p_kst 1.816667e-03   p_cons 8.619444e-02   p_joint 1.816667e-03

Joint ci ratio: 1.508550e-01	ci left: 1.684187e-03	ci right 1.961547e-03	k: 673	n:370000
Cons ci ratio: 2.098175e-02	ci left: 8.530025e-02	ci right 8.711164e-02	k: 31895	n:370000
KS ci ratio: 1.508550e-01	ci left: 1.684187e-03	ci right 1.961547e-03	k: 673	n:370000
TADA2A   370000 perm   111 sec   (3321 perm/sec)   p_kst 1.818919e-03   p_cons 8.620270e-02   p_joint 1.818919e-03

Joint ci ratio: 1.488801e-01	ci left: 1.685458e-03	ci right 1.959070e-03	k: 691	n:380000
Cons ci ratio: 2.070559e-02	ci left: 8.529901e-02	ci right 8.708625e-02	k: 32752	n:380000
KS ci ratio: 1.488801e-01	ci left: 1.685458e-03	ci right 1.959070e-03	k: 691	n:380000
TADA2A   380000 perm   116 sec   (3286 perm/sec)   p_kst 1.818421e-03   p_cons 8.618947e-02   p_joint 1.818421e-03

Joint ci ratio: 1.476070e-01	ci left: 1.671868e-03	ci right 1.940749e-03	k: 703	n:390000
Cons ci ratio: 2.044604e-02	ci left: 8.525205e-02	ci right 8.701564e-02	k: 33591	n:390000
KS ci ratio: 1.476070e-01	ci left: 1.671868e-03	ci right 1.940749e-03	k: 703	n:390000
TADA2A   390000 perm   120 sec   (3253 perm/sec)   p_kst 1.802564e-03   p_cons 8.613077e-02   p_joint 1.802564e-03

Joint ci ratio: 1.454530e-01	ci left: 1.680647e-03	ci right 1.946653e-03	k: 724	n:400000
Cons ci ratio: 2.019440e-02	ci left: 8.522001e-02	ci right 8.696099e-02	k: 34435	n:400000
KS ci ratio: 1.454530e-01	ci left: 1.680647e-03	ci right 1.946653e-03	k: 724	n:400000
TADA2A   400000 perm   124 sec   (3220 perm/sec)   p_kst 1.810000e-03   p_cons 8.608750e-02   p_joint 1.810000e-03

Joint ci ratio: 1.435835e-01	ci left: 1.684322e-03	ci right 1.947189e-03	k: 743	n:410000
Cons ci ratio: 1.994781e-02	ci left: 8.522122e-02	ci right 8.694073e-02	k: 35292	n:410000
KS ci ratio: 1.435835e-01	ci left: 1.684322e-03	ci right 1.947189e-03	k: 743	n:410000
TADA2A   410000 perm   129 sec   (3187 perm/sec)   p_kst 1.812195e-03   p_cons 8.607805e-02   p_joint 1.812195e-03

Joint ci ratio: 1.412292e-01	ci left: 1.701623e-03	ci right 1.962469e-03	k: 768	n:420000
Cons ci ratio: 1.970319e-02	ci left: 8.527702e-02	ci right 8.697631e-02	k: 36172	n:420000
KS ci ratio: 1.412292e-01	ci left: 1.701623e-03	ci right 1.962469e-03	k: 768	n:420000
TADA2A   420000 perm   133 sec   (3153 perm/sec)   p_kst 1.828571e-03   p_cons 8.612381e-02   p_joint 1.828571e-03

Joint ci ratio: 1.402310e-01	ci left: 1.686730e-03	ci right 1.943313e-03	k: 779	n:430000
Cons ci ratio: 1.948058e-02	ci left: 8.522384e-02	ci right 8.690267e-02	k: 37006	n:430000
KS ci ratio: 1.402310e-01	ci left: 1.686730e-03	ci right 1.943313e-03	k: 779	n:430000
TADA2A   430000 perm   138 sec   (3121 perm/sec)   p_kst 1.811628e-03   p_cons 8.606047e-02   p_joint 1.811628e-03

Joint ci ratio: 1.393419e-01	ci left: 1.670327e-03	ci right 1.922670e-03	k: 789	n:440000
Cons ci ratio: 1.926368e-02	ci left: 8.518676e-02	ci right 8.684597e-02	k: 37846	n:440000
KS ci ratio: 1.393419e-01	ci left: 1.670327e-03	ci right 1.922670e-03	k: 789	n:440000
TADA2A   440000 perm   142 sec   (3089 perm/sec)   p_kst 1.793182e-03   p_cons 8.601364e-02   p_joint 1.793182e-03

Joint ci ratio: 1.369348e-01	ci left: 1.693282e-03	ci right 1.944313e-03	k: 817	n:450000
Cons ci ratio: 1.904633e-02	ci left: 8.521338e-02	ci right 8.685418e-02	k: 38714	n:450000
KS ci ratio: 1.369348e-01	ci left: 1.693282e-03	ci right 1.944313e-03	k: 817	n:450000
TADA2A   450000 perm   147 sec   (3058 perm/sec)   p_kst 1.815556e-03   p_cons 8.603111e-02   p_joint 1.815556e-03

Joint ci ratio: 1.353715e-01	ci left: 1.696369e-03	ci right 1.944756e-03	k: 836	n:460000
Cons ci ratio: 1.883409e-02	ci left: 8.525626e-02	ci right 8.687939e-02	k: 39590	n:460000
KS ci ratio: 1.353715e-01	ci left: 1.696369e-03	ci right 1.944756e-03	k: 836	n:460000
TADA2A   460000 perm   152 sec   (3027 perm/sec)   p_kst 1.817391e-03   p_cons 8.606522e-02   p_joint 1.817391e-03

Joint ci ratio: 1.335484e-01	ci left: 1.707567e-03	ci right 1.953959e-03	k: 859	n:470000
Cons ci ratio: 1.862727e-02	ci left: 8.531013e-02	ci right 8.691626e-02	k: 40472	n:470000
KS ci ratio: 1.335484e-01	ci left: 1.707567e-03	ci right 1.953959e-03	k: 859	n:470000
TADA2A   470000 perm   157 sec   (2998 perm/sec)   p_kst 1.827660e-03   p_cons 8.611064e-02   p_joint 1.827660e-03

Joint ci ratio: 1.314989e-01	ci left: 1.726379e-03	ci right 1.971364e-03	k: 886	n:480000
Cons ci ratio: 1.841690e-02	ci left: 8.544898e-02	ci right 8.703936e-02	k: 41396	n:480000
KS ci ratio: 1.314989e-01	ci left: 1.726379e-03	ci right 1.971364e-03	k: 886	n:480000
TADA2A   480000 perm   162 sec   (2969 perm/sec)   p_kst 1.845833e-03   p_cons 8.624167e-02   p_joint 1.845833e-03

Joint ci ratio: 1.303290e-01	ci left: 1.722730e-03	ci right 1.964854e-03	k: 902	n:490000
Cons ci ratio: 1.822315e-02	ci left: 8.549892e-02	ci right 8.707332e-02	k: 42279	n:490000
KS ci ratio: 1.303290e-01	ci left: 1.722730e-03	ci right 1.964854e-03	k: 902	n:490000
TADA2A   490000 perm   167 sec   (2941 perm/sec)   p_kst 1.840816e-03   p_cons 8.628367e-02   p_joint 1.840816e-03

Joint ci ratio: 1.294016e-01	ci left: 1.713430e-03	ci right 1.952402e-03	k: 915	n:500000
Cons ci ratio: 1.804844e-02	ci left: 8.543342e-02	ci right 8.699137e-02	k: 43105	n:500000
KS ci ratio: 1.294016e-01	ci left: 1.713430e-03	ci right 1.952402e-03	k: 915	n:500000
TADA2A   500000 perm   172 sec   (2913 perm/sec)   p_kst 1.830000e-03   p_cons 8.621000e-02   p_joint 1.830000e-03

Joint ci ratio: 1.274669e-01	ci left: 1.732973e-03	ci right 1.970783e-03	k: 943	n:510000
Cons ci ratio: 1.787509e-02	ci left: 8.540181e-02	ci right 8.694407e-02	k: 43947	n:510000
KS ci ratio: 1.274669e-01	ci left: 1.732973e-03	ci right 1.970783e-03	k: 943	n:510000
TADA2A   510000 perm   177 sec   (2884 perm/sec)   p_kst 1.849020e-03   p_cons 8.617059e-02   p_joint 1.849020e-03

Joint ci ratio: 1.265326e-01	ci left: 1.725713e-03	ci right 1.960662e-03	k: 957	n:520000
Cons ci ratio: 1.770968e-02	ci left: 8.534467e-02	ci right 8.687149e-02	k: 44775	n:520000
KS ci ratio: 1.265326e-01	ci left: 1.725713e-03	ci right 1.960662e-03	k: 957	n:520000
TADA2A   520000 perm   182 sec   (2857 perm/sec)   p_kst 1.840385e-03   p_cons 8.610577e-02   p_joint 1.840385e-03

Joint ci ratio: 1.255539e-01	ci left: 1.720562e-03	ci right 1.952862e-03	k: 972	n:530000
Cons ci ratio: 1.754540e-02	ci left: 8.531981e-02	ci right 8.683189e-02	k: 45619	n:530000
KS ci ratio: 1.255539e-01	ci left: 1.720562e-03	ci right 1.952862e-03	k: 972	n:530000
TADA2A   530000 perm   187 sec   (2830 perm/sec)   p_kst 1.833962e-03   p_cons 8.607358e-02   p_joint 1.833962e-03

Joint ci ratio: 1.245976e-01	ci left: 1.715608e-03	ci right 1.945345e-03	k: 987	n:540000
Cons ci ratio: 1.738602e-02	ci left: 8.529225e-02	ci right 8.678997e-02	k: 46461	n:540000
KS ci ratio: 1.245976e-01	ci left: 1.715608e-03	ci right 1.945345e-03	k: 987	n:540000
TADA2A   540000 perm   193 sec   (2804 perm/sec)   p_kst 1.827778e-03   p_cons 8.603889e-02   p_joint 1.827778e-03

Joint ci ratio: 1.237864e-01	ci left: 1.707317e-03	ci right 1.934346e-03	k: 1000	n:550000
Cons ci ratio: 1.722692e-02	ci left: 8.530198e-02	ci right 8.678602e-02	k: 47323	n:550000
KS ci ratio: 1.237864e-01	ci left: 1.707317e-03	ci right 1.934346e-03	k: 1000	n:550000
TADA2A   550000 perm   198 sec   (2779 perm/sec)   p_kst 1.818182e-03   p_cons 8.604182e-02   p_joint 1.818182e-03

Joint ci ratio: 1.226883e-01	ci left: 1.707981e-03	ci right 1.932937e-03	k: 1018	n:560000
Cons ci ratio: 1.707716e-02	ci left: 8.526517e-02	ci right 8.673555e-02	k: 48159	n:560000
KS ci ratio: 1.226883e-01	ci left: 1.707981e-03	ci right 1.932937e-03	k: 1018	n:560000
TADA2A   560000 perm   203 sec   (2754 perm/sec)   p_kst 1.817857e-03   p_cons 8.599821e-02   p_joint 1.817857e-03

Joint ci ratio: 1.216776e-01	ci left: 1.706929e-03	ci right 1.929762e-03	k: 1035	n:570000
Cons ci ratio: 1.692216e-02	ci left: 8.531359e-02	ci right 8.677132e-02	k: 49043	n:570000
KS ci ratio: 1.216776e-01	ci left: 1.706929e-03	ci right 1.929762e-03	k: 1035	n:570000
TADA2A   570000 perm   209 sec   (2729 perm/sec)   p_kst 1.815789e-03   p_cons 8.604035e-02   p_joint 1.815789e-03

Joint ci ratio: 1.208066e-01	ci left: 1.702577e-03	ci right 1.923136e-03	k: 1050	n:580000
Cons ci ratio: 1.677058e-02	ci left: 8.536727e-02	ci right 8.681273e-02	k: 49931	n:580000
KS ci ratio: 1.208066e-01	ci left: 1.702577e-03	ci right 1.923136e-03	k: 1050	n:580000
TADA2A   580000 perm   214 sec   (2706 perm/sec)   p_kst 1.810345e-03   p_cons 8.608793e-02   p_joint 1.810345e-03

Joint ci ratio: 1.198413e-01	ci left: 1.701666e-03	ci right 1.920221e-03	k: 1067	n:590000
Cons ci ratio: 1.662998e-02	ci left: 8.535333e-02	ci right 8.678633e-02	k: 50780	n:590000
KS ci ratio: 1.198413e-01	ci left: 1.701666e-03	ci right 1.920221e-03	k: 1067	n:590000
TADA2A   590000 perm   220 sec   (2683 perm/sec)   p_kst 1.808475e-03   p_cons 8.606780e-02   p_joint 1.808475e-03

Joint ci ratio: 1.188440e-01	ci left: 1.702410e-03	ci right 1.919113e-03	k: 1085	n:600000
Cons ci ratio: 1.648570e-02	ci left: 8.540799e-02	ci right 8.682934e-02	k: 51670	n:600000
KS ci ratio: 1.188440e-01	ci left: 1.702410e-03	ci right 1.919113e-03	k: 1085	n:600000
TADA2A   600000 perm   226 sec   (2660 perm/sec)   p_kst 1.808333e-03   p_cons 8.611667e-02   p_joint 1.808333e-03

Joint ci ratio: 1.174457e-01	ci left: 1.715865e-03	ci right 1.931533e-03	k: 1111	n:610000
Cons ci ratio: 1.634255e-02	ci left: 8.548541e-02	ci right 8.689558e-02	k: 52575	n:610000
KS ci ratio: 1.174457e-01	ci left: 1.715865e-03	ci right 1.931533e-03	k: 1111	n:610000
TADA2A   610000 perm   231 sec   (2637 perm/sec)   p_kst 1.821311e-03   p_cons 8.618852e-02   p_joint 1.821311e-03

Joint ci ratio: 1.160445e-01	ci left: 1.730467e-03	ci right 1.945198e-03	k: 1138	n:620000
Cons ci ratio: 1.621369e-02	ci left: 8.545753e-02	ci right 8.685602e-02	k: 53416	n:620000
KS ci ratio: 1.160445e-01	ci left: 1.730467e-03	ci right 1.945198e-03	k: 1138	n:620000
TADA2A   620000 perm   237 sec   (2615 perm/sec)   p_kst 1.835484e-03   p_cons 8.615484e-02   p_joint 1.835484e-03

Joint ci ratio: 1.148899e-01	ci left: 1.738454e-03	ci right 1.951883e-03	k: 1161	n:630000
Cons ci ratio: 1.608556e-02	ci left: 8.545272e-02	ci right 8.683998e-02	k: 54271	n:630000
KS ci ratio: 1.148899e-01	ci left: 1.738454e-03	ci right 1.951883e-03	k: 1161	n:630000
TADA2A   630000 perm   243 sec   (2592 perm/sec)   p_kst 1.842857e-03   p_cons 8.614444e-02   p_joint 1.842857e-03

Joint ci ratio: 1.135772e-01	ci left: 1.752273e-03	ci right 1.964777e-03	k: 1188	n:640000
Cons ci ratio: 1.595615e-02	ci left: 8.549014e-02	ci right 8.686674e-02	k: 55153	n:640000
KS ci ratio: 1.135772e-01	ci left: 1.752273e-03	ci right 1.964777e-03	k: 1188	n:640000
TADA2A   640000 perm   249 sec   (2570 perm/sec)   p_kst 1.856250e-03   p_cons 8.617656e-02   p_joint 1.856250e-03

Joint ci ratio: 1.124475e-01	ci left: 1.761195e-03	ci right 1.972515e-03	k: 1212	n:650000
Cons ci ratio: 1.582424e-02	ci left: 8.558163e-02	ci right 8.694821e-02	k: 56071	n:650000
KS ci ratio: 1.124475e-01	ci left: 1.761195e-03	ci right 1.972515e-03	k: 1212	n:650000
TADA2A   650000 perm   255 sec   (2549 perm/sec)   p_kst 1.864615e-03   p_cons 8.626308e-02   p_joint 1.864615e-03

Joint ci ratio: 1.116224e-01	ci left: 1.761019e-03	ci right 1.970665e-03	k: 1230	n:660000
Cons ci ratio: 1.570476e-02	ci left: 8.557831e-02	ci right 8.693442e-02	k: 56928	n:660000
KS ci ratio: 1.116224e-01	ci left: 1.761019e-03	ci right 1.970665e-03	k: 1230	n:660000
TADA2A   660000 perm   261 sec   (2529 perm/sec)   p_kst 1.863636e-03   p_cons 8.625455e-02   p_joint 1.863636e-03

Joint ci ratio: 1.108152e-01	ci left: 1.760853e-03	ci right 1.968865e-03	k: 1248	n:670000
Cons ci ratio: 1.558278e-02	ci left: 8.562717e-02	ci right 8.697342e-02	k: 57820	n:670000
KS ci ratio: 1.108152e-01	ci left: 1.760853e-03	ci right 1.968865e-03	k: 1248	n:670000
TADA2A   670000 perm   267 sec   (2507 perm/sec)   p_kst 1.862687e-03   p_cons 8.629851e-02   p_joint 1.862687e-03

Joint ci ratio: 1.101560e-01	ci left: 1.756407e-03	ci right 1.962580e-03	k: 1263	n:680000
Cons ci ratio: 1.546878e-02	ci left: 8.562188e-02	ci right 8.695812e-02	k: 58676	n:680000
KS ci ratio: 1.101560e-01	ci left: 1.756407e-03	ci right 1.962580e-03	k: 1263	n:680000
TADA2A   680000 perm   274 sec   (2486 perm/sec)   p_kst 1.857353e-03   p_cons 8.628824e-02   p_joint 1.857353e-03

Joint ci ratio: 1.095084e-01	ci left: 1.752094e-03	ci right 1.956473e-03	k: 1278	n:690000
Cons ci ratio: 1.535232e-02	ci left: 8.566733e-02	ci right 8.699412e-02	k: 59567	n:690000
KS ci ratio: 1.095084e-01	ci left: 1.752094e-03	ci right 1.956473e-03	k: 1278	n:690000
TADA2A   690000 perm   280 sec   (2466 perm/sec)   p_kst 1.852174e-03   p_cons 8.632899e-02   p_joint 1.852174e-03

Joint ci ratio: 1.086620e-01	ci left: 1.754856e-03	ci right 1.957874e-03	k: 1298	n:700000
Cons ci ratio: 1.524534e-02	ci left: 8.564033e-02	ci right 8.695738e-02	k: 60408	n:700000
KS ci ratio: 1.086620e-01	ci left: 1.754856e-03	ci right 1.957874e-03	k: 1298	n:700000
TADA2A   700000 perm   286 sec   (2446 perm/sec)   p_kst 1.854286e-03   p_cons 8.629714e-02   p_joint 1.854286e-03

Joint ci ratio: 1.079170e-01	ci left: 1.754805e-03	ci right 1.956337e-03	k: 1316	n:710000
Cons ci ratio: 1.514368e-02	ci left: 8.558184e-02	ci right 8.688914e-02	k: 61226	n:710000
KS ci ratio: 1.079170e-01	ci left: 1.754805e-03	ci right 1.956337e-03	k: 1316	n:710000
TADA2A   710000 perm   293 sec   (2425 perm/sec)   p_kst 1.853521e-03   p_cons 8.623380e-02   p_joint 1.853521e-03

Joint ci ratio: 1.073887e-01	ci left: 1.748002e-03	ci right 1.947707e-03	k: 1329	n:720000
Cons ci ratio: 1.504112e-02	ci left: 8.555546e-02	ci right 8.685343e-02	k: 62066	n:720000
KS ci ratio: 1.073887e-01	ci left: 1.748002e-03	ci right 1.947707e-03	k: 1329	n:720000
TADA2A   720000 perm   299 sec   (2406 perm/sec)   p_kst 1.845833e-03   p_cons 8.620278e-02   p_joint 1.845833e-03

Joint ci ratio: 1.067487e-01	ci left: 1.745387e-03	ci right 1.943531e-03	k: 1345	n:730000
Cons ci ratio: 1.494073e-02	ci left: 8.552847e-02	ci right 8.681729e-02	k: 62905	n:730000
KS ci ratio: 1.067487e-01	ci left: 1.745387e-03	ci right 1.943531e-03	k: 1345	n:730000
TADA2A   730000 perm   306 sec   (2388 perm/sec)   p_kst 1.842466e-03   p_cons 8.617123e-02   p_joint 1.842466e-03

Joint ci ratio: 1.059642e-01	ci left: 1.748109e-03	ci right 1.945012e-03	k: 1365	n:740000
Cons ci ratio: 1.483877e-02	ci left: 8.553994e-02	ci right 8.682006e-02	k: 63772	n:740000
KS ci ratio: 1.059642e-01	ci left: 1.748109e-03	ci right 1.945012e-03	k: 1365	n:740000
TADA2A   740000 perm   313 sec   (2368 perm/sec)   p_kst 1.844595e-03   p_cons 8.617838e-02   p_joint 1.844595e-03

Joint ci ratio: 1.050072e-01	ci left: 1.757255e-03	ci right 1.953291e-03	k: 1390	n:750000
Cons ci ratio: 1.474073e-02	ci left: 8.553120e-02	ci right 8.680266e-02	k: 64624	n:750000
KS ci ratio: 1.050072e-01	ci left: 1.757255e-03	ci right 1.953291e-03	k: 1390	n:750000
TADA2A   750000 perm   319 sec   (2350 perm/sec)   p_kst 1.853333e-03   p_cons 8.616533e-02   p_joint 1.853333e-03

Joint ci ratio: 1.042973e-01	ci left: 1.758479e-03	ci right 1.953244e-03	k: 1409	n:760000
Cons ci ratio: 1.464254e-02	ci left: 8.554502e-02	ci right 8.680814e-02	k: 65493	n:760000
KS ci ratio: 1.042973e-01	ci left: 1.758479e-03	ci right 1.953244e-03	k: 1409	n:760000
TADA2A   760000 perm   326 sec   (2332 perm/sec)   p_kst 1.853947e-03   p_cons 8.617500e-02   p_joint 1.853947e-03

Joint ci ratio: 1.034566e-01	ci left: 1.764736e-03	ci right 1.958523e-03	k: 1432	n:770000
Cons ci ratio: 1.454795e-02	ci left: 8.554038e-02	ci right 8.679521e-02	k: 66348	n:770000
KS ci ratio: 1.034566e-01	ci left: 1.764736e-03	ci right 1.958523e-03	k: 1432	n:770000
TADA2A   770000 perm   333 sec   (2315 perm/sec)   p_kst 1.859740e-03   p_cons 8.616623e-02   p_joint 1.859740e-03

Joint ci ratio: 1.029552e-01	ci left: 1.759597e-03	ci right 1.951825e-03	k: 1446	n:780000
Cons ci ratio: 1.445424e-02	ci left: 8.554611e-02	ci right 8.679287e-02	k: 67211	n:780000
KS ci ratio: 1.029552e-01	ci left: 1.759597e-03	ci right 1.951825e-03	k: 1446	n:780000
TADA2A   780000 perm   340 sec   (2296 perm/sec)   p_kst 1.853846e-03   p_cons 8.616795e-02   p_joint 1.853846e-03

Joint ci ratio: 1.022858e-01	ci left: 1.760757e-03	ci right 1.951786e-03	k: 1465	n:790000
Cons ci ratio: 1.436024e-02	ci left: 8.557442e-02	ci right 8.681342e-02	k: 68092	n:790000
KS ci ratio: 1.022858e-01	ci left: 1.760757e-03	ci right 1.951786e-03	k: 1465	n:790000
TADA2A   790000 perm   347 sec   (2279 perm/sec)   p_kst 1.854430e-03   p_cons 8.619241e-02   p_joint 1.854430e-03

Joint ci ratio: 1.014925e-01	ci left: 1.766765e-03	ci right 1.956871e-03	k: 1488	n:800000
Cons ci ratio: 1.427054e-02	ci left: 8.557465e-02	ci right 8.680585e-02	k: 68951	n:800000
KS ci ratio: 1.014925e-01	ci left: 1.766765e-03	ci right 1.956871e-03	k: 1488	n:800000
TADA2A   800000 perm   354 sec   (2262 perm/sec)   p_kst 1.860000e-03   p_cons 8.618875e-02   p_joint 1.860000e-03

Joint ci ratio: 1.004846e-01	ci left: 1.781055e-03	ci right 1.970684e-03	k: 1518	n:810000
Cons ci ratio: 1.418394e-02	ci left: 8.555890e-02	ci right 8.678234e-02	k: 69797	n:810000
KS ci ratio: 1.004846e-01	ci left: 1.781055e-03	ci right 1.970684e-03	k: 1518	n:810000
TADA2A   810000 perm   361 sec   (2244 perm/sec)   p_kst 1.874074e-03   p_cons 8.616914e-02   p_joint 1.874074e-03

Joint ci ratio: 9.986193e-02	ci left: 1.781925e-03	ci right 1.970402e-03	k: 1537	n:820000
Cons ci ratio: 1.409770e-02	ci left: 8.555692e-02	ci right 8.677283e-02	k: 70654	n:820000
KS ci ratio: 9.986193e-02	ci left: 1.781925e-03	ci right 1.970402e-03	k: 1537	n:820000
TADA2A   820000 perm   368 sec   (2228 perm/sec)   p_kst 1.874390e-03   p_cons 8.616341e-02   p_joint 1.874390e-03

Outputting figure to mutsig2_images.part000000000170/TADA2A.2_1487_820000_0.0018744_0.086163_0.0018744.png
                gene_name: TADA2A
               theta_stop: 0.100 
                    nperm: 820000 
                     p_ks: 0.0019 
        ci_ks_bounds_left: 0.0018 
       ci_ks_bounds_right: 0.0020 
                   p_cons: 0.086 
      ci_cons_bounds_left: 0.086 
     ci_cons_bounds_right: 0.087 
                  p_joint: 0.0019 
     ci_joint_bounds_left: 0.0018 
    ci_joint_bounds_right: 0.0020 

Current progress: 75 percent done.
TAF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.731015e-02	ci left: 6.639075e-01	ci right 6.823916e-01	k: 6732	n:10000
KS ci ratio: 3.878868e-02	ci left: 4.953504e-01	ci right 5.150466e-01	k: 5052	n:10000
TAF1   10000 perm   2 sec   (5815 perm/sec)   p_kst 5.052000e-01   p_cons 6.732000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000170/TAF1.2_5834_10000_0.5052_0.6732_1.png
                gene_name: TAF1
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000170
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 170 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1427>
Subject: Job 4398448: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1427>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000171> was used as the working directory.
Started at Wed Oct 24 16:17:25 2012
Results reported at Wed Oct 24 16:19:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000171.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000171.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 171  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000171.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    177.99 sec.
    Max Memory :      1266 MB
    Max Swap   :      3976 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
171
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 171
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 171: processing genes 15252 - 15340
Calculating significance of each gene.
Using projection method.
15252	TAF10	1
15253	TAF11	1
15254	TAF12	7.691588e-03
15255	TAF13	1
15256	TAF15	1
15257	TAF1A	1
15258	TAF1B	1
15259	TAF1C	1
15260	TAF1D	1
15261	TAF1L	1
15262	TAF2	1
15263	TAF3	1
15264	TAF4	2.854183e-01
15265	TAF4B	1
15266	TAF5	1
15267	TAF5L	1
15268	TAF6	2.360424e-01
15269	TAF6L	1
15270	TAF7	1
15271	TAF7L	4.187201e-02
15272	TAF8	1
15273	TAF9	1
15274	TAF9B	5.918020e-02
15275	TAGAP	1
15276	TAGLN	1
15277	TAGLN2	1
15278	TAGLN3	1
15279	TAL1	1
15280	TAL2	1
15281	TALDO1	1
15282	TANC1	6.450491e-01
15283	TANC2	3.640759e-01
15284	TANK	1
15285	TAOK1	2.571456e-01
15286	TAOK2	4.261357e-01
15287	TAOK3	4.002029e-01
15288	TAP1	1
15289	TAP2	1.579907e-01
15290	TAPBP	1
15291	TAPBPL	1
15292	TAPT1	1
15293	TARBP1	1
15294	TARBP2	1
15295	TARDBP	1.997822e-01
15296	TARP	1
15297	TARS	1
15298	TARS2	3.629052e-02
15299	TARSL2	1.214081e-01
15300	TAS1R1	1
15301	TAS1R2	1
15302	TAS1R3	1
15303	TAS2R1	1.544729e-01
15304	TAS2R10	1
15305	TAS2R13	1
15306	TAS2R14	1
15307	TAS2R16	3.322679e-02
15308	TAS2R19	2.210417e-02
15309	TAS2R20	1
15310	TAS2R3	1
15311	TAS2R30	1
15312	TAS2R31	1
15313	TAS2R38	1
15314	TAS2R39	1
15315	TAS2R4	1
15316	TAS2R40	1
15317	TAS2R41	1
15318	TAS2R42	1
15319	TAS2R43	3.604454e-02
15320	TAS2R46	1
15321	TAS2R5	1
15322	TAS2R50	1
15323	TAS2R60	1
15324	TAS2R7	1
15325	TAS2R8	1
15326	TAS2R9	1
15327	TASP1	1
15328	TAT	5.773206e-02
15329	TATDN1	1
15330	TATDN2	1
15331	TATDN3	1
15332	TAX1BP1	1
15333	TAX1BP3	1
15334	TAZ	1
15335	TBC1D1	1
15336	TBC1D10A	1.169259e-01
15337	TBC1D10C	1
15338	TBC1D12	1
15339	TBC1D13	1
15340	TBC1D14	2.751735e-01
Done

Running MutSig 2:
Scatter job 171: processing genes 15252 - 15340
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TANC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.221280e-01	ci left: 2.683859e-02	ci right 3.363872e-02	k: 301	n:10000
Cons ci ratio: 4.412626e-02	ci left: 4.312370e-01	ci right 4.507974e-01	k: 4410	n:10000
KS ci ratio: 2.221280e-01	ci left: 2.683859e-02	ci right 3.363872e-02	k: 301	n:10000
TANC1   10000 perm   2 sec   (4151 perm/sec)   p_kst 3.010000e-02   p_cons 4.410000e-01   p_joint 3.010000e-02

Joint ci ratio: 1.556167e-01	ci left: 2.835269e-02	ci right 3.318501e-02	k: 614	n:20000
Cons ci ratio: 3.122052e-02	ci left: 4.338533e-01	ci right 4.476639e-01	k: 8815	n:20000
KS ci ratio: 1.556167e-01	ci left: 2.835269e-02	ci right 3.318501e-02	k: 614	n:20000
TANC1   20000 perm   8 sec   (2439 perm/sec)   p_kst 3.070000e-02   p_cons 4.407500e-01   p_joint 3.070000e-02

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 2.551547e-02	ci left: 4.346719e-01	ci right 4.459397e-01	k: 13209	n:30000
KS ci ratio: 1.270970e-01	ci left: 2.877686e-02	ci right 3.271471e-02	k: 921	n:30000
TANC1   30000 perm   11 sec   (2723 perm/sec)   p_kst 3.070000e-02   p_cons 4.403000e-01   p_joint 1

Joint ci ratio: 9.799510e-05	ci left: 9.999078e-01	ci right 1	k: 40000	n:40000
Cons ci ratio: 2.212990e-02	ci left: 4.347030e-01	ci right 4.444557e-01	k: 17583	n:40000
KS ci ratio: 1.104565e-01	ci left: 2.883649e-02	ci right 3.223212e-02	k: 1220	n:40000
TANC1   40000 perm   14 sec   (2870 perm/sec)   p_kst 3.050000e-02   p_cons 4.395750e-01   p_joint 1

Joint ci ratio: 3.518898e-02	ci left: 1.953293e-01	ci right 2.023457e-01	k: 9941	n:50000
Cons ci ratio: 1.982733e-02	ci left: 4.343841e-01	ci right 4.431030e-01	k: 21937	n:50000
KS ci ratio: 9.887077e-02	ci left: 2.897101e-02	ci right 3.200382e-02	k: 1523	n:50000
TANC1   50000 perm   17 sec   (2952 perm/sec)   p_kst 3.046000e-02   p_cons 4.387400e-01   p_joint 1.988200e-01

Outputting figure to mutsig2_images.part000000000171/TANC1.2_5691_50000_0.03046_0.43874_0.19882.png
                gene_name: TANC1
               theta_stop: 0.099 
                    nperm: 50000 
                     p_ks: 0.030 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.20 

Current progress: 50 percent done.
TARS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.001785e-02	ci left: 4.797565e-01	ci right 4.994495e-01	k: 4896	n:10000
Cons ci ratio: 5.709069e-02	ci left: 3.111584e-01	ci right 3.295464e-01	k: 3203	n:10000
KS ci ratio: 8.621708e-02	ci left: 1.638637e-01	ci right 1.787283e-01	k: 1712	n:10000
TARS2   10000 perm   2 sec   (5749 perm/sec)   p_kst 1.712000e-01   p_cons 3.203000e-01   p_joint 4.896000e-01

Outputting figure to mutsig2_images.part000000000171/TARS2.2_2229_10000_0.1712_0.3203_0.4896.png
                gene_name: TARS2
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000171
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 171 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4398452: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000172> was used as the working directory.
Started at Wed Oct 24 16:52:42 2012
Results reported at Wed Oct 24 17:30:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000172.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000172.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 172  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000172.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :   2341.23 sec.
    Max Memory :      1436 MB
    Max Swap   :      3970 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
172
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 172
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 172: processing genes 15341 - 15430
Calculating significance of each gene.
Using projection method.
15341	TBC1D15	1
15342	TBC1D16	1
15343	TBC1D17	1
15344	TBC1D19	1
15345	TBC1D2	1
15346	TBC1D20	1
15347	TBC1D21	1
15348	TBC1D22A	1
15349	TBC1D22B	1
15350	TBC1D23	1
15351	TBC1D24	1
15352	TBC1D25	1
15353	TBC1D26	1
15354	TBC1D28	1
15355	TBC1D29	1
15356	TBC1D2B	4.399616e-02
15357	TBC1D3B	1
15358	TBC1D4	5.169999e-01
15359	TBC1D5	7.446481e-02
15360	TBC1D7	1
15361	TBC1D8	1
15362	TBC1D8B	1
15363	TBC1D9	1
15364	TBC1D9B	1
15365	TBCA	1
15366	TBCB	1
15367	TBCC	1
15368	TBCCD1	1
15369	TBCD	1
15370	TBCE	1
15371	TBCEL	1
15372	TBCK	1
15373	TBK1	1
15374	TBKBP1	1
15375	TBL1X	1
15376	TBL1XR1	1.067811e-01
15377	TBL2	1
15378	TBL3	1
15379	TBP	1
15380	TBPL1	1
15381	TBPL2	1
15382	TBR1	1
15383	TBRG1	1
15384	TBRG4	1
15385	TBX1	1
15386	TBX10	1
15387	TBX15	1
15388	TBX18	1
15389	TBX19	2.243296e-01
15390	TBX2	1
15391	TBX20	1
15392	TBX21	1
15393	TBX22	1
15394	TBX3	1
15395	TBX4	1.424975e-01
15396	TBX5	1
15397	TBX6	1
15398	TBXA2R	1
15399	TBXAS1	1
15400	TC2N	1
15401	TCAP	1
15402	TCEA1	1
15403	TCEA2	1
15404	TCEA3	1
15405	TCEAL1	1
15406	TCEAL2	1
15407	TCEAL3	1
15408	TCEAL4	1
15409	TCEAL5	1
15410	TCEAL6	1
15411	TCEAL7	4.282955e-02
15412	TCEAL8	1
15413	TCEANC	1
15414	TCEB1	1
15415	TCEB2	1
15416	TCEB3	1.621028e-01
15417	TCEB3B	7.368972e-02
15418	TCEB3C	1
15419	TCERG1	1
15420	TCERG1L	5.126086e-03
15421	TCF12	1
15422	TCF19	1
15423	TCF20	1.022358e-01
15424	TCF21	1.100200e-02
15425	TCF23	4.214661e-02
15426	TCF25	1
15427	TCF3	1
15428	TCF4	1
15429	TCF7	1
15430	TCF7L1	1
Done

Running MutSig 2:
Scatter job 172: processing genes 15341 - 15430
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TCF20
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.816794e-02	ci left: 8.155790e-01	ci right 8.306323e-01	k: 8232	n:10000
Cons ci ratio: 2.143030e-02	ci left: 7.615226e-01	ci right 7.781199e-01	k: 7699	n:10000
KS ci ratio: 2.882575e-02	ci left: 6.395531e-01	ci right 6.583601e-01	k: 6490	n:10000
TCF20   10000 perm   2 sec   (4549 perm/sec)   p_kst 6.490000e-01   p_cons 7.699000e-01   p_joint 8.232000e-01

Outputting figure to mutsig2_images.part000000000172/TCF20.3_5921_10000_0.649_0.7699_0.8232.png
                gene_name: TCF20
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.82 
    ci_joint_bounds_right: 0.83 

Current progress: 25 percent done.
TBC1D2B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.731880e-02	ci left: 5.146560e-01	ci right 5.343297e-01	k: 5245	n:10000
KS ci ratio: 3.703552e-02	ci left: 5.184588e-01	ci right 5.381247e-01	k: 5283	n:10000
TBC1D2B   10000 perm   2 sec   (5981 perm/sec)   p_kst 5.283000e-01   p_cons 5.245000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000172/TBC1D2B.2_2944_10000_0.5283_0.5245_1.png
                gene_name: TBC1D2B
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
TCEB3B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.677370e-01	ci left: 1.618501e-03	ci right 3.688296e-03	k: 25	n:10000
Cons ci ratio: 5.972766e-03	ci left: 9.742942e-01	ci right 9.802233e-01	k: 9774	n:10000
KS ci ratio: 1.481028e+00	ci left: 2.202202e-04	ci right 1.305486e-03	k: 6	n:10000
TCEB3B   10000 perm   2 sec   (6014 perm/sec)   p_kst 6.000000e-04   p_cons 9.774000e-01   p_joint 2.500000e-03

Joint ci ratio: 7.034894e-01	ci left: 1.012265e-03	ci right 2.140657e-03	k: 30	n:20000
Cons ci ratio: 4.219154e-03	ci left: 9.752445e-01	ci right 9.794152e-01	k: 19548	n:20000
KS ci ratio: 1.086832e+00	ci left: 3.100660e-04	ci right 1.047844e-03	k: 12	n:20000
TCEB3B   20000 perm   4 sec   (5369 perm/sec)   p_kst 6.000000e-04   p_cons 9.774000e-01   p_joint 1.500000e-03

Joint ci ratio: 4.646599e-01	ci left: 1.819386e-03	ci right 2.947120e-03	k: 70	n:30000
Cons ci ratio: 3.719240e-03	ci left: 9.718604e-01	ci right 9.755137e-01	k: 29212	n:30000
KS ci ratio: 9.504544e-01	ci left: 3.048758e-04	ci right 8.659558e-04	k: 16	n:30000
TCEB3B   30000 perm   6 sec   (5116 perm/sec)   p_kst 5.333333e-04   p_cons 9.737333e-01   p_joint 2.333333e-03

Joint ci ratio: 3.500628e-01	ci left: 2.579060e-03	ci right 3.695006e-03	k: 124	n:40000
Cons ci ratio: 3.239842e-03	ci left: 9.718015e-01	ci right 9.749792e-01	k: 38937	n:40000
KS ci ratio: 7.276527e-01	ci left: 4.651937e-04	ci right 1.011537e-03	k: 28	n:40000
TCEB3B   40000 perm   8 sec   (4961 perm/sec)   p_kst 7.000000e-04   p_cons 9.734250e-01   p_joint 3.100000e-03

Joint ci ratio: 3.123554e-01	ci left: 2.650208e-03	ci right 3.648858e-03	k: 156	n:50000
Cons ci ratio: 2.897839e-03	ci left: 9.719723e-01	ci right 9.748124e-01	k: 48671	n:50000
KS ci ratio: 6.530916e-01	ci left: 4.876226e-04	ci right 9.733974e-04	k: 35	n:50000
TCEB3B   50000 perm   10 sec   (4839 perm/sec)   p_kst 7.000000e-04   p_cons 9.734200e-01   p_joint 3.120000e-03

Joint ci ratio: 2.746620e-01	ci left: 2.919007e-03	ci right 3.863370e-03	k: 202	n:60000
Cons ci ratio: 2.637703e-03	ci left: 9.722516e-01	ci right 9.748357e-01	k: 58414	n:60000
KS ci ratio: 5.777461e-01	ci left: 5.471061e-04	ci right 1.003432e-03	k: 45	n:60000
TCEB3B   60000 perm   13 sec   (4733 perm/sec)   p_kst 7.500000e-04   p_cons 9.735667e-01   p_joint 3.366667e-03

Joint ci ratio: 2.029748e-01	ci left: 4.762007e-03	ci right 5.851048e-03	k: 370	n:70000
Cons ci ratio: 2.426769e-03	ci left: 9.726774e-01	ci right 9.750546e-01	k: 68172	n:70000
KS ci ratio: 5.541697e-01	ci left: 5.179073e-04	ci right 9.253328e-04	k: 49	n:70000
TCEB3B   70000 perm   15 sec   (4635 perm/sec)   p_kst 7.000000e-04   p_cons 9.738857e-01   p_joint 5.285714e-03

Joint ci ratio: 1.150649e-01	ci left: 1.347655e-02	ci right 1.513395e-02	k: 1143	n:80000
Cons ci ratio: 2.274342e-03	ci left: 9.726568e-01	ci right 9.748836e-01	k: 77903	n:80000
KS ci ratio: 5.101491e-01	ci left: 5.505675e-04	ci right 9.371312e-04	k: 58	n:80000
TCEB3B   80000 perm   18 sec   (4544 perm/sec)   p_kst 7.250000e-04   p_cons 9.737875e-01   p_joint 1.428750e-02

Joint ci ratio: 2.422885e-01	ci left: 2.548799e-03	ci right 3.261618e-03	k: 260	n:90000
Cons ci ratio: 2.149753e-03	ci left: 9.725883e-01	ci right 9.746922e-01	k: 87629	n:90000
KS ci ratio: 4.650323e-01	ci left: 6.063646e-04	ci right 9.825747e-04	k: 70	n:90000
TCEB3B   90000 perm   20 sec   (4460 perm/sec)   p_kst 7.777778e-04   p_cons 9.736556e-01   p_joint 2.888889e-03

Joint ci ratio: 2.466242e-01	ci left: 2.209382e-03	ci right 2.840026e-03	k: 251	n:100000
Cons ci ratio: 2.045569e-03	ci left: 9.724857e-01	ci right 9.744867e-01	k: 97350	n:100000
KS ci ratio: 4.494817e-01	ci left: 5.899669e-04	ci right 9.400421e-04	k: 75	n:100000
TCEB3B   100000 perm   23 sec   (4380 perm/sec)   p_kst 7.500000e-04   p_cons 9.735000e-01   p_joint 2.510000e-03

Joint ci ratio: 2.496493e-01	ci left: 1.957343e-03	ci right 2.523959e-03	k: 245	n:110000
Cons ci ratio: 1.947594e-03	ci left: 9.726077e-01	ci right 9.745127e-01	k: 107093	n:110000
KS ci ratio: 4.301116e-01	ci left: 5.929247e-04	ci right 9.252224e-04	k: 82	n:110000
TCEB3B   110000 perm   26 sec   (4302 perm/sec)   p_kst 7.454545e-04   p_cons 9.735727e-01   p_joint 2.227273e-03

Joint ci ratio: 2.387376e-01	ci left: 1.974176e-03	ci right 2.516994e-03	k: 268	n:120000
Cons ci ratio: 1.865177e-03	ci left: 9.726349e-01	ci right 9.744588e-01	k: 116827	n:120000
KS ci ratio: 4.107701e-01	ci left: 6.031304e-04	ci right 9.217981e-04	k: 90	n:120000
TCEB3B   120000 perm   28 sec   (4230 perm/sec)   p_kst 7.500000e-04   p_cons 9.735583e-01   p_joint 2.233333e-03

Joint ci ratio: 2.283595e-01	ci left: 2.003380e-03	ci right 2.526910e-03	k: 293	n:130000
Cons ci ratio: 1.794013e-03	ci left: 9.726124e-01	ci right 9.743664e-01	k: 126555	n:130000
KS ci ratio: 3.999340e-01	ci left: 5.912749e-04	ci right 8.932549e-04	k: 95	n:130000
TCEB3B   130000 perm   31 sec   (4159 perm/sec)   p_kst 7.307692e-04   p_cons 9.735000e-01   p_joint 2.253846e-03

Joint ci ratio: 1.803193e-01	ci left: 3.060900e-03	ci right 3.674239e-03	k: 470	n:140000
Cons ci ratio: 1.730413e-03	ci left: 9.725944e-01	ci right 9.742859e-01	k: 136283	n:140000
KS ci ratio: 3.861056e-01	ci left: 5.941008e-04	ci right 8.843671e-04	k: 102	n:140000
TCEB3B   140000 perm   34 sec   (4093 perm/sec)   p_kst 7.285714e-04   p_cons 9.734500e-01   p_joint 3.357143e-03

Joint ci ratio: 1.383093e-01	ci left: 4.958126e-03	ci right 5.701192e-03	k: 798	n:150000
Cons ci ratio: 1.674847e-03	ci left: 9.725258e-01	ci right 9.741625e-01	k: 146003	n:150000
KS ci ratio: 3.686224e-01	ci left: 6.148415e-04	ci right 8.983658e-04	k: 112	n:150000
TCEB3B   150000 perm   37 sec   (4029 perm/sec)   p_kst 7.466667e-04   p_cons 9.733533e-01   p_joint 5.320000e-03

Joint ci ratio: 1.325382e-01	ci left: 5.076984e-03	ci right 5.803614e-03	k: 869	n:160000
Cons ci ratio: 1.624489e-03	ci left: 9.724603e-01	ci right 9.740475e-01	k: 155722	n:160000
KS ci ratio: 3.504774e-01	ci left: 6.446449e-04	ci right 9.239581e-04	k: 124	n:160000
TCEB3B   160000 perm   40 sec   (3967 perm/sec)   p_kst 7.750000e-04   p_cons 9.732625e-01   p_joint 5.431250e-03

Joint ci ratio: 1.288880e-01	ci left: 5.062836e-03	ci right 5.765958e-03	k: 919	n:170000
Cons ci ratio: 1.574306e-03	ci left: 9.725405e-01	ci right 9.740786e-01	k: 165464	n:170000
KS ci ratio: 3.450048e-01	ci left: 6.281981e-04	ci right 8.951858e-04	k: 128	n:170000
TCEB3B   170000 perm   44 sec   (3907 perm/sec)   p_kst 7.529412e-04   p_cons 9.733176e-01   p_joint 5.405882e-03

Joint ci ratio: 8.463388e-02	ci left: 1.127904e-02	ci right 1.228122e-02	k: 2119	n:180000
Cons ci ratio: 1.528170e-03	ci left: 9.726237e-01	ci right 9.741166e-01	k: 175208	n:180000
KS ci ratio: 3.360093e-01	ci left: 6.288625e-04	ci right 8.876546e-04	k: 135	n:180000
TCEB3B   180000 perm   47 sec   (3848 perm/sec)   p_kst 7.500000e-04   p_cons 9.733778e-01   p_joint 1.177222e-02

Joint ci ratio: 8.207607e-02	ci left: 1.137600e-02	ci right 1.235477e-02	k: 2253	n:190000
Cons ci ratio: 1.487522e-03	ci left: 9.726399e-01	ci right 9.740930e-01	k: 184941	n:190000
KS ci ratio: 3.265420e-01	ci left: 6.343689e-04	ci right 8.865297e-04	k: 143	n:190000
TCEB3B   190000 perm   50 sec   (3789 perm/sec)   p_kst 7.526316e-04   p_cons 9.733737e-01   p_joint 1.185789e-02

Joint ci ratio: 7.803480e-02	ci left: 1.197352e-02	ci right 1.295068e-02	k: 2491	n:200000
Cons ci ratio: 1.449254e-03	ci left: 9.726803e-01	ci right 9.740959e-01	k: 194679	n:200000
KS ci ratio: 3.157602e-01	ci left: 6.486220e-04	ci right 8.962181e-04	k: 153	n:200000
TCEB3B   200000 perm   54 sec   (3734 perm/sec)   p_kst 7.650000e-04   p_cons 9.733950e-01   p_joint 1.245500e-02

Joint ci ratio: 7.563775e-02	ci left: 1.215066e-02	ci right 1.311048e-02	k: 2651	n:210000
Cons ci ratio: 1.410540e-03	ci left: 9.728378e-01	ci right 9.742157e-01	k: 204442	n:210000
KS ci ratio: 3.050509e-01	ci left: 6.660384e-04	ci right 9.099868e-04	k: 164	n:210000
TCEB3B   210000 perm   57 sec   (3681 perm/sec)   p_kst 7.809524e-04   p_cons 9.735333e-01   p_joint 1.262381e-02

Joint ci ratio: 7.403765e-02	ci left: 1.211576e-02	ci right 1.305170e-02	k: 2767	n:220000
Cons ci ratio: 1.378631e-03	ci left: 9.728341e-01	ci right 9.741807e-01	k: 214173	n:220000
KS ci ratio: 2.970562e-01	ci left: 6.735843e-04	ci right 9.126125e-04	k: 173	n:220000
TCEB3B   220000 perm   61 sec   (3627 perm/sec)   p_kst 7.863636e-04   p_cons 9.735136e-01   p_joint 1.257727e-02

Joint ci ratio: 7.312786e-02	ci left: 1.188768e-02	ci right 1.279424e-02	k: 2837	n:230000
Cons ci ratio: 1.348112e-03	ci left: 9.728574e-01	ci right 9.741741e-01	k: 223910	n:230000
KS ci ratio: 2.945312e-01	ci left: 6.563728e-04	ci right 8.869437e-04	k: 176	n:230000
TCEB3B   230000 perm   64 sec   (3575 perm/sec)   p_kst 7.652174e-04   p_cons 9.735217e-01   p_joint 1.233478e-02

Joint ci ratio: 7.155626e-02	ci left: 1.190787e-02	ci right 1.279563e-02	k: 2963	n:240000
Cons ci ratio: 1.320919e-03	ci left: 9.728243e-01	ci right 9.741142e-01	k: 233634	n:240000
KS ci ratio: 2.857828e-01	ci left: 6.715233e-04	ci right 8.991458e-04	k: 187	n:240000
TCEB3B   240000 perm   68 sec   (3526 perm/sec)   p_kst 7.791667e-04   p_cons 9.734750e-01   p_joint 1.234583e-02

Joint ci ratio: 7.033577e-02	ci left: 1.184016e-02	ci right 1.270720e-02	k: 3067	n:250000
Cons ci ratio: 1.291895e-03	ci left: 9.729317e-01	ci right 9.741933e-01	k: 243392	n:250000
KS ci ratio: 2.806070e-01	ci left: 6.706740e-04	ci right 8.931633e-04	k: 194	n:250000
TCEB3B   250000 perm   72 sec   (3478 perm/sec)   p_kst 7.760000e-04   p_cons 9.735680e-01   p_joint 1.226800e-02

Joint ci ratio: 9.872748e-02	ci left: 5.729259e-03	ci right 6.327987e-03	k: 1566	n:260000
Cons ci ratio: 1.267247e-03	ci left: 9.729260e-01	ci right 9.741635e-01	k: 253123	n:260000
KS ci ratio: 2.777745e-01	ci left: 6.591859e-04	ci right 8.752707e-04	k: 198	n:260000
TCEB3B   260000 perm   76 sec   (3432 perm/sec)   p_kst 7.615385e-04   p_cons 9.735500e-01   p_joint 6.023077e-03

Joint ci ratio: 9.710039e-02	ci left: 5.708550e-03	ci right 6.294722e-03	k: 1619	n:270000
Cons ci ratio: 1.242974e-03	ci left: 9.729621e-01	ci right 9.741759e-01	k: 262865	n:270000
KS ci ratio: 2.736802e-01	ci left: 6.554574e-04	ci right 8.666083e-04	k: 204	n:270000
TCEB3B   270000 perm   80 sec   (3387 perm/sec)   p_kst 7.555556e-04   p_cons 9.735741e-01   p_joint 5.996296e-03

Joint ci ratio: 9.509477e-02	ci left: 5.745185e-03	ci right 6.322255e-03	k: 1688	n:280000
Cons ci ratio: 1.220213e-03	ci left: 9.729886e-01	ci right 9.741801e-01	k: 272605	n:280000
KS ci ratio: 2.684913e-01	ci left: 6.586781e-04	ci right 8.661663e-04	k: 212	n:280000
TCEB3B   280000 perm   84 sec   (3344 perm/sec)   p_kst 7.571429e-04   p_cons 9.735893e-01   p_joint 6.028571e-03

Joint ci ratio: 9.355716e-02	ci left: 5.735621e-03	ci right 6.301905e-03	k: 1744	n:290000
Cons ci ratio: 1.200425e-03	ci left: 9.729368e-01	ci right 9.741089e-01	k: 282323	n:290000
KS ci ratio: 2.647886e-01	ci left: 6.552717e-04	ci right 8.583682e-04	k: 218	n:290000
TCEB3B   290000 perm   88 sec   (3300 perm/sec)   p_kst 7.517241e-04   p_cons 9.735276e-01   p_joint 6.013793e-03

Joint ci ratio: 9.140502e-02	ci left: 5.814713e-03	ci right 6.374893e-03	k: 1827	n:300000
Cons ci ratio: 1.179045e-03	ci left: 9.729998e-01	ci right 9.741510e-01	k: 292074	n:300000
KS ci ratio: 2.583776e-01	ci left: 6.676927e-04	ci right 8.688203e-04	k: 229	n:300000
TCEB3B   300000 perm   92 sec   (3258 perm/sec)   p_kst 7.633333e-04   p_cons 9.735800e-01   p_joint 6.090000e-03

Joint ci ratio: 8.974991e-02	ci left: 5.841531e-03	ci right 6.393570e-03	k: 1895	n:310000
Cons ci ratio: 1.159492e-03	ci left: 9.730263e-01	ci right 9.741584e-01	k: 301815	n:310000
KS ci ratio: 2.567108e-01	ci left: 6.552064e-04	ci right 8.510955e-04	k: 232	n:310000
TCEB3B   310000 perm   96 sec   (3218 perm/sec)   p_kst 7.483871e-04   p_cons 9.735968e-01   p_joint 6.112903e-03

Joint ci ratio: 1.416510e-01	ci left: 2.218351e-03	ci right 2.559511e-03	k: 763	n:320000
Cons ci ratio: 1.140672e-03	ci left: 9.730608e-01	ci right 9.741744e-01	k: 311559	n:320000
KS ci ratio: 2.540010e-01	ci left: 6.493560e-04	ci right 8.411220e-04	k: 237	n:320000
TCEB3B   320000 perm   101 sec   (3181 perm/sec)   p_kst 7.406250e-04   p_cons 9.736219e-01   p_joint 2.384375e-03

Joint ci ratio: 8.740970e-02	ci left: 5.792700e-03	ci right 6.325121e-03	k: 1998	n:330000
Cons ci ratio: 1.124726e-03	ci left: 9.730014e-01	ci right 9.740994e-01	k: 321273	n:330000
KS ci ratio: 2.513751e-01	ci left: 6.438704e-04	ci right 8.317429e-04	k: 242	n:330000
TCEB3B   330000 perm   105 sec   (3144 perm/sec)   p_kst 7.333333e-04   p_cons 9.735545e-01   p_joint 6.054545e-03

Joint ci ratio: 1.667105e-01	ci left: 1.488177e-03	ci right 1.761606e-03	k: 551	n:340000
Cons ci ratio: 1.107715e-03	ci left: 9.730259e-01	ci right 9.741072e-01	k: 331014	n:340000
KS ci ratio: 2.498393e-01	ci left: 6.332019e-04	ci right 8.166571e-04	k: 245	n:340000
TCEB3B   340000 perm   110 sec   (3105 perm/sec)   p_kst 7.205882e-04   p_cons 9.735706e-01   p_joint 1.620588e-03

Joint ci ratio: 1.644909e-01	ci left: 1.486738e-03	ci right 1.755907e-03	k: 566	n:350000
Cons ci ratio: 1.091939e-03	ci left: 9.730260e-01	ci right 9.740919e-01	k: 340747	n:350000
KS ci ratio: 2.483312e-01	ci left: 6.231464e-04	ci right 8.024300e-04	k: 248	n:350000
TCEB3B   350000 perm   114 sec   (3068 perm/sec)   p_kst 7.085714e-04   p_cons 9.735629e-01   p_joint 1.617143e-03

Joint ci ratio: 1.619401e-01	ci left: 1.493398e-03	ci right 1.759171e-03	k: 584	n:360000
Cons ci ratio: 1.075248e-03	ci left: 9.731019e-01	ci right 9.741515e-01	k: 350507	n:360000
KS ci ratio: 2.439607e-01	ci left: 6.292952e-04	ci right 8.066789e-04	k: 257	n:360000
TCEB3B   360000 perm   119 sec   (3034 perm/sec)   p_kst 7.138889e-04   p_cons 9.736306e-01   p_joint 1.622222e-03

Joint ci ratio: 1.588461e-01	ci left: 1.512705e-03	ci right 1.776280e-03	k: 607	n:370000
Cons ci ratio: 1.060466e-03	ci left: 9.731165e-01	ci right 9.741517e-01	k: 360246	n:370000
KS ci ratio: 2.380355e-01	ci left: 6.453017e-04	ci right 8.221283e-04	k: 270	n:370000
TCEB3B   370000 perm   123 sec   (3002 perm/sec)   p_kst 7.297297e-04   p_cons 9.736378e-01   p_joint 1.640541e-03

Joint ci ratio: 1.562955e-01	ci left: 1.523454e-03	ci right 1.784240e-03	k: 627	n:380000
Cons ci ratio: 1.046332e-03	ci left: 9.731278e-01	ci right 9.741492e-01	k: 369984	n:380000
KS ci ratio: 2.350197e-01	ci left: 6.456496e-04	ci right 8.200040e-04	k: 277	n:380000
TCEB3B   380000 perm   128 sec   (2969 perm/sec)   p_kst 7.289474e-04   p_cons 9.736421e-01   p_joint 1.650000e-03

Joint ci ratio: 1.533905e-01	ci left: 1.543546e-03	ci right 1.802410e-03	k: 651	n:390000
Cons ci ratio: 1.033469e-03	ci left: 9.731024e-01	ci right 9.741111e-01	k: 379708	n:390000
KS ci ratio: 2.293145e-01	ci left: 6.629050e-04	ci right 8.369588e-04	k: 291	n:390000
TCEB3B   390000 perm   133 sec   (2939 perm/sec)   p_kst 7.461538e-04   p_cons 9.736103e-01   p_joint 1.669231e-03

Joint ci ratio: 7.408814e-02	ci left: 6.692421e-03	ci right 7.209760e-03	k: 2779	n:400000
Cons ci ratio: 9.486997e-04	ci left: 9.766418e-01	ci right 9.775713e-01	k: 390844	n:400000
KS ci ratio: 2.273767e-01	ci left: 6.581172e-04	ci right 8.292489e-04	k: 296	n:400000
TCEB3B   400000 perm   138 sec   (2909 perm/sec)   p_kst 7.400000e-04   p_cons 9.771100e-01   p_joint 6.947500e-03

Joint ci ratio: 7.317259e-02	ci left: 6.696780e-03	ci right 7.207787e-03	k: 2849	n:410000
Cons ci ratio: 9.374714e-04	ci left: 9.766277e-01	ci right 9.775461e-01	k: 400607	n:410000
KS ci ratio: 2.243748e-01	ci left: 6.604739e-04	ci right 8.296375e-04	k: 304	n:410000
TCEB3B   410000 perm   143 sec   (2876 perm/sec)   p_kst 7.414634e-04   p_cons 9.770902e-01   p_joint 6.948780e-03

Joint ci ratio: 7.242766e-02	ci left: 6.675249e-03	ci right 7.179209e-03	k: 2908	n:420000
Cons ci ratio: 9.263857e-04	ci left: 9.766263e-01	ci right 9.775338e-01	k: 410375	n:420000
KS ci ratio: 2.229187e-01	ci left: 6.537383e-04	ci right 8.199411e-04	k: 308	n:420000
TCEB3B   420000 perm   148 sec   (2830 perm/sec)   p_kst 7.333333e-04   p_cons 9.770833e-01   p_joint 6.923810e-03

Joint ci ratio: 7.159580e-02	ci left: 6.675302e-03	ci right 7.173237e-03	k: 2976	n:430000
Cons ci ratio: 9.155890e-04	ci left: 9.766297e-01	ci right 9.775266e-01	k: 420145	n:430000
KS ci ratio: 2.204359e-01	ci left: 6.539103e-04	ci right 8.180542e-04	k: 315	n:430000
TCEB3B   430000 perm   153 sec   (2803 perm/sec)   p_kst 7.325581e-04   p_cons 9.770814e-01   p_joint 6.920930e-03

Joint ci ratio: 7.079196e-02	ci left: 6.675385e-03	ci right 7.167506e-03	k: 3044	n:440000
Cons ci ratio: 9.057580e-04	ci left: 9.766033e-01	ci right 9.774905e-01	k: 429902	n:440000
KS ci ratio: 2.193980e-01	ci left: 6.454910e-04	ci right 8.066557e-04	k: 318	n:440000
TCEB3B   440000 perm   159 sec   (2776 perm/sec)   p_kst 7.227273e-04   p_cons 9.770500e-01   p_joint 6.918182e-03

Joint ci ratio: 7.003726e-02	ci left: 6.671126e-03	ci right 7.157477e-03	k: 3110	n:450000
Cons ci ratio: 8.957032e-04	ci left: 9.766049e-01	ci right 9.774822e-01	k: 439671	n:450000
KS ci ratio: 2.176991e-01	ci left: 6.416496e-04	ci right 8.004486e-04	k: 323	n:450000
TCEB3B   450000 perm   164 sec   (2748 perm/sec)   p_kst 7.177778e-04   p_cons 9.770467e-01   p_joint 6.911111e-03

Joint ci ratio: 5.614263e-02	ci left: 1.019243e-02	ci right 1.078332e-02	k: 4823	n:460000
Cons ci ratio: 8.849880e-04	ci left: 9.766570e-01	ci right 9.775239e-01	k: 449463	n:460000
KS ci ratio: 2.160391e-01	ci left: 6.379797e-04	ci right 7.945067e-04	k: 328	n:460000
TCEB3B   460000 perm   170 sec   (2707 perm/sec)   p_kst 7.130435e-04   p_cons 9.770935e-01   p_joint 1.048478e-02

Joint ci ratio: 5.548456e-02	ci left: 1.021684e-02	ci right 1.080198e-02	k: 4938	n:470000
Cons ci ratio: 8.753526e-04	ci left: 9.766705e-01	ci right 9.775279e-01	k: 459238	n:470000
KS ci ratio: 2.140959e-01	ci left: 6.364840e-04	ci right 7.910550e-04	k: 334	n:470000
TCEB3B   470000 perm   175 sec   (2680 perm/sec)   p_kst 7.106383e-04   p_cons 9.771021e-01   p_joint 1.050638e-02

Joint ci ratio: 5.494256e-02	ci left: 1.020534e-02	ci right 1.078393e-02	k: 5036	n:480000
Cons ci ratio: 8.657832e-04	ci left: 9.766960e-01	ci right 9.775440e-01	k: 469019	n:480000
KS ci ratio: 2.122043e-01	ci left: 6.350566e-04	ci right 7.877410e-04	k: 340	n:480000
TCEB3B   480000 perm   181 sec   (2655 perm/sec)   p_kst 7.083333e-04   p_cons 9.771229e-01   p_joint 1.049167e-02

Joint ci ratio: 5.437870e-02	ci left: 1.020842e-02	ci right 1.078106e-02	k: 5141	n:490000
Cons ci ratio: 8.567157e-04	ci left: 9.767103e-01	ci right 9.775494e-01	k: 478795	n:490000
KS ci ratio: 2.091590e-01	ci left: 6.414280e-04	ci right 7.931477e-04	k: 350	n:490000
TCEB3B   490000 perm   187 sec   (2621 perm/sec)   p_kst 7.142857e-04   p_cons 9.771327e-01   p_joint 1.049184e-02

Joint ci ratio: 5.382667e-02	ci left: 1.021339e-02	ci right 1.078031e-02	k: 5247	n:500000
Cons ci ratio: 8.478134e-04	ci left: 9.767300e-01	ci right 9.775604e-01	k: 488574	n:500000
KS ci ratio: 2.065275e-01	ci left: 6.456628e-04	ci right 7.962201e-04	k: 359	n:500000
TCEB3B   500000 perm   193 sec   (2596 perm/sec)   p_kst 7.180000e-04   p_cons 9.771480e-01   p_joint 1.049400e-02

Joint ci ratio: 5.330621e-02	ci left: 1.021238e-02	ci right 1.077359e-02	k: 5350	n:510000
Cons ci ratio: 8.395879e-04	ci left: 9.767273e-01	ci right 9.775496e-01	k: 498342	n:510000
KS ci ratio: 2.059573e-01	ci left: 6.367214e-04	ci right 7.847321e-04	k: 361	n:510000
TCEB3B   510000 perm   198 sec   (2572 perm/sec)   p_kst 7.078431e-04   p_cons 9.771412e-01   p_joint 1.049020e-02

Joint ci ratio: 5.290358e-02	ci left: 1.017158e-02	ci right 1.072620e-02	k: 5432	n:520000
Cons ci ratio: 8.306305e-04	ci left: 9.767771e-01	ci right 9.775907e-01	k: 508137	n:520000
KS ci ratio: 2.048294e-01	ci left: 6.317733e-04	ci right 7.777288e-04	k: 365	n:520000
TCEB3B   520000 perm   204 sec   (2547 perm/sec)   p_kst 7.019231e-04   p_cons 9.771865e-01   p_joint 1.044615e-02

Joint ci ratio: 5.241877e-02	ci left: 1.016772e-02	ci right 1.071690e-02	k: 5533	n:530000
Cons ci ratio: 8.230998e-04	ci left: 9.767622e-01	ci right 9.775684e-01	k: 517899	n:530000
KS ci ratio: 2.028983e-01	ci left: 6.323864e-04	ci right 7.769355e-04	k: 372	n:530000
TCEB3B   530000 perm   210 sec   (2522 perm/sec)   p_kst 7.018868e-04   p_cons 9.771679e-01   p_joint 1.043962e-02

Joint ci ratio: 5.190982e-02	ci left: 1.017865e-02	ci right 1.072292e-02	k: 5642	n:540000
Cons ci ratio: 8.151269e-04	ci left: 9.767834e-01	ci right 9.775818e-01	k: 527680	n:540000
KS ci ratio: 2.018196e-01	ci left: 6.277075e-04	ci right 7.703302e-04	k: 376	n:540000
TCEB3B   540000 perm   216 sec   (2499 perm/sec)   p_kst 6.962963e-04   p_cons 9.771852e-01   p_joint 1.044815e-02

Joint ci ratio: 5.145158e-02	ci left: 1.017485e-02	ci right 1.071396e-02	k: 5743	n:550000
Cons ci ratio: 8.080065e-04	ci left: 9.767691e-01	ci right 9.775604e-01	k: 537442	n:550000
KS ci ratio: 1.994525e-01	ci left: 6.318364e-04	ci right 7.735087e-04	k: 385	n:550000
TCEB3B   550000 perm   222 sec   (2473 perm/sec)   p_kst 7.000000e-04   p_cons 9.771673e-01   p_joint 1.044182e-02

Joint ci ratio: 5.097883e-02	ci left: 1.018178e-02	ci right 1.071616e-02	k: 5850	n:560000
Cons ci ratio: 8.005564e-04	ci left: 9.767841e-01	ci right 9.775681e-01	k: 547220	n:560000
KS ci ratio: 1.974171e-01	ci left: 6.341296e-04	ci right 7.746905e-04	k: 393	n:560000
TCEB3B   560000 perm   228 sec   (2452 perm/sec)   p_kst 7.017857e-04   p_cons 9.771786e-01   p_joint 1.044643e-02

Joint ci ratio: 5.053603e-02	ci left: 1.018156e-02	ci right 1.071115e-02	k: 5953	n:570000
Cons ci ratio: 7.935893e-04	ci left: 9.767827e-01	ci right 9.775599e-01	k: 556989	n:570000
KS ci ratio: 1.961766e-01	ci left: 6.313442e-04	ci right 7.703032e-04	k: 398	n:570000
TCEB3B   570000 perm   235 sec   (2429 perm/sec)   p_kst 6.982456e-04   p_cons 9.771737e-01   p_joint 1.044386e-02

Joint ci ratio: 5.017157e-02	ci left: 1.015412e-02	ci right 1.067837e-02	k: 6040	n:580000
Cons ci ratio: 7.861928e-04	ci left: 9.768161e-01	ci right 9.775860e-01	k: 566778	n:580000
KS ci ratio: 1.944781e-01	ci left: 6.319377e-04	ci right 7.696805e-04	k: 405	n:580000
TCEB3B   580000 perm   241 sec   (2410 perm/sec)   p_kst 6.982759e-04   p_cons 9.772034e-01   p_joint 1.041379e-02

Joint ci ratio: 4.974930e-02	ci left: 1.015441e-02	ci right 1.067414e-02	k: 6143	n:590000
Cons ci ratio: 7.789980e-04	ci left: 9.768484e-01	ci right 9.776113e-01	k: 576567	n:590000
KS ci ratio: 1.937642e-01	ci left: 6.260643e-04	ci right 7.619669e-04	k: 408	n:590000
TCEB3B   590000 perm   247 sec   (2389 perm/sec)   p_kst 6.915254e-04   p_cons 9.772322e-01   p_joint 1.041186e-02

Joint ci ratio: 4.932953e-02	ci left: 1.015801e-02	ci right 1.067340e-02	k: 6248	n:600000
Cons ci ratio: 7.725169e-04	ci left: 9.768494e-01	ci right 9.776060e-01	k: 586338	n:600000
KS ci ratio: 1.916665e-01	ci left: 6.299063e-04	ci right 7.649901e-04	k: 417	n:600000
TCEB3B   600000 perm   254 sec   (2361 perm/sec)   p_kst 6.950000e-04   p_cons 9.772300e-01   p_joint 1.041333e-02

Joint ci ratio: 4.842588e-02	ci left: 1.037043e-02	ci right 1.088669e-02	k: 6482	n:610000
Cons ci ratio: 7.664771e-04	ci left: 9.768339e-01	ci right 9.775845e-01	k: 596099	n:610000
KS ci ratio: 1.900815e-01	ci left: 6.305071e-04	ci right 7.644724e-04	k: 424	n:610000
TCEB3B   610000 perm   261 sec   (2340 perm/sec)   p_kst 6.950820e-04   p_cons 9.772115e-01   p_joint 1.062623e-02

Joint ci ratio: 4.801638e-02	ci left: 1.038004e-02	ci right 1.089229e-02	k: 6593	n:620000
Cons ci ratio: 7.605762e-04	ci left: 9.768189e-01	ci right 9.775637e-01	k: 605860	n:620000
KS ci ratio: 1.887540e-01	ci left: 6.295561e-04	ci right 7.622780e-04	k: 430	n:620000
TCEB3B   620000 perm   267 sec   (2321 perm/sec)   p_kst 6.935484e-04   p_cons 9.771935e-01   p_joint 1.063387e-02

Joint ci ratio: 4.760992e-02	ci left: 1.039250e-02	ci right 1.090091e-02	k: 6706	n:630000
Cons ci ratio: 7.551313e-04	ci left: 9.767852e-01	ci right 9.775247e-01	k: 615609	n:630000
KS ci ratio: 1.868132e-01	ci left: 6.331774e-04	ci right 7.651347e-04	k: 439	n:630000
TCEB3B   630000 perm   274 sec   (2302 perm/sec)   p_kst 6.968254e-04   p_cons 9.771571e-01   p_joint 1.064444e-02

Joint ci ratio: 4.720661e-02	ci left: 1.040767e-02	ci right 1.091239e-02	k: 6821	n:640000
Cons ci ratio: 7.489348e-04	ci left: 9.768046e-01	ci right 9.775380e-01	k: 625391	n:640000
KS ci ratio: 1.857611e-01	ci left: 6.307321e-04	ci right 7.613560e-04	k: 444	n:640000
TCEB3B   640000 perm   280 sec   (2282 perm/sec)   p_kst 6.937500e-04   p_cons 9.771734e-01   p_joint 1.065781e-02

Joint ci ratio: 4.690916e-02	ci left: 1.037982e-02	ci right 1.087994e-02	k: 6908	n:650000
Cons ci ratio: 7.426316e-04	ci left: 9.768389e-01	ci right 9.775661e-01	k: 635183	n:650000
KS ci ratio: 1.851386e-01	ci left: 6.254295e-04	ci right 7.544725e-04	k: 447	n:650000
TCEB3B   650000 perm   288 sec   (2261 perm/sec)   p_kst 6.876923e-04   p_cons 9.772046e-01   p_joint 1.062769e-02

Joint ci ratio: 4.653665e-02	ci left: 1.038877e-02	ci right 1.088523e-02	k: 7019	n:660000
Cons ci ratio: 7.374109e-04	ci left: 9.768157e-01	ci right 9.775377e-01	k: 644938	n:660000
KS ci ratio: 1.831059e-01	ci left: 6.304067e-04	ci right 7.588900e-04	k: 457	n:660000
TCEB3B   660000 perm   295 sec   (2237 perm/sec)   p_kst 6.924242e-04   p_cons 9.771788e-01   p_joint 1.063485e-02

Joint ci ratio: 4.622861e-02	ci left: 1.037239e-02	ci right 1.086470e-02	k: 7113	n:670000
Cons ci ratio: 7.324691e-04	ci left: 9.767826e-01	ci right 9.774998e-01	k: 654686	n:670000
KS ci ratio: 1.815272e-01	ci left: 6.323930e-04	ci right 7.600478e-04	k: 465	n:670000
TCEB3B   670000 perm   302 sec   (2215 perm/sec)   p_kst 6.940299e-04   p_cons 9.771433e-01   p_joint 1.061642e-02

Joint ci ratio: 4.585272e-02	ci left: 1.038993e-02	ci right 1.087896e-02	k: 7230	n:680000
Cons ci ratio: 7.266425e-04	ci left: 9.768113e-01	ci right 9.775228e-01	k: 664475	n:680000
KS ci ratio: 1.799887e-01	ci left: 6.343256e-04	ci right 7.611670e-04	k: 473	n:680000
TCEB3B   680000 perm   310 sec   (2196 perm/sec)   p_kst 6.955882e-04   p_cons 9.771691e-01   p_joint 1.063235e-02

Joint ci ratio: 4.552971e-02	ci left: 1.038692e-02	ci right 1.087227e-02	k: 7333	n:690000
Cons ci ratio: 7.215610e-04	ci left: 9.768013e-01	ci right 9.775078e-01	k: 674238	n:690000
KS ci ratio: 1.786742e-01	ci left: 6.348220e-04	ci right 7.607354e-04	k: 480	n:690000
TCEB3B   690000 perm   317 sec   (2178 perm/sec)   p_kst 6.956522e-04   p_cons 9.771565e-01   p_joint 1.062754e-02

Joint ci ratio: 4.517048e-02	ci left: 1.040379e-02	ci right 1.088599e-02	k: 7450	n:700000
Cons ci ratio: 7.158738e-04	ci left: 9.768361e-01	ci right 9.775371e-01	k: 684032	n:700000
KS ci ratio: 1.766650e-01	ci left: 6.407688e-04	ci right 7.662800e-04	k: 491	n:700000
TCEB3B   700000 perm   324 sec   (2160 perm/sec)   p_kst 7.014286e-04   p_cons 9.771886e-01   p_joint 1.064286e-02

Joint ci ratio: 4.487059e-02	ci left: 1.039651e-02	ci right 1.087510e-02	k: 7550	n:710000
Cons ci ratio: 7.103849e-04	ci left: 9.768658e-01	ci right 9.775613e-01	k: 693823	n:710000
KS ci ratio: 1.757744e-01	ci left: 6.384755e-04	ci right 7.628399e-04	k: 496	n:710000
TCEB3B   710000 perm   332 sec   (2141 perm/sec)   p_kst 6.985915e-04   p_cons 9.772155e-01   p_joint 1.063380e-02

Joint ci ratio: 4.457364e-02	ci left: 1.039082e-02	ci right 1.086590e-02	k: 7651	n:720000
Cons ci ratio: 7.051295e-04	ci left: 9.768876e-01	ci right 9.775780e-01	k: 703609	n:720000
KS ci ratio: 1.747230e-01	ci left: 6.375755e-04	ci right 7.609435e-04	k: 502	n:720000
TCEB3B   720000 perm   339 sec   (2125 perm/sec)   p_kst 6.972222e-04   p_cons 9.772347e-01   p_joint 1.062639e-02

Joint ci ratio: 4.425080e-02	ci left: 1.040021e-02	ci right 1.087218e-02	k: 7763	n:730000
Cons ci ratio: 7.004629e-04	ci left: 9.768785e-01	ci right 9.775643e-01	k: 713373	n:730000
KS ci ratio: 1.735198e-01	ci left: 6.380128e-04	ci right 7.605261e-04	k: 509	n:730000
TCEB3B   730000 perm   346 sec   (2110 perm/sec)   p_kst 6.972603e-04   p_cons 9.772233e-01   p_joint 1.063425e-02

Joint ci ratio: 4.391515e-02	ci left: 1.041870e-02	ci right 1.088784e-02	k: 7882	n:740000
Cons ci ratio: 6.956763e-04	ci left: 9.768832e-01	ci right 9.775644e-01	k: 723147	n:740000
KS ci ratio: 1.725081e-01	ci left: 6.371480e-04	ci right 7.587076e-04	k: 515	n:740000
TCEB3B   740000 perm   353 sec   (2095 perm/sec)   p_kst 6.959459e-04   p_cons 9.772257e-01   p_joint 1.065135e-02

Joint ci ratio: 4.359804e-02	ci left: 1.043145e-02	ci right 1.089768e-02	k: 7997	n:750000
Cons ci ratio: 6.908417e-04	ci left: 9.768973e-01	ci right 9.775737e-01	k: 732928	n:750000
KS ci ratio: 1.718437e-01	ci left: 6.337561e-04	ci right 7.541546e-04	k: 519	n:750000
TCEB3B   750000 perm   361 sec   (2079 perm/sec)   p_kst 6.920000e-04   p_cons 9.772373e-01   p_joint 1.066267e-02

Joint ci ratio: 4.330389e-02	ci left: 1.043605e-02	ci right 1.089927e-02	k: 8106	n:760000
Cons ci ratio: 6.861266e-04	ci left: 9.769096e-01	ci right 9.775814e-01	k: 742708	n:760000
KS ci ratio: 1.700540e-01	ci left: 6.392718e-04	ci right 7.593237e-04	k: 530	n:760000
TCEB3B   760000 perm   368 sec   (2064 perm/sec)   p_kst 6.973684e-04   p_cons 9.772474e-01   p_joint 1.066579e-02

Joint ci ratio: 4.307394e-02	ci left: 1.041228e-02	ci right 1.087193e-02	k: 8193	n:770000
Cons ci ratio: 6.820837e-04	ci left: 9.768838e-01	ci right 9.775516e-01	k: 752459	n:770000
KS ci ratio: 1.689440e-01	ci left: 6.396748e-04	ci right 7.589385e-04	k: 537	n:770000
TCEB3B   770000 perm   376 sec   (2047 perm/sec)   p_kst 6.974026e-04   p_cons 9.772195e-01   p_joint 1.064026e-02

Joint ci ratio: 4.281627e-02	ci left: 1.040435e-02	ci right 1.086083e-02	k: 8292	n:780000
Cons ci ratio: 6.775448e-04	ci left: 9.768960e-01	ci right 9.775594e-01	k: 762239	n:780000
KS ci ratio: 1.675482e-01	ci left: 6.425265e-04	ci right 7.612323e-04	k: 546	n:780000
TCEB3B   780000 perm   384 sec   (2033 perm/sec)   p_kst 7.000000e-04   p_cons 9.772295e-01   p_joint 1.063077e-02

Joint ci ratio: 4.256317e-02	ci left: 1.039663e-02	ci right 1.085001e-02	k: 8391	n:790000
Cons ci ratio: 6.731142e-04	ci left: 9.769067e-01	ci right 9.775657e-01	k: 772018	n:790000
KS ci ratio: 1.663362e-01	ci left: 6.440968e-04	ci right 7.621457e-04	k: 554	n:790000
TCEB3B   790000 perm   392 sec   (2017 perm/sec)   p_kst 7.012658e-04   p_cons 9.772380e-01   p_joint 1.062152e-02

Joint ci ratio: 4.230192e-02	ci left: 1.039529e-02	ci right 1.084576e-02	k: 8495	n:800000
Cons ci ratio: 6.689386e-04	ci left: 9.769058e-01	ci right 9.775607e-01	k: 781788	n:800000
KS ci ratio: 1.651501e-01	ci left: 6.456309e-04	ci right 7.630332e-04	k: 562	n:800000
TCEB3B   800000 perm   399 sec   (2003 perm/sec)   p_kst 7.025000e-04   p_cons 9.772350e-01   p_joint 1.061875e-02

Joint ci ratio: 3.658693e-02	ci left: 1.371834e-02	ci right 1.423082e-02	k: 11318	n:810000
Cons ci ratio: 6.651162e-04	ci left: 9.768863e-01	ci right 9.775375e-01	k: 791543	n:810000
KS ci ratio: 1.642771e-01	ci left: 6.447622e-04	ci right 7.613256e-04	k: 568	n:810000
TCEB3B   810000 perm   407 sec   (1989 perm/sec)   p_kst 7.012346e-04   p_cons 9.772136e-01   p_joint 1.397284e-02

Joint ci ratio: 4.178141e-02	ci left: 1.039877e-02	ci right 1.084372e-02	k: 8708	n:820000
Cons ci ratio: 6.608694e-04	ci left: 9.769004e-01	ci right 9.775474e-01	k: 801325	n:820000
KS ci ratio: 1.627115e-01	ci left: 6.497651e-04	ci right 7.660040e-04	k: 579	n:820000
TCEB3B   820000 perm   415 sec   (1975 perm/sec)   p_kst 7.060976e-04   p_cons 9.772256e-01   p_joint 1.061951e-02

Joint ci ratio: 3.614103e-02	ci left: 1.372326e-02	ci right 1.422954e-02	k: 11599	n:830000
Cons ci ratio: 6.570406e-04	ci left: 9.768912e-01	ci right 9.775344e-01	k: 811088	n:830000
KS ci ratio: 1.620148e-01	ci left: 6.477159e-04	ci right 7.630437e-04	k: 584	n:830000
TCEB3B   830000 perm   424 sec   (1960 perm/sec)   p_kst 7.036145e-04   p_cons 9.772145e-01   p_joint 1.397470e-02

Joint ci ratio: 3.590629e-02	ci left: 1.373921e-02	ci right 1.424272e-02	k: 11751	n:840000
Cons ci ratio: 6.529631e-04	ci left: 9.769037e-01	ci right 9.775430e-01	k: 820869	n:840000
KS ci ratio: 1.614641e-01	ci left: 6.445741e-04	ci right 7.589145e-04	k: 588	n:840000
TCEB3B   840000 perm   432 sec   (1945 perm/sec)   p_kst 7.000000e-04   p_cons 9.772250e-01   p_joint 1.398929e-02

Joint ci ratio: 3.586907e-02	ci left: 1.360787e-02	ci right 1.410604e-02	k: 11777	n:850000
Cons ci ratio: 6.489948e-04	ci left: 9.769136e-01	ci right 9.775490e-01	k: 830648	n:850000
KS ci ratio: 1.607832e-01	ci left: 6.426360e-04	ci right 7.561055e-04	k: 593	n:850000
TCEB3B   850000 perm   440 sec   (1930 perm/sec)   p_kst 6.976471e-04   p_cons 9.772329e-01   p_joint 1.385529e-02

Joint ci ratio: 3.601176e-02	ci left: 1.334589e-02	ci right 1.383646e-02	k: 11687	n:860000
Cons ci ratio: 6.449798e-04	ci left: 9.769315e-01	ci right 9.775630e-01	k: 840434	n:860000
KS ci ratio: 1.602449e-01	ci left: 6.396277e-04	ci right 7.521515e-04	k: 597	n:860000
TCEB3B   860000 perm   449 sec   (1917 perm/sec)   p_kst 6.941860e-04   p_cons 9.772488e-01   p_joint 1.358953e-02

Joint ci ratio: 3.581480e-02	ci left: 1.333944e-02	ci right 1.382703e-02	k: 11816	n:870000
Cons ci ratio: 6.410548e-04	ci left: 9.769478e-01	ci right 9.775754e-01	k: 850219	n:870000
KS ci ratio: 1.594471e-01	ci left: 6.388963e-04	ci right 7.506783e-04	k: 603	n:870000
TCEB3B   870000 perm   457 sec   (1904 perm/sec)   p_kst 6.931034e-04   p_cons 9.772632e-01   p_joint 1.358161e-02

Joint ci ratio: 3.528862e-02	ci left: 1.358433e-02	ci right 1.407343e-02	k: 12168	n:880000
Cons ci ratio: 6.373143e-04	ci left: 9.769558e-01	ci right 9.775797e-01	k: 859997	n:880000
KS ci ratio: 1.584014e-01	ci left: 6.403655e-04	ci right 7.516000e-04	k: 611	n:880000
TCEB3B   880000 perm   465 sec   (1891 perm/sec)   p_kst 6.943182e-04   p_cons 9.772693e-01   p_joint 1.382727e-02

Joint ci ratio: 3.540959e-02	ci left: 1.334257e-02	ci right 1.382465e-02	k: 12088	n:890000
Cons ci ratio: 6.338950e-04	ci left: 9.769455e-01	ci right 9.775660e-01	k: 869759	n:890000
KS ci ratio: 1.572492e-01	ci left: 6.428835e-04	ci right 7.536664e-04	k: 620	n:890000
TCEB3B   890000 perm   474 sec   (1878 perm/sec)   p_kst 6.966292e-04   p_cons 9.772573e-01   p_joint 1.358202e-02

Joint ci ratio: 3.521061e-02	ci left: 1.334520e-02	ci right 1.382461e-02	k: 12225	n:900000
Cons ci ratio: 6.305142e-04	ci left: 9.769365e-01	ci right 9.775538e-01	k: 879522	n:900000
KS ci ratio: 1.568711e-01	ci left: 6.389426e-04	ci right 7.487567e-04	k: 623	n:900000
TCEB3B   900000 perm   482 sec   (1865 perm/sec)   p_kst 6.922222e-04   p_cons 9.772467e-01   p_joint 1.358333e-02

Joint ci ratio: 4.009752e-02	ci left: 1.018496e-02	ci right 1.060278e-02	k: 9457	n:910000
Cons ci ratio: 6.267374e-04	ci left: 9.769598e-01	ci right 9.775734e-01	k: 889314	n:910000
KS ci ratio: 1.556288e-01	ci left: 6.424807e-04	ci right 7.519468e-04	k: 633	n:910000
TCEB3B   910000 perm   491 sec   (1852 perm/sec)   p_kst 6.956044e-04   p_cons 9.772681e-01   p_joint 1.039231e-02

Joint ci ratio: 3.989573e-02	ci left: 1.017755e-02	ci right 1.059293e-02	k: 9553	n:920000
Cons ci ratio: 6.231034e-04	ci left: 9.769772e-01	ci right 9.775872e-01	k: 899101	n:920000
KS ci ratio: 1.551404e-01	ci left: 6.396759e-04	ci right 7.482903e-04	k: 637	n:920000
TCEB3B   920000 perm   500 sec   (1840 perm/sec)   p_kst 6.923913e-04   p_cons 9.772837e-01   p_joint 1.038370e-02

Joint ci ratio: 3.457779e-02	ci left: 1.339543e-02	ci right 1.386782e-02	k: 12676	n:930000
Cons ci ratio: 6.199218e-04	ci left: 9.769660e-01	ci right 9.775729e-01	k: 908862	n:930000
KS ci ratio: 1.539384e-01	ci left: 6.431346e-04	ci right 7.514122e-04	k: 647	n:930000
TCEB3B   930000 perm   509 sec   (1827 perm/sec)   p_kst 6.956989e-04   p_cons 9.772710e-01   p_joint 1.363011e-02

Joint ci ratio: 3.401364e-02	ci left: 1.369594e-02	ci right 1.417089e-02	k: 13096	n:940000
Cons ci ratio: 6.166259e-04	ci left: 9.769669e-01	ci right 9.775706e-01	k: 918634	n:940000
KS ci ratio: 1.526479e-01	ci left: 6.475461e-04	ci right 7.555690e-04	k: 658	n:940000
TCEB3B   940000 perm   518 sec   (1815 perm/sec)   p_kst 7.000000e-04   p_cons 9.772702e-01   p_joint 1.393191e-02

Joint ci ratio: 3.383458e-02	ci left: 1.369685e-02	ci right 1.416928e-02	k: 13235	n:950000
Cons ci ratio: 6.135272e-04	ci left: 9.769572e-01	ci right 9.775578e-01	k: 928396	n:950000
KS ci ratio: 1.521870e-01	ci left: 6.447797e-04	ci right 7.519867e-04	k: 662	n:950000
TCEB3B   950000 perm   527 sec   (1802 perm/sec)   p_kst 6.968421e-04   p_cons 9.772589e-01   p_joint 1.393158e-02

Joint ci ratio: 3.349991e-02	ci left: 1.382687e-02	ci right 1.429898e-02	k: 13499	n:960000
Cons ci ratio: 6.103317e-04	ci left: 9.769582e-01	ci right 9.775556e-01	k: 938168	n:960000
KS ci ratio: 1.515031e-01	ci left: 6.440758e-04	ci right 7.506408e-04	k: 668	n:960000
TCEB3B   960000 perm   536 sec   (1791 perm/sec)   p_kst 6.958333e-04   p_cons 9.772583e-01   p_joint 1.406146e-02

Joint ci ratio: 3.349608e-02	ci left: 1.368942e-02	ci right 1.415679e-02	k: 13504	n:970000
Cons ci ratio: 6.069744e-04	ci left: 9.769747e-01	ci right 9.775689e-01	k: 947955	n:970000
KS ci ratio: 1.508283e-01	ci left: 6.433874e-04	ci right 7.493216e-04	k: 674	n:970000
TCEB3B   970000 perm   545 sec   (1780 perm/sec)   p_kst 6.948454e-04   p_cons 9.772732e-01   p_joint 1.392165e-02

Joint ci ratio: 3.330276e-02	ci left: 1.370860e-02	ci right 1.417387e-02	k: 13661	n:980000
Cons ci ratio: 6.039212e-04	ci left: 9.769724e-01	ci right 9.775636e-01	k: 957724	n:980000
KS ci ratio: 1.501624e-01	ci left: 6.427141e-04	ci right 7.480283e-04	k: 680	n:980000
TCEB3B   980000 perm   554 sec   (1769 perm/sec)   p_kst 6.938776e-04   p_cons 9.772694e-01   p_joint 1.393980e-02

Joint ci ratio: 3.312368e-02	ci left: 1.371839e-02	ci right 1.418143e-02	k: 13809	n:990000
Cons ci ratio: 6.011049e-04	ci left: 9.769559e-01	ci right 9.775443e-01	k: 967479	n:990000
KS ci ratio: 1.496144e-01	ci left: 6.410831e-04	ci right 7.457123e-04	k: 685	n:990000
TCEB3B   990000 perm   563 sec   (1758 perm/sec)   p_kst 6.919192e-04   p_cons 9.772515e-01   p_joint 1.394848e-02

Joint ci ratio: 3.279175e-02	ci left: 1.385792e-02	ci right 1.432090e-02	k: 14088	n:1000000
Cons ci ratio: 5.982870e-04	ci left: 9.769428e-01	ci right 9.775284e-01	k: 977237	n:1000000
KS ci ratio: 1.486423e-01	ci left: 6.433365e-04	ci right 7.475907e-04	k: 694	n:1000000
TCEB3B   1000000 perm   572 sec   (1748 perm/sec)   p_kst 6.940000e-04   p_cons 9.772370e-01   p_joint 1.408800e-02

Joint ci ratio: 3.260681e-02	ci left: 1.387783e-02	ci right 1.433882e-02	k: 14248	n:1010000
Cons ci ratio: 5.952961e-04	ci left: 9.769459e-01	ci right 9.775286e-01	k: 987011	n:1010000
KS ci ratio: 1.473751e-01	ci left: 6.484082e-04	ci right 7.525096e-04	k: 706	n:1010000
TCEB3B   1010000 perm   581 sec   (1737 perm/sec)   p_kst 6.990099e-04   p_cons 9.772386e-01   p_joint 1.410693e-02

Joint ci ratio: 3.243981e-02	ci left: 1.388472e-02	ci right 1.434353e-02	k: 14395	n:1020000
Cons ci ratio: 5.924279e-04	ci left: 9.769430e-01	ci right 9.775229e-01	k: 996779	n:1020000
KS ci ratio: 1.464458e-01	ci left: 6.505505e-04	ci right 7.542796e-04	k: 715	n:1020000
TCEB3B   1020000 perm   591 sec   (1727 perm/sec)   p_kst 7.009804e-04   p_cons 9.772343e-01   p_joint 1.411275e-02

Joint ci ratio: 3.227423e-02	ci left: 1.389245e-02	ci right 1.434912e-02	k: 14543	n:1030000
Cons ci ratio: 5.893306e-04	ci left: 9.769607e-01	ci right 9.775376e-01	k: 1006568	n:1030000
KS ci ratio: 1.455338e-01	ci left: 6.526532e-04	ci right 7.560132e-04	k: 724	n:1030000
TCEB3B   1030000 perm   600 sec   (1716 perm/sec)   p_kst 7.029126e-04   p_cons 9.772505e-01   p_joint 1.411942e-02

Joint ci ratio: 3.211892e-02	ci left: 1.389335e-02	ci right 1.434782e-02	k: 14684	n:1040000
Cons ci ratio: 5.864967e-04	ci left: 9.769616e-01	ci right 9.775357e-01	k: 1016340	n:1040000
KS ci ratio: 1.444419e-01	ci left: 6.565710e-04	ci right 7.597041e-04	k: 735	n:1040000
TCEB3B   1040000 perm   610 sec   (1706 perm/sec)   p_kst 7.067308e-04   p_cons 9.772500e-01   p_joint 1.411923e-02

Joint ci ratio: 3.193634e-02	ci left: 1.391976e-02	ci right 1.437245e-02	k: 14852	n:1050000
Cons ci ratio: 5.837409e-04	ci left: 9.769597e-01	ci right 9.775310e-01	k: 1026109	n:1050000
KS ci ratio: 1.431825e-01	ci left: 6.622536e-04	ci right 7.652948e-04	k: 748	n:1050000
TCEB3B   1050000 perm   619 sec   (1696 perm/sec)   p_kst 7.123810e-04   p_cons 9.772467e-01   p_joint 1.414476e-02

Joint ci ratio: 3.148683e-02	ci left: 1.418436e-02	ci right 1.463905e-02	k: 15275	n:1060000
Cons ci ratio: 5.808509e-04	ci left: 9.769710e-01	ci right 9.775396e-01	k: 1035892	n:1060000
KS ci ratio: 1.423298e-01	ci left: 6.641932e-04	ci right 7.668686e-04	k: 757	n:1060000
TCEB3B   1060000 perm   629 sec   (1686 perm/sec)   p_kst 7.141509e-04   p_cons 9.772566e-01   p_joint 1.441038e-02

Joint ci ratio: 3.134256e-02	ci left: 1.418254e-02	ci right 1.463505e-02	k: 15416	n:1070000
Cons ci ratio: 5.781127e-04	ci left: 9.769737e-01	ci right 9.775396e-01	k: 1045666	n:1070000
KS ci ratio: 1.417699e-01	ci left: 6.633940e-04	ci right 7.655083e-04	k: 763	n:1070000
TCEB3B   1070000 perm   638 sec   (1676 perm/sec)   p_kst 7.130841e-04   p_cons 9.772579e-01   p_joint 1.440748e-02

Joint ci ratio: 3.119822e-02	ci left: 1.418259e-02	ci right 1.463298e-02	k: 15559	n:1080000
Cons ci ratio: 5.754249e-04	ci left: 9.769754e-01	ci right 9.775387e-01	k: 1055439	n:1080000
KS ci ratio: 1.414004e-01	ci left: 6.608239e-04	ci right 7.622551e-04	k: 767	n:1080000
TCEB3B   1080000 perm   648 sec   (1666 perm/sec)   p_kst 7.101852e-04   p_cons 9.772583e-01   p_joint 1.440648e-02

Joint ci ratio: 3.104382e-02	ci left: 1.419357e-02	ci right 1.464204e-02	k: 15714	n:1090000
Cons ci ratio: 5.725851e-04	ci left: 9.769919e-01	ci right 9.775524e-01	k: 1065228	n:1090000
KS ci ratio: 1.405790e-01	ci left: 6.627270e-04	ci right 7.638098e-04	k: 776	n:1090000
TCEB3B   1090000 perm   658 sec   (1656 perm/sec)   p_kst 7.119266e-04   p_cons 9.772734e-01   p_joint 1.441651e-02

Joint ci ratio: 3.089861e-02	ci left: 1.419804e-02	ci right 1.464452e-02	k: 15862	n:1100000
Cons ci ratio: 5.699266e-04	ci left: 9.769971e-01	ci right 9.775549e-01	k: 1075005	n:1100000
KS ci ratio: 1.401290e-01	ci left: 6.610880e-04	ci right 7.615711e-04	k: 781	n:1100000
TCEB3B   1100000 perm   668 sec   (1647 perm/sec)   p_kst 7.100000e-04   p_cons 9.772773e-01   p_joint 1.442000e-02

Joint ci ratio: 3.075152e-02	ci left: 1.420601e-02	ci right 1.465058e-02	k: 16014	n:1110000
Cons ci ratio: 5.674314e-04	ci left: 9.769922e-01	ci right 9.775476e-01	k: 1084771	n:1110000
KS ci ratio: 1.391535e-01	ci left: 6.646960e-04	ci right 7.649659e-04	k: 792	n:1110000
TCEB3B   1110000 perm   678 sec   (1637 perm/sec)   p_kst 7.135135e-04   p_cons 9.772712e-01   p_joint 1.442703e-02

Joint ci ratio: 3.059979e-02	ci left: 1.422005e-02	ci right 1.466282e-02	k: 16173	n:1120000
Cons ci ratio: 5.649687e-04	ci left: 9.769874e-01	ci right 9.775404e-01	k: 1094537	n:1120000
KS ci ratio: 1.381980e-01	ci left: 6.682420e-04	ci right 7.682977e-04	k: 803	n:1120000
TCEB3B   1120000 perm   688 sec   (1628 perm/sec)   p_kst 7.169643e-04   p_cons 9.772652e-01   p_joint 1.444018e-02

Joint ci ratio: 3.047111e-02	ci left: 1.421452e-02	ci right 1.465523e-02	k: 16310	n:1130000
Cons ci ratio: 5.623584e-04	ci left: 9.769970e-01	ci right 9.775474e-01	k: 1104319	n:1130000
KS ci ratio: 1.377705e-01	ci left: 6.666003e-04	ci right 7.660761e-04	k: 808	n:1130000
TCEB3B   1130000 perm   698 sec   (1619 perm/sec)   p_kst 7.150442e-04   p_cons 9.772735e-01   p_joint 1.443363e-02

Joint ci ratio: 3.034779e-02	ci left: 1.420561e-02	ci right 1.464423e-02	k: 16443	n:1140000
Cons ci ratio: 5.597840e-04	ci left: 9.770064e-01	ci right 9.775543e-01	k: 1114101	n:1140000
KS ci ratio: 1.374313e-01	ci left: 6.641409e-04	ci right 7.629857e-04	k: 812	n:1140000
TCEB3B   1140000 perm   708 sec   (1609 perm/sec)   p_kst 7.122807e-04   p_cons 9.772816e-01   p_joint 1.442368e-02

Joint ci ratio: 3.013203e-02	ci left: 1.428490e-02	ci right 1.472277e-02	k: 16678	n:1150000
Cons ci ratio: 5.575719e-04	ci left: 9.769894e-01	ci right 9.775351e-01	k: 1123853	n:1150000
KS ci ratio: 1.366768e-01	ci left: 6.659235e-04	ci right 7.644453e-04	k: 821	n:1150000
TCEB3B   1150000 perm   719 sec   (1600 perm/sec)   p_kst 7.139130e-04   p_cons 9.772635e-01   p_joint 1.450261e-02

Joint ci ratio: 3.005997e-02	ci left: 1.423105e-02	ci right 1.466621e-02	k: 16759	n:1160000
Cons ci ratio: 5.550516e-04	ci left: 9.769996e-01	ci right 9.775429e-01	k: 1133636	n:1160000
KS ci ratio: 1.358527e-01	ci left: 6.685097e-04	ci right 7.667696e-04	k: 831	n:1160000
TCEB3B   1160000 perm   729 sec   (1591 perm/sec)   p_kst 7.163793e-04   p_cons 9.772724e-01   p_joint 1.444741e-02

Joint ci ratio: 2.992718e-02	ci left: 1.423581e-02	ci right 1.466916e-02	k: 16908	n:1170000
Cons ci ratio: 5.526715e-04	ci left: 9.770010e-01	ci right 9.775419e-01	k: 1143409	n:1170000
KS ci ratio: 1.356901e-01	ci left: 6.644472e-04	ci right 7.619835e-04	k: 833	n:1170000
TCEB3B   1170000 perm   739 sec   (1582 perm/sec)   p_kst 7.119658e-04   p_cons 9.772726e-01   p_joint 1.445128e-02

Joint ci ratio: 3.008830e-02	ci left: 1.396711e-02	ci right 1.439460e-02	k: 16732	n:1180000
Cons ci ratio: 5.505107e-04	ci left: 9.769870e-01	ci right 9.775259e-01	k: 1153164	n:1180000
KS ci ratio: 1.350439e-01	ci left: 6.653664e-04	ci right 7.625351e-04	k: 841	n:1180000
TCEB3B   1180000 perm   750 sec   (1574 perm/sec)   p_kst 7.127119e-04   p_cons 9.772576e-01   p_joint 1.417966e-02

Joint ci ratio: 2.996414e-02	ci left: 1.396567e-02	ci right 1.439133e-02	k: 16871	n:1190000
Cons ci ratio: 5.482505e-04	ci left: 9.769835e-01	ci right 9.775201e-01	k: 1162931	n:1190000
KS ci ratio: 1.341701e-01	ci left: 6.687075e-04	ci right 7.656820e-04	k: 852	n:1190000
TCEB3B   1190000 perm   761 sec   (1565 perm/sec)   p_kst 7.159664e-04   p_cons 9.772529e-01   p_joint 1.417731e-02

Joint ci ratio: 2.983706e-02	ci left: 1.396839e-02	ci right 1.439229e-02	k: 17015	n:1200000
Cons ci ratio: 5.458029e-04	ci left: 9.769976e-01	ci right 9.775318e-01	k: 1172719	n:1200000
KS ci ratio: 1.339350e-01	ci left: 6.655511e-04	ci right 7.618852e-04	k: 855	n:1200000
TCEB3B   1200000 perm   772 sec   (1555 perm/sec)   p_kst 7.125000e-04   p_cons 9.772658e-01   p_joint 1.417917e-02

Joint ci ratio: 2.973179e-02	ci left: 1.395220e-02	ci right 1.437410e-02	k: 17136	n:1210000
Cons ci ratio: 5.435696e-04	ci left: 9.769965e-01	ci right 9.775285e-01	k: 1182489	n:1210000
KS ci ratio: 1.330824e-01	ci left: 6.688380e-04	ci right 7.649829e-04	k: 866	n:1210000
TCEB3B   1210000 perm   783 sec   (1545 perm/sec)   p_kst 7.157025e-04   p_cons 9.772636e-01   p_joint 1.416198e-02

Joint ci ratio: 2.962154e-02	ci left: 1.394198e-02	ci right 1.436197e-02	k: 17264	n:1220000
Cons ci ratio: 5.412537e-04	ci left: 9.770045e-01	ci right 9.775342e-01	k: 1192270	n:1220000
KS ci ratio: 1.327767e-01	ci left: 6.665253e-04	ci right 7.621003e-04	k: 870	n:1220000
TCEB3B   1220000 perm   794 sec   (1537 perm/sec)   p_kst 7.131148e-04   p_cons 9.772705e-01   p_joint 1.415082e-02

Joint ci ratio: 2.949789e-02	ci left: 1.394564e-02	ci right 1.436397e-02	k: 17409	n:1230000
Cons ci ratio: 5.389474e-04	ci left: 9.770140e-01	ci right 9.775415e-01	k: 1202053	n:1230000
KS ci ratio: 1.321710e-01	ci left: 6.673950e-04	ci right 7.626238e-04	k: 878	n:1230000
TCEB3B   1230000 perm   805 sec   (1528 perm/sec)   p_kst 7.138211e-04   p_cons 9.772789e-01   p_joint 1.415366e-02

Joint ci ratio: 2.937917e-02	ci left: 1.394605e-02	ci right 1.436267e-02	k: 17550	n:1240000
Cons ci ratio: 5.366312e-04	ci left: 9.770266e-01	ci right 9.775518e-01	k: 1211840	n:1240000
KS ci ratio: 1.317968e-01	ci left: 6.659118e-04	ci right 7.606390e-04	k: 883	n:1240000
TCEB3B   1240000 perm   817 sec   (1518 perm/sec)   p_kst 7.120968e-04   p_cons 9.772903e-01   p_joint 1.415323e-02

Joint ci ratio: 2.925684e-02	ci left: 1.395122e-02	ci right 1.436623e-02	k: 17697	n:1250000
Cons ci ratio: 5.346335e-04	ci left: 9.770149e-01	ci right 9.775381e-01	k: 1221597	n:1250000
KS ci ratio: 1.312781e-01	ci left: 6.660003e-04	ci right 7.603380e-04	k: 890	n:1250000
TCEB3B   1250000 perm   828 sec   (1510 perm/sec)   p_kst 7.120000e-04   p_cons 9.772776e-01   p_joint 1.415760e-02

Joint ci ratio: 2.914182e-02	ci left: 1.395080e-02	ci right 1.436414e-02	k: 17837	n:1260000
Cons ci ratio: 5.326577e-04	ci left: 9.770033e-01	ci right 9.775246e-01	k: 1231354	n:1260000
KS ci ratio: 1.303304e-01	ci left: 6.706945e-04	ci right 7.649583e-04	k: 903	n:1260000
TCEB3B   1260000 perm   839 sec   (1502 perm/sec)   p_kst 7.166667e-04   p_cons 9.772651e-01   p_joint 1.415635e-02

Joint ci ratio: 2.904126e-02	ci left: 1.393787e-02	ci right 1.434939e-02	k: 17961	n:1270000
Cons ci ratio: 5.307223e-04	ci left: 9.769904e-01	ci right 9.775098e-01	k: 1241109	n:1270000
KS ci ratio: 1.300432e-01	ci left: 6.684604e-04	ci right 7.621872e-04	k: 907	n:1270000
TCEB3B   1270000 perm   850 sec   (1494 perm/sec)   p_kst 7.141732e-04   p_cons 9.772512e-01   p_joint 1.414252e-02

Joint ci ratio: 2.893281e-02	ci left: 1.393369e-02	ci right 1.434351e-02	k: 18096	n:1280000
Cons ci ratio: 5.284361e-04	ci left: 9.770091e-01	ci right 9.775263e-01	k: 1250904	n:1280000
KS ci ratio: 1.296157e-01	ci left: 6.677733e-04	ci right 7.610723e-04	k: 913	n:1280000
TCEB3B   1280000 perm   861 sec   (1486 perm/sec)   p_kst 7.132813e-04   p_cons 9.772688e-01   p_joint 1.413750e-02

Joint ci ratio: 2.880634e-02	ci left: 1.394804e-02	ci right 1.435647e-02	k: 18255	n:1290000
Cons ci ratio: 5.264820e-04	ci left: 9.770018e-01	ci right 9.775170e-01	k: 1260666	n:1290000
KS ci ratio: 1.291222e-01	ci left: 6.678475e-04	ci right 7.607744e-04	k: 920	n:1290000
TCEB3B   1290000 perm   873 sec   (1478 perm/sec)   p_kst 7.131783e-04   p_cons 9.772605e-01   p_joint 1.415116e-02

Joint ci ratio: 2.869574e-02	ci left: 1.394843e-02	ci right 1.435528e-02	k: 18396	n:1300000
Cons ci ratio: 5.244132e-04	ci left: 9.770062e-01	ci right 9.775194e-01	k: 1270443	n:1300000
KS ci ratio: 1.287037e-01	ci left: 6.671768e-04	ci right 7.596865e-04	k: 926	n:1300000
TCEB3B   1300000 perm   884 sec   (1470 perm/sec)   p_kst 7.123077e-04   p_cons 9.772638e-01   p_joint 1.415077e-02

Joint ci ratio: 2.857156e-02	ci left: 1.396322e-02	ci right 1.436870e-02	k: 18556	n:1310000
Cons ci ratio: 5.224584e-04	ci left: 9.770028e-01	ci right 9.775141e-01	k: 1280210	n:1310000
KS ci ratio: 1.281519e-01	ci left: 6.679945e-04	ci right 7.601903e-04	k: 934	n:1310000
TCEB3B   1310000 perm   896 sec   (1462 perm/sec)   p_kst 7.129771e-04   p_cons 9.772595e-01   p_joint 1.416489e-02

Joint ci ratio: 2.847213e-02	ci left: 1.395522e-02	ci right 1.435904e-02	k: 18686	n:1320000
Cons ci ratio: 5.205695e-04	ci left: 9.769957e-01	ci right 9.775052e-01	k: 1289972	n:1320000
KS ci ratio: 1.276749e-01	ci left: 6.680673e-04	ci right 7.599039e-04	k: 941	n:1320000
TCEB3B   1320000 perm   909 sec   (1453 perm/sec)   p_kst 7.128788e-04   p_cons 9.772515e-01   p_joint 1.415606e-02

Joint ci ratio: 2.836380e-02	ci left: 1.395705e-02	ci right 1.435936e-02	k: 18829	n:1330000
Cons ci ratio: 5.184027e-04	ci left: 9.770145e-01	ci right 9.775218e-01	k: 1299768	n:1330000
KS ci ratio: 1.272031e-01	ci left: 6.681396e-04	ci right 7.596212e-04	k: 948	n:1330000
TCEB3B   1330000 perm   920 sec   (1445 perm/sec)   p_kst 7.127820e-04   p_cons 9.772692e-01   p_joint 1.415714e-02

Joint ci ratio: 2.825821e-02	ci left: 1.395737e-02	ci right 1.435817e-02	k: 18970	n:1340000
Cons ci ratio: 5.163319e-04	ci left: 9.770269e-01	ci right 9.775322e-01	k: 1309556	n:1340000
KS ci ratio: 1.266041e-01	ci left: 6.696567e-04	ci right 7.608818e-04	k: 957	n:1340000
TCEB3B   1340000 perm   932 sec   (1437 perm/sec)   p_kst 7.141791e-04   p_cons 9.772806e-01   p_joint 1.415672e-02

Joint ci ratio: 2.816873e-02	ci left: 1.394298e-02	ci right 1.434207e-02	k: 19091	n:1350000
Cons ci ratio: 5.144744e-04	ci left: 9.770228e-01	ci right 9.775263e-01	k: 1319322	n:1350000
KS ci ratio: 1.262096e-01	ci left: 6.690002e-04	ci right 7.598306e-04	k: 963	n:1350000
TCEB3B   1350000 perm   944 sec   (1429 perm/sec)   p_kst 7.133333e-04   p_cons 9.772756e-01   p_joint 1.414148e-02

Joint ci ratio: 2.807714e-02	ci left: 1.393172e-02	ci right 1.432918e-02	k: 19216	n:1360000
Cons ci ratio: 5.125518e-04	ci left: 9.770261e-01	ci right 9.775277e-01	k: 1329098	n:1360000
KS ci ratio: 1.257538e-01	ci left: 6.690659e-04	ci right 7.595528e-04	k: 970	n:1360000
TCEB3B   1360000 perm   957 sec   (1422 perm/sec)   p_kst 7.132353e-04   p_cons 9.772779e-01   p_joint 1.412941e-02

Joint ci ratio: 2.797031e-02	ci left: 1.393658e-02	ci right 1.433263e-02	k: 19363	n:1370000
Cons ci ratio: 5.107094e-04	ci left: 9.770243e-01	ci right 9.775241e-01	k: 1338867	n:1370000
KS ci ratio: 1.251750e-01	ci left: 6.705454e-04	ci right 7.607840e-04	k: 979	n:1370000
TCEB3B   1370000 perm   969 sec   (1414 perm/sec)   p_kst 7.145985e-04   p_cons 9.772752e-01   p_joint 1.413358e-02

Joint ci ratio: 2.786976e-02	ci left: 1.393633e-02	ci right 1.433093e-02	k: 19503	n:1380000
Cons ci ratio: 5.088453e-04	ci left: 9.770261e-01	ci right 9.775241e-01	k: 1348641	n:1380000
KS ci ratio: 1.248570e-01	ci left: 6.691962e-04	ci right 7.590076e-04	k: 984	n:1380000
TCEB3B   1380000 perm   981 sec   (1407 perm/sec)   p_kst 7.130435e-04   p_cons 9.772761e-01   p_joint 1.413261e-02

Joint ci ratio: 2.776383e-02	ci left: 1.394252e-02	ci right 1.433577e-02	k: 19652	n:1390000
Cons ci ratio: 5.069685e-04	ci left: 9.770308e-01	ci right 9.775269e-01	k: 1358419	n:1390000
KS ci ratio: 1.246044e-01	ci left: 6.671698e-04	ci right 7.565146e-04	k: 988	n:1390000
TCEB3B   1390000 perm   993 sec   (1400 perm/sec)   p_kst 7.107914e-04   p_cons 9.772799e-01   p_joint 1.413813e-02

Joint ci ratio: 2.766335e-02	ci left: 1.394436e-02	ci right 1.433622e-02	k: 19795	n:1400000
Cons ci ratio: 5.049498e-04	ci left: 9.770498e-01	ci right 9.775440e-01	k: 1368217	n:1400000
KS ci ratio: 1.243533e-01	ci left: 6.651724e-04	ci right 7.540570e-04	k: 992	n:1400000
TCEB3B   1400000 perm   1005 sec   (1393 perm/sec)   p_kst 7.085714e-04   p_cons 9.772979e-01   p_joint 1.413929e-02

Joint ci ratio: 2.755485e-02	ci left: 1.395534e-02	ci right 1.434595e-02	k: 19951	n:1410000
Cons ci ratio: 5.032844e-04	ci left: 9.770393e-01	ci right 9.775318e-01	k: 1377974	n:1410000
KS ci ratio: 1.237935e-01	ci left: 6.666398e-04	ci right 7.552900e-04	k: 1001	n:1410000
TCEB3B   1410000 perm   1018 sec   (1385 perm/sec)   p_kst 7.099291e-04   p_cons 9.772865e-01   p_joint 1.414965e-02

Joint ci ratio: 2.745246e-02	ci left: 1.396127e-02	ci right 1.435057e-02	k: 20100	n:1420000
Cons ci ratio: 5.015558e-04	ci left: 9.770360e-01	ci right 9.775268e-01	k: 1387741	n:1420000
KS ci ratio: 1.235472e-01	ci left: 6.646748e-04	ci right 7.528751e-04	k: 1005	n:1420000
TCEB3B   1420000 perm   1030 sec   (1378 perm/sec)   p_kst 7.077465e-04   p_cons 9.772824e-01   p_joint 1.415493e-02

Joint ci ratio: 2.736423e-02	ci left: 1.395393e-02	ci right 1.434175e-02	k: 20230	n:1430000
Cons ci ratio: 4.998842e-04	ci left: 9.770293e-01	ci right 9.775185e-01	k: 1397503	n:1430000
KS ci ratio: 1.231196e-01	ci left: 6.647708e-04	ci right 7.526563e-04	k: 1012	n:1430000
TCEB3B   1430000 perm   1044 sec   (1370 perm/sec)   p_kst 7.076923e-04   p_cons 9.772748e-01   p_joint 1.414685e-02

Joint ci ratio: 2.741580e-02	ci left: 1.380666e-02	ci right 1.419113e-02	k: 20157	n:1440000
Cons ci ratio: 4.981512e-04	ci left: 9.770296e-01	ci right 9.775171e-01	k: 1407275	n:1440000
KS ci ratio: 1.228170e-01	ci left: 6.635198e-04	ci right 7.510086e-04	k: 1017	n:1440000
TCEB3B   1440000 perm   1056 sec   (1363 perm/sec)   p_kst 7.062500e-04   p_cons 9.772743e-01   p_joint 1.399792e-02

Joint ci ratio: 2.732109e-02	ci left: 1.380734e-02	ci right 1.419047e-02	k: 20297	n:1450000
Cons ci ratio: 4.962820e-04	ci left: 9.770438e-01	ci right 9.775295e-01	k: 1417067	n:1450000
KS ci ratio: 1.226366e-01	ci left: 6.609492e-04	ci right 7.479617e-04	k: 1020	n:1450000
TCEB3B   1450000 perm   1070 sec   (1356 perm/sec)   p_kst 7.034483e-04   p_cons 9.772876e-01   p_joint 1.399793e-02

Joint ci ratio: 2.721723e-02	ci left: 1.381821e-02	ci right 1.420016e-02	k: 20452	n:1460000
Cons ci ratio: 4.945327e-04	ci left: 9.770488e-01	ci right 9.775328e-01	k: 1426846	n:1460000
KS ci ratio: 1.219811e-01	ci left: 6.637259e-04	ci right 7.506032e-04	k: 1031	n:1460000
TCEB3B   1460000 perm   1083 sec   (1348 perm/sec)   p_kst 7.061644e-04   p_cons 9.772918e-01   p_joint 1.400822e-02

Joint ci ratio: 2.768130e-02	ci left: 1.327218e-02	ci right 1.364539e-02	k: 19783	n:1470000
Cons ci ratio: 4.928471e-04	ci left: 9.770497e-01	ci right 9.775321e-01	k: 1436619	n:1470000
KS ci ratio: 1.215110e-01	ci left: 6.644872e-04	ci right 7.511049e-04	k: 1039	n:1470000
TCEB3B   1470000 perm   1096 sec   (1341 perm/sec)   p_kst 7.068027e-04   p_cons 9.772918e-01   p_joint 1.345782e-02

Joint ci ratio: 2.702687e-02	ci left: 1.382542e-02	ci right 1.420486e-02	k: 20741	n:1480000
Cons ci ratio: 4.909916e-04	ci left: 9.770676e-01	ci right 9.775481e-01	k: 1446417	n:1480000
KS ci ratio: 1.209885e-01	ci left: 6.658941e-04	ci right 7.522953e-04	k: 1048	n:1480000
TCEB3B   1480000 perm   1109 sec   (1335 perm/sec)   p_kst 7.081081e-04   p_cons 9.773088e-01   p_joint 1.401419e-02

Joint ci ratio: 2.749640e-02	ci left: 1.327198e-02	ci right 1.364266e-02	k: 20050	n:1490000
Cons ci ratio: 4.892233e-04	ci left: 9.770791e-01	ci right 9.775579e-01	k: 1456206	n:1490000
KS ci ratio: 1.205298e-01	ci left: 6.666320e-04	ci right 7.527775e-04	k: 1056	n:1490000
TCEB3B   1490000 perm   1122 sec   (1328 perm/sec)   p_kst 7.087248e-04   p_cons 9.773195e-01   p_joint 1.345638e-02

Joint ci ratio: 2.740774e-02	ci left: 1.326958e-02	ci right 1.363897e-02	k: 20180	n:1500000
Cons ci ratio: 4.875473e-04	ci left: 9.770838e-01	ci right 9.775610e-01	k: 1465985	n:1500000
KS ci ratio: 1.203025e-01	ci left: 6.647741e-04	ci right 7.505060e-04	k: 1060	n:1500000
TCEB3B   1500000 perm   1135 sec   (1322 perm/sec)   p_kst 7.066667e-04   p_cons 9.773233e-01   p_joint 1.345333e-02

Joint ci ratio: 2.731993e-02	ci left: 1.326720e-02	ci right 1.363533e-02	k: 20310	n:1510000
Cons ci ratio: 4.858520e-04	ci left: 9.770918e-01	ci right 9.775673e-01	k: 1475769	n:1510000
KS ci ratio: 1.199638e-01	ci left: 6.642257e-04	ci right 7.496286e-04	k: 1066	n:1510000
TCEB3B   1510000 perm   1148 sec   (1315 perm/sec)   p_kst 7.059603e-04   p_cons 9.773305e-01   p_joint 1.345033e-02

Joint ci ratio: 2.723701e-02	ci left: 1.326094e-02	ci right 1.362776e-02	k: 20434	n:1520000
Cons ci ratio: 4.841670e-04	ci left: 9.771003e-01	ci right 9.775742e-01	k: 1485554	n:1520000
KS ci ratio: 1.195722e-01	ci left: 6.643231e-04	ci right 7.494400e-04	k: 1073	n:1520000
TCEB3B   1520000 perm   1162 sec   (1308 perm/sec)   p_kst 7.059211e-04   p_cons 9.773382e-01   p_joint 1.344342e-02

Joint ci ratio: 2.713612e-02	ci left: 1.327294e-02	ci right 1.363871e-02	k: 20586	n:1530000
Cons ci ratio: 4.824353e-04	ci left: 9.771147e-01	ci right 9.775868e-01	k: 1495348	n:1530000
KS ci ratio: 1.189096e-01	ci left: 6.675904e-04	ci right 7.526186e-04	k: 1085	n:1530000
TCEB3B   1530000 perm   1175 sec   (1302 perm/sec)   p_kst 7.091503e-04   p_cons 9.773516e-01   p_joint 1.345490e-02

Joint ci ratio: 2.705552e-02	ci left: 1.326608e-02	ci right 1.363056e-02	k: 20709	n:1540000
Cons ci ratio: 4.808136e-04	ci left: 9.771203e-01	ci right 9.775909e-01	k: 1505129	n:1540000
KS ci ratio: 1.187458e-01	ci left: 6.651455e-04	ci right 7.497375e-04	k: 1088	n:1540000
TCEB3B   1540000 perm   1188 sec   (1296 perm/sec)   p_kst 7.064935e-04   p_cons 9.773565e-01   p_joint 1.344740e-02

Joint ci ratio: 2.696645e-02	ci left: 1.326828e-02	ci right 1.363160e-02	k: 20846	n:1550000
Cons ci ratio: 4.791731e-04	ci left: 9.771291e-01	ci right 9.775981e-01	k: 1514915	n:1550000
KS ci ratio: 1.184742e-01	ci left: 6.639843e-04	ci right 7.482220e-04	k: 1093	n:1550000
TCEB3B   1550000 perm   1201 sec   (1290 perm/sec)   p_kst 7.051613e-04   p_cons 9.773645e-01   p_joint 1.344903e-02

Joint ci ratio: 2.687825e-02	ci left: 1.327046e-02	ci right 1.363263e-02	k: 20983	n:1560000
Cons ci ratio: 4.777431e-04	ci left: 9.771198e-01	ci right 9.775874e-01	k: 1524673	n:1560000
KS ci ratio: 1.182584e-01	ci left: 6.622161e-04	ci right 7.460657e-04	k: 1097	n:1560000
TCEB3B   1560000 perm   1214 sec   (1285 perm/sec)   p_kst 7.032051e-04   p_cons 9.773545e-01   p_joint 1.345064e-02

Joint ci ratio: 2.678128e-02	ci left: 1.328210e-02	ci right 1.364327e-02	k: 21135	n:1570000
Cons ci ratio: 4.763462e-04	ci left: 9.771087e-01	ci right 9.775749e-01	k: 1534428	n:1570000
KS ci ratio: 1.177234e-01	ci left: 6.641797e-04	ci right 7.478710e-04	k: 1107	n:1570000
TCEB3B   1570000 perm   1228 sec   (1279 perm/sec)   p_kst 7.050955e-04   p_cons 9.773427e-01   p_joint 1.346178e-02

Joint ci ratio: 2.669234e-02	ci left: 1.328668e-02	ci right 1.364675e-02	k: 21276	n:1580000
Cons ci ratio: 4.747374e-04	ci left: 9.771187e-01	ci right 9.775833e-01	k: 1544216	n:1580000
KS ci ratio: 1.175645e-01	ci left: 6.618188e-04	ci right 7.450922e-04	k: 1110	n:1580000
TCEB3B   1580000 perm   1241 sec   (1273 perm/sec)   p_kst 7.025316e-04   p_cons 9.773519e-01   p_joint 1.346582e-02

Joint ci ratio: 2.660680e-02	ci left: 1.328871e-02	ci right 1.364766e-02	k: 21413	n:1590000
Cons ci ratio: 4.734002e-04	ci left: 9.771046e-01	ci right 9.775679e-01	k: 1553966	n:1590000
KS ci ratio: 1.170388e-01	ci left: 6.637613e-04	ci right 7.468798e-04	k: 1120	n:1590000
TCEB3B   1590000 perm   1255 sec   (1267 perm/sec)   p_kst 7.044025e-04   p_cons 9.773371e-01   p_joint 1.346730e-02

Joint ci ratio: 2.652083e-02	ci left: 1.329195e-02	ci right 1.364981e-02	k: 21552	n:1600000
Cons ci ratio: 4.715480e-04	ci left: 9.771403e-01	ci right 9.776018e-01	k: 1563795	n:1600000
KS ci ratio: 1.165202e-01	ci left: 6.656802e-04	ci right 7.486443e-04	k: 1130	n:1600000
TCEB3B   1600000 perm   1269 sec   (1261 perm/sec)   p_kst 7.062500e-04   p_cons 9.773719e-01   p_joint 1.347000e-02

Joint ci ratio: 2.644001e-02	ci left: 1.329084e-02	ci right 1.364756e-02	k: 21684	n:1610000
Cons ci ratio: 4.700398e-04	ci left: 9.771449e-01	ci right 9.776049e-01	k: 1573575	n:1610000
KS ci ratio: 1.161102e-01	ci left: 6.663700e-04	ci right 7.491077e-04	k: 1138	n:1610000
TCEB3B   1610000 perm   1283 sec   (1255 perm/sec)   p_kst 7.068323e-04   p_cons 9.773758e-01   p_joint 1.346832e-02

Joint ci ratio: 2.635686e-02	ci left: 1.329280e-02	ci right 1.364845e-02	k: 21821	n:1620000
Cons ci ratio: 4.686702e-04	ci left: 9.771377e-01	ci right 9.775964e-01	k: 1583336	n:1620000
KS ci ratio: 1.158563e-01	ci left: 6.652534e-04	ci right 7.476596e-04	k: 1143	n:1620000
TCEB3B   1620000 perm   1297 sec   (1249 perm/sec)   p_kst 7.055556e-04   p_cons 9.773679e-01   p_joint 1.346975e-02

Joint ci ratio: 2.626843e-02	ci left: 1.330084e-02	ci right 1.365549e-02	k: 21968	n:1630000
Cons ci ratio: 4.672865e-04	ci left: 9.771331e-01	ci right 9.775904e-01	k: 1593101	n:1630000
KS ci ratio: 1.153531e-01	ci left: 6.671297e-04	ci right 7.493849e-04	k: 1153	n:1630000
TCEB3B   1630000 perm   1311 sec   (1244 perm/sec)   p_kst 7.073620e-04   p_cons 9.773626e-01   p_joint 1.347730e-02

Joint ci ratio: 2.617969e-02	ci left: 1.331000e-02	ci right 1.366367e-02	k: 22117	n:1640000
Cons ci ratio: 4.659086e-04	ci left: 9.771291e-01	ci right 9.775851e-01	k: 1602867	n:1640000
KS ci ratio: 1.151538e-01	ci left: 6.654305e-04	ci right 7.473249e-04	k: 1157	n:1640000
TCEB3B   1640000 perm   1325 sec   (1238 perm/sec)   p_kst 7.054878e-04   p_cons 9.773579e-01   p_joint 1.348598e-02

Joint ci ratio: 2.610313e-02	ci left: 1.330761e-02	ci right 1.366017e-02	k: 22247	n:1650000
Cons ci ratio: 4.644537e-04	ci left: 9.771337e-01	ci right 9.775882e-01	k: 1612647	n:1650000
KS ci ratio: 1.145126e-01	ci left: 6.690502e-04	ci right 7.509005e-04	k: 1170	n:1650000
TCEB3B   1650000 perm   1339 sec   (1232 perm/sec)   p_kst 7.090909e-04   p_cons 9.773618e-01   p_joint 1.348303e-02

Joint ci ratio: 2.603609e-02	ci left: 1.329626e-02	ci right 1.364760e-02	k: 22362	n:1660000
Cons ci ratio: 4.631007e-04	ci left: 9.771298e-01	ci right 9.775830e-01	k: 1622413	n:1660000
KS ci ratio: 1.142204e-01	ci left: 6.685308e-04	ci right 7.500949e-04	k: 1176	n:1660000
TCEB3B   1660000 perm   1354 sec   (1226 perm/sec)   p_kst 7.084337e-04   p_cons 9.773572e-01   p_joint 1.347108e-02

Joint ci ratio: 2.595142e-02	ci left: 1.330350e-02	ci right 1.365388e-02	k: 22508	n:1670000
Cons ci ratio: 4.614969e-04	ci left: 9.771512e-01	ci right 9.776028e-01	k: 1632221	n:1670000
KS ci ratio: 1.138342e-01	ci left: 6.691814e-04	ci right 7.505302e-04	k: 1184	n:1670000
TCEB3B   1670000 perm   1368 sec   (1221 perm/sec)   p_kst 7.089820e-04   p_cons 9.773778e-01   p_joint 1.347784e-02

Joint ci ratio: 2.587626e-02	ci left: 1.330179e-02	ci right 1.365108e-02	k: 22639	n:1680000
Cons ci ratio: 4.599961e-04	ci left: 9.771640e-01	ci right 9.776141e-01	k: 1642015	n:1680000
KS ci ratio: 1.134518e-01	ci left: 6.698248e-04	ci right 7.509600e-04	k: 1192	n:1680000
TCEB3B   1680000 perm   1383 sec   (1215 perm/sec)   p_kst 7.095238e-04   p_cons 9.773899e-01   p_joint 1.347560e-02

Joint ci ratio: 3.167733e-02	ci left: 8.837614e-03	ci right 9.122653e-03	k: 15175	n:1690000
Cons ci ratio: 4.586079e-04	ci left: 9.771671e-01	ci right 9.776159e-01	k: 1651793	n:1690000
KS ci ratio: 1.132149e-01	ci left: 6.687360e-04	ci right 7.495589e-04	k: 1197	n:1690000
TCEB3B   1690000 perm   1397 sec   (1210 perm/sec)   p_kst 7.082840e-04   p_cons 9.773923e-01   p_joint 8.979290e-03

Joint ci ratio: 2.571082e-02	ci left: 1.331595e-02	ci right 1.366335e-02	k: 22931	n:1700000
Cons ci ratio: 4.573053e-04	ci left: 9.771631e-01	ci right 9.776106e-01	k: 1661559	n:1700000
KS ci ratio: 1.130265e-01	ci left: 6.670886e-04	ci right 7.475692e-04	k: 1201	n:1700000
TCEB3B   1700000 perm   1412 sec   (1204 perm/sec)   p_kst 7.064706e-04   p_cons 9.773876e-01   p_joint 1.348882e-02

Joint ci ratio: 2.563096e-02	ci left: 1.332117e-02	ci right 1.366761e-02	k: 23074	n:1710000
Cons ci ratio: 4.559292e-04	ci left: 9.771673e-01	ci right 9.776135e-01	k: 1671339	n:1710000
KS ci ratio: 1.125127e-01	ci left: 6.694389e-04	ci right 7.498116e-04	k: 1212	n:1710000
TCEB3B   1710000 perm   1427 sec   (1199 perm/sec)   p_kst 7.087719e-04   p_cons 9.773912e-01   p_joint 1.349357e-02

Joint ci ratio: 3.138284e-02	ci left: 8.848438e-03	ci right 9.131126e-03	k: 15461	n:1720000
Cons ci ratio: 4.544996e-04	ci left: 9.771780e-01	ci right 9.776228e-01	k: 1681130	n:1720000
KS ci ratio: 1.119601e-01	ci left: 6.723277e-04	ci right 7.526246e-04	k: 1224	n:1720000
TCEB3B   1720000 perm   1442 sec   (1193 perm/sec)   p_kst 7.116279e-04   p_cons 9.774012e-01   p_joint 8.988953e-03

Joint ci ratio: 3.130307e-02	ci left: 8.842598e-03	ci right 9.124367e-03	k: 15540	n:1730000
Cons ci ratio: 4.533798e-04	ci left: 9.771594e-01	ci right 9.776031e-01	k: 1690871	n:1730000
KS ci ratio: 1.117324e-01	ci left: 6.712507e-04	ci right 7.512452e-04	k: 1229	n:1730000
TCEB3B   1730000 perm   1456 sec   (1188 perm/sec)   p_kst 7.104046e-04   p_cons 9.773821e-01   p_joint 8.982659e-03

Joint ci ratio: 3.122795e-02	ci left: 8.834544e-03	ci right 9.115370e-03	k: 15615	n:1740000
Cons ci ratio: 4.520976e-04	ci left: 9.771579e-01	ci right 9.776003e-01	k: 1700641	n:1740000
KS ci ratio: 1.115060e-01	ci left: 6.701863e-04	ci right 7.498815e-04	k: 1234	n:1740000
TCEB3B   1740000 perm   1471 sec   (1183 perm/sec)   p_kst 7.091954e-04   p_cons 9.773799e-01   p_joint 8.974138e-03

Joint ci ratio: 3.114334e-02	ci left: 8.832254e-03	ci right 9.112232e-03	k: 15700	n:1750000
Cons ci ratio: 4.508261e-04	ci left: 9.771563e-01	ci right 9.775975e-01	k: 1710411	n:1750000
KS ci ratio: 1.110572e-01	ci left: 6.719119e-04	ci right 7.514697e-04	k: 1244	n:1750000
TCEB3B   1750000 perm   1486 sec   (1178 perm/sec)   p_kst 7.108571e-04   p_cons 9.773777e-01   p_joint 8.971429e-03

Joint ci ratio: 3.105149e-02	ci left: 8.834501e-03	ci right 9.113710e-03	k: 15793	n:1760000
Cons ci ratio: 4.495942e-04	ci left: 9.771520e-01	ci right 9.775919e-01	k: 1720176	n:1760000
KS ci ratio: 1.106138e-01	ci left: 6.736186e-04	ci right 7.530392e-04	k: 1254	n:1760000
TCEB3B   1760000 perm   1501 sec   (1173 perm/sec)   p_kst 7.125000e-04   p_cons 9.773727e-01   p_joint 8.973295e-03

Joint ci ratio: 3.096929e-02	ci left: 8.831678e-03	ci right 9.110045e-03	k: 15877	n:1770000
Cons ci ratio: 4.483780e-04	ci left: 9.771471e-01	ci right 9.775858e-01	k: 1729940	n:1770000
KS ci ratio: 1.104819e-01	ci left: 6.714608e-04	ci right 7.505266e-04	k: 1257	n:1770000
TCEB3B   1770000 perm   1516 sec   (1168 perm/sec)   p_kst 7.101695e-04   p_cons 9.773672e-01   p_joint 8.970056e-03

Joint ci ratio: 2.512224e-02	ci left: 1.332428e-02	ci right 1.366382e-02	k: 24018	n:1780000
Cons ci ratio: 4.471149e-04	ci left: 9.771479e-01	ci right 9.775854e-01	k: 1739714	n:1780000
KS ci ratio: 1.101758e-01	ci left: 6.715126e-04	ci right 7.503512e-04	k: 1264	n:1780000
TCEB3B   1780000 perm   1531 sec   (1162 perm/sec)   p_kst 7.101124e-04   p_cons 9.773674e-01   p_joint 1.349326e-02

Joint ci ratio: 3.079523e-02	ci left: 8.832782e-03	ci right 9.109592e-03	k: 16057	n:1790000
Cons ci ratio: 4.457666e-04	ci left: 9.771582e-01	ci right 9.775944e-01	k: 1749505	n:1790000
KS ci ratio: 1.098723e-01	ci left: 6.715642e-04	ci right 7.501775e-04	k: 1271	n:1790000
TCEB3B   1790000 perm   1547 sec   (1157 perm/sec)   p_kst 7.100559e-04   p_cons 9.773771e-01   p_joint 8.970391e-03

Joint ci ratio: 3.070161e-02	ci left: 8.837737e-03	ci right 9.113846e-03	k: 16155	n:1800000
Cons ci ratio: 4.444583e-04	ci left: 9.771656e-01	ci right 9.776006e-01	k: 1759291	n:1800000
KS ci ratio: 1.095712e-01	ci left: 6.716154e-04	ci right 7.500054e-04	k: 1278	n:1800000
TCEB3B   1800000 perm   1562 sec   (1152 perm/sec)   p_kst 7.100000e-04   p_cons 9.773839e-01   p_joint 8.975000e-03

Joint ci ratio: 3.062121e-02	ci left: 8.835511e-03	ci right 9.110815e-03	k: 16240	n:1810000
Cons ci ratio: 4.431670e-04	ci left: 9.771724e-01	ci right 9.776061e-01	k: 1769076	n:1810000
KS ci ratio: 1.090606e-01	ci left: 6.743535e-04	ci right 7.526727e-04	k: 1290	n:1810000
TCEB3B   1810000 perm   1577 sec   (1148 perm/sec)   p_kst 7.127072e-04   p_cons 9.773901e-01   p_joint 8.972376e-03

Joint ci ratio: 3.054143e-02	ci left: 8.833310e-03	ci right 9.107816e-03	k: 16325	n:1820000
Cons ci ratio: 4.420077e-04	ci left: 9.771670e-01	ci right 9.775996e-01	k: 1778839	n:1820000
KS ci ratio: 1.086824e-01	ci left: 6.754587e-04	ci right 7.536167e-04	k: 1299	n:1820000
TCEB3B   1820000 perm   1593 sec   (1143 perm/sec)   p_kst 7.137363e-04   p_cons 9.773841e-01   p_joint 8.969780e-03

Joint ci ratio: 2.426992e-02	ci left: 1.388459e-02	ci right 1.422624e-02	k: 25720	n:1830000
Cons ci ratio: 4.408683e-04	ci left: 9.771606e-01	ci right 9.775920e-01	k: 1788600	n:1830000
KS ci ratio: 1.084325e-01	ci left: 6.749573e-04	ci right 7.528663e-04	k: 1305	n:1830000
TCEB3B   1830000 perm   1608 sec   (1138 perm/sec)   p_kst 7.131148e-04   p_cons 9.773770e-01   p_joint 1.405464e-02

Joint ci ratio: 3.039675e-02	ci left: 8.821432e-03	ci right 9.094247e-03	k: 16481	n:1840000
Cons ci ratio: 4.396890e-04	ci left: 9.771591e-01	ci right 9.775894e-01	k: 1798370	n:1840000
KS ci ratio: 1.081019e-01	ci left: 6.755191e-04	ci right 7.532401e-04	k: 1313	n:1840000
TCEB3B   1840000 perm   1624 sec   (1133 perm/sec)   p_kst 7.135870e-04   p_cons 9.773750e-01   p_joint 8.957065e-03

Joint ci ratio: 3.031871e-02	ci left: 8.819346e-03	ci right 9.091384e-03	k: 16566	n:1850000
Cons ci ratio: 4.385459e-04	ci left: 9.771549e-01	ci right 9.775841e-01	k: 1808135	n:1850000
KS ci ratio: 1.075709e-01	ci left: 6.787052e-04	ci right 7.563850e-04	k: 1326	n:1850000
TCEB3B   1850000 perm   1639 sec   (1129 perm/sec)   p_kst 7.167568e-04   p_cons 9.773703e-01   p_joint 8.954595e-03

Joint ci ratio: 2.408726e-02	ci left: 1.387012e-02	ci right 1.420881e-02	k: 26112	n:1860000
Cons ci ratio: 4.373266e-04	ci left: 9.771595e-01	ci right 9.775874e-01	k: 1817916	n:1860000
KS ci ratio: 1.072079e-01	ci left: 6.797651e-04	ci right 7.572870e-04	k: 1335	n:1860000
TCEB3B   1860000 perm   1655 sec   (1124 perm/sec)   p_kst 7.177419e-04   p_cons 9.773742e-01   p_joint 1.403871e-02

Joint ci ratio: 2.402109e-02	ci left: 1.387249e-02	ci right 1.421030e-02	k: 26256	n:1870000
Cons ci ratio: 4.362440e-04	ci left: 9.771511e-01	ci right 9.775779e-01	k: 1827673	n:1870000
KS ci ratio: 1.070478e-01	ci left: 6.782116e-04	ci right 7.554337e-04	k: 1339	n:1870000
TCEB3B   1870000 perm   1671 sec   (1119 perm/sec)   p_kst 7.160428e-04   p_cons 9.773652e-01   p_joint 1.404064e-02

Joint ci ratio: 2.396146e-02	ci left: 1.386796e-02	ci right 1.420481e-02	k: 26387	n:1880000
Cons ci ratio: 4.350437e-04	ci left: 9.771556e-01	ci right 9.775813e-01	k: 1837454	n:1880000
KS ci ratio: 1.067693e-01	ci left: 6.782280e-04	ci right 7.552384e-04	k: 1346	n:1880000
TCEB3B   1880000 perm   1687 sec   (1114 perm/sec)   p_kst 7.159574e-04   p_cons 9.773691e-01   p_joint 1.403564e-02

Joint ci ratio: 2.389495e-02	ci left: 1.387190e-02	ci right 1.420790e-02	k: 26534	n:1890000
Cons ci ratio: 4.339727e-04	ci left: 9.771478e-01	ci right 9.775724e-01	k: 1847212	n:1890000
KS ci ratio: 1.066507e-01	ci left: 6.761844e-04	ci right 7.528721e-04	k: 1349	n:1890000
TCEB3B   1890000 perm   1703 sec   (1110 perm/sec)   p_kst 7.137566e-04   p_cons 9.773608e-01   p_joint 1.403915e-02

Joint ci ratio: 2.381904e-02	ci left: 1.388731e-02	ci right 1.422260e-02	k: 26703	n:1900000
Cons ci ratio: 4.328528e-04	ci left: 9.771459e-01	ci right 9.775695e-01	k: 1856981	n:1900000
KS ci ratio: 1.064932e-01	ci left: 6.746746e-04	ci right 7.510710e-04	k: 1353	n:1900000
TCEB3B   1900000 perm   1719 sec   (1105 perm/sec)   p_kst 7.121053e-04   p_cons 9.773584e-01   p_joint 1.405421e-02

Joint ci ratio: 2.376044e-02	ci left: 1.388330e-02	ci right 1.421765e-02	k: 26835	n:1910000
Cons ci ratio: 4.318080e-04	ci left: 9.771372e-01	ci right 9.775598e-01	k: 1866737	n:1910000
KS ci ratio: 1.061799e-01	ci left: 6.752194e-04	ci right 7.514385e-04	k: 1361	n:1910000
TCEB3B   1910000 perm   1735 sec   (1101 perm/sec)   p_kst 7.125654e-04   p_cons 9.773492e-01   p_joint 1.404974e-02

Joint ci ratio: 2.370227e-02	ci left: 1.387933e-02	ci right 1.421276e-02	k: 26967	n:1920000
Cons ci ratio: 4.305680e-04	ci left: 9.771496e-01	ci right 9.775709e-01	k: 1876533	n:1920000
KS ci ratio: 1.061022e-01	ci left: 6.727166e-04	ci right 7.485941e-04	k: 1363	n:1920000
TCEB3B   1920000 perm   1751 sec   (1096 perm/sec)   p_kst 7.098958e-04   p_cons 9.773609e-01   p_joint 1.404531e-02

Joint ci ratio: 2.364807e-02	ci left: 1.387129e-02	ci right 1.420375e-02	k: 27091	n:1930000
Cons ci ratio: 4.294541e-04	ci left: 9.771498e-01	ci right 9.775700e-01	k: 1886306	n:1930000
KS ci ratio: 1.058310e-01	ci left: 6.727618e-04	ci right 7.484384e-04	k: 1370	n:1930000
TCEB3B   1930000 perm   1768 sec   (1092 perm/sec)   p_kst 7.098446e-04   p_cons 9.773606e-01   p_joint 1.403679e-02

Joint ci ratio: 2.408265e-02	ci left: 1.331092e-02	ci right 1.363590e-02	k: 26137	n:1940000
Cons ci ratio: 4.283688e-04	ci left: 9.771479e-01	ci right 9.775671e-01	k: 1896075	n:1940000
KS ci ratio: 1.056386e-01	ci left: 6.718031e-04	ci right 7.472260e-04	k: 1375	n:1940000
TCEB3B   1940000 perm   1784 sec   (1087 perm/sec)   p_kst 7.087629e-04   p_cons 9.773582e-01   p_joint 1.347268e-02

Joint ci ratio: 2.807458e-02	ci left: 9.759985e-03	ci right 1.003840e-02	k: 19302	n:1950000
Cons ci ratio: 4.587226e-04	ci left: 9.737674e-01	ci right 9.742147e-01	k: 1899284	n:1950000
KS ci ratio: 1.052948e-01	ci left: 6.728517e-04	ci right 7.481311e-04	k: 1384	n:1950000
TCEB3B   1950000 perm   1801 sec   (1083 perm/sec)   p_kst 7.097436e-04   p_cons 9.739918e-01   p_joint 9.898462e-03

Joint ci ratio: 2.800141e-02	ci left: 9.761358e-03	ci right 1.003907e-02	k: 19403	n:1960000
Cons ci ratio: 4.577117e-04	ci left: 9.737501e-01	ci right 9.741964e-01	k: 1908989	n:1960000
KS ci ratio: 1.050675e-01	ci left: 6.723994e-04	ci right 7.474559e-04	k: 1390	n:1960000
TCEB3B   1960000 perm   1818 sec   (1078 perm/sec)   p_kst 7.091837e-04   p_cons 9.739740e-01   p_joint 9.899490e-03

Joint ci ratio: 2.792808e-02	ci left: 9.763223e-03	ci right 1.004025e-02	k: 19505	n:1970000
Cons ci ratio: 4.564559e-04	ci left: 9.737610e-01	ci right 9.742061e-01	k: 1918749	n:1970000
KS ci ratio: 1.047666e-01	ci left: 6.729406e-04	ci right 7.478291e-04	k: 1398	n:1970000
TCEB3B   1970000 perm   1834 sec   (1074 perm/sec)   p_kst 7.096447e-04   p_cons 9.739843e-01   p_joint 9.901015e-03

Joint ci ratio: 2.786034e-02	ci left: 9.761559e-03	ci right 1.003786e-02	k: 19600	n:1980000
Cons ci ratio: 4.552511e-04	ci left: 9.737673e-01	ci right 9.742112e-01	k: 1928500	n:1980000
KS ci ratio: 1.046172e-01	ci left: 6.715092e-04	ci right 7.461253e-04	k: 1402	n:1980000
TCEB3B   1980000 perm   1851 sec   (1070 perm/sec)   p_kst 7.080808e-04   p_cons 9.739899e-01   p_joint 9.898990e-03

Joint ci ratio: 2.779096e-02	ci left: 9.761409e-03	ci right 1.003700e-02	k: 19698	n:1990000
Cons ci ratio: 4.541189e-04	ci left: 9.737664e-01	ci right 9.742092e-01	k: 1938237	n:1990000
KS ci ratio: 1.044314e-01	ci left: 6.705816e-04	ci right 7.449542e-04	k: 1407	n:1990000
TCEB3B   1990000 perm   1868 sec   (1065 perm/sec)   p_kst 7.070352e-04   p_cons 9.739884e-01   p_joint 9.898492e-03

Joint ci ratio: 2.773271e-02	ci left: 9.753814e-03	ci right 1.002861e-02	k: 19781	n:2000000
Cons ci ratio: 4.529190e-04	ci left: 9.737740e-01	ci right 9.742156e-01	k: 1947991	n:2000000
KS ci ratio: 1.042834e-01	ci left: 6.691765e-04	ci right 7.432816e-04	k: 1411	n:2000000
TCEB3B   2000000 perm   1885 sec   (1061 perm/sec)   p_kst 7.055000e-04   p_cons 9.739955e-01   p_joint 9.890500e-03

Joint ci ratio: 2.765655e-02	ci left: 9.759141e-03	ci right 1.003332e-02	k: 19890	n:2010000
Cons ci ratio: 4.517641e-04	ci left: 9.737776e-01	ci right 9.742181e-01	k: 1957737	n:2010000
KS ci ratio: 1.040259e-01	ci left: 6.692391e-04	ci right 7.431570e-04	k: 1418	n:2010000
TCEB3B   2010000 perm   1902 sec   (1057 perm/sec)   p_kst 7.054726e-04   p_cons 9.739985e-01   p_joint 9.895522e-03

Joint ci ratio: 2.802891e-02	ci left: 9.455666e-03	ci right 9.724951e-03	k: 19371	n:2020000
Cons ci ratio: 4.506797e-04	ci left: 9.737742e-01	ci right 9.742136e-01	k: 1967469	n:2020000
KS ci ratio: 1.037339e-01	ci left: 6.697836e-04	ci right 7.435412e-04	k: 1426	n:2020000
TCEB3B   2020000 perm   1919 sec   (1053 perm/sec)   p_kst 7.059406e-04   p_cons 9.739946e-01   p_joint 9.589604e-03

Joint ci ratio: 2.795392e-02	ci left: 9.459959e-03	ci right 9.728635e-03	k: 19475	n:2030000
Cons ci ratio: 4.494849e-04	ci left: 9.737841e-01	ci right 9.742224e-01	k: 1977228	n:2030000
KS ci ratio: 1.034082e-01	ci left: 6.708028e-04	ci right 7.444267e-04	k: 1435	n:2030000
TCEB3B   2030000 perm   1935 sec   (1049 perm/sec)   p_kst 7.068966e-04   p_cons 9.740039e-01   p_joint 9.593596e-03

Joint ci ratio: 2.789463e-02	ci left: 9.453989e-03	ci right 9.721916e-03	k: 19558	n:2040000
Cons ci ratio: 4.483386e-04	ci left: 9.737896e-01	ci right 9.742267e-01	k: 1986978	n:2040000
KS ci ratio: 1.030500e-01	ci left: 6.722900e-04	ci right 7.458060e-04	k: 1445	n:2040000
TCEB3B   2040000 perm   1953 sec   (1045 perm/sec)   p_kst 7.083333e-04   p_cons 9.740088e-01   p_joint 9.587255e-03

Joint ci ratio: 2.782285e-02	ci left: 9.456797e-03	ci right 9.724103e-03	k: 19659	n:2050000
Cons ci ratio: 4.471968e-04	ci left: 9.737954e-01	ci right 9.742315e-01	k: 1996729	n:2050000
KS ci ratio: 1.027661e-01	ci left: 6.728125e-04	ci right 7.461708e-04	k: 1453	n:2050000
TCEB3B   2050000 perm   1970 sec   (1041 perm/sec)   p_kst 7.087805e-04   p_cons 9.740141e-01   p_joint 9.589756e-03

Joint ci ratio: 2.775304e-02	ci left: 9.458615e-03	ci right 9.725291e-03	k: 19758	n:2060000
Cons ci ratio: 4.461020e-04	ci left: 9.737969e-01	ci right 9.742319e-01	k: 2006471	n:2060000
KS ci ratio: 1.024494e-01	ci left: 6.738033e-04	ci right 7.470296e-04	k: 1462	n:2060000
TCEB3B   2060000 perm   1987 sec   (1037 perm/sec)   p_kst 7.097087e-04   p_cons 9.740150e-01   p_joint 9.591262e-03

Joint ci ratio: 2.768164e-02	ci left: 9.461855e-03	ci right 9.727925e-03	k: 19860	n:2070000
Cons ci ratio: 4.450535e-04	ci left: 9.737940e-01	ci right 9.742279e-01	k: 2016204	n:2070000
KS ci ratio: 1.022052e-01	ci left: 6.738433e-04	ci right 7.468889e-04	k: 1469	n:2070000
TCEB3B   2070000 perm   2004 sec   (1033 perm/sec)   p_kst 7.096618e-04   p_cons 9.740116e-01   p_joint 9.594203e-03

Joint ci ratio: 2.760312e-02	ci left: 9.470317e-03	ci right 9.735858e-03	k: 19973	n:2080000
Cons ci ratio: 4.439660e-04	ci left: 9.737964e-01	ci right 9.742293e-01	k: 2025948	n:2080000
KS ci ratio: 1.019973e-01	ci left: 6.734146e-04	ci right 7.462563e-04	k: 1475	n:2080000
TCEB3B   2080000 perm   2022 sec   (1029 perm/sec)   p_kst 7.091346e-04   p_cons 9.740135e-01   p_joint 9.602404e-03

Joint ci ratio: 2.753494e-02	ci left: 9.472047e-03	ci right 9.736970e-03	k: 20072	n:2090000
Cons ci ratio: 4.429074e-04	ci left: 9.737963e-01	ci right 9.742282e-01	k: 2035687	n:2090000
KS ci ratio: 1.017563e-01	ci left: 6.734565e-04	ci right 7.461203e-04	k: 1482	n:2090000
TCEB3B   2090000 perm   2040 sec   (1024 perm/sec)   p_kst 7.090909e-04   p_cons 9.740129e-01   p_joint 9.603828e-03

Joint ci ratio: 2.746659e-02	ci left: 9.474234e-03	ci right 9.738550e-03	k: 20172	n:2100000
Cons ci ratio: 4.418521e-04	ci left: 9.737968e-01	ci right 9.742276e-01	k: 2045427	n:2100000
KS ci ratio: 1.014149e-01	ci left: 6.748905e-04	ci right 7.474502e-04	k: 1492	n:2100000
TCEB3B   2100000 perm   2057 sec   (1021 perm/sec)   p_kst 7.104762e-04   p_cons 9.740129e-01   p_joint 9.605714e-03

Joint ci ratio: 2.740556e-02	ci left: 9.471693e-03	ci right 9.735342e-03	k: 20262	n:2110000
Cons ci ratio: 4.408084e-04	ci left: 9.737968e-01	ci right 9.742266e-01	k: 2055166	n:2110000
KS ci ratio: 1.011442e-01	ci left: 6.753874e-04	ci right 7.477952e-04	k: 1500	n:2110000
TCEB3B   2110000 perm   2075 sec   (1017 perm/sec)   p_kst 7.109005e-04   p_cons 9.740123e-01   p_joint 9.602844e-03

Joint ci ratio: 2.734087e-02	ci left: 9.471989e-03	ci right 9.735014e-03	k: 20358	n:2120000
Cons ci ratio: 4.397476e-04	ci left: 9.737996e-01	ci right 9.742284e-01	k: 2064911	n:2120000
KS ci ratio: 1.009762e-01	ci left: 6.745005e-04	ci right 7.466860e-04	k: 1505	n:2120000
TCEB3B   2120000 perm   2093 sec   (1013 perm/sec)   p_kst 7.099057e-04   p_cons 9.740146e-01   p_joint 9.602830e-03

Joint ci ratio: 2.728809e-02	ci left: 9.464355e-03	ci right 9.726653e-03	k: 20437	n:2130000
Cons ci ratio: 4.386780e-04	ci left: 9.738043e-01	ci right 9.742320e-01	k: 2074660	n:2130000
KS ci ratio: 1.007757e-01	ci left: 6.740796e-04	ci right 7.460684e-04	k: 1511	n:2130000
TCEB3B   2130000 perm   2111 sec   (1009 perm/sec)   p_kst 7.093897e-04   p_cons 9.740188e-01   p_joint 9.594836e-03

Joint ci ratio: 2.721620e-02	ci left: 9.470253e-03	ci right 9.732012e-03	k: 20545	n:2140000
Cons ci ratio: 4.377536e-04	ci left: 9.737930e-01	ci right 9.742198e-01	k: 2084375	n:2140000
KS ci ratio: 1.003781e-01	ci left: 6.763962e-04	ci right 7.483305e-04	k: 1523	n:2140000
TCEB3B   2140000 perm   2129 sec   (1005 perm/sec)   p_kst 7.116822e-04   p_cons 9.740070e-01   p_joint 9.600467e-03

Joint ci ratio: 2.715084e-02	ci left: 9.471939e-03	ci right 9.733106e-03	k: 20644	n:2150000
Cons ci ratio: 4.368229e-04	ci left: 9.737831e-01	ci right 9.742091e-01	k: 2094093	n:2150000
KS ci ratio: 1.001483e-01	ci left: 6.764244e-04	ci right 7.481873e-04	k: 1530	n:2150000
TCEB3B   2150000 perm   2146 sec   (1002 perm/sec)   p_kst 7.116279e-04   p_cons 9.739967e-01   p_joint 9.601860e-03

Joint ci ratio: 2.709585e-02	ci left: 9.466712e-03	ci right 9.727198e-03	k: 20728	n:2160000
Cons ci ratio: 4.358981e-04	ci left: 9.737734e-01	ci right 9.741984e-01	k: 2103811	n:2160000
KS ci ratio: 9.985521e-02	ci left: 6.773552e-04	ci right 7.489943e-04	k: 1539	n:2160000
TCEB3B   2160000 perm   2164 sec   (998 perm/sec)   p_kst 7.125000e-04   p_cons 9.739866e-01   p_joint 9.596296e-03

Outputting figure to mutsig2_images.part000000000172/TCEB3B.2_2266_2160000_0.0007125_0.97399_0.0095963.png
                gene_name: TCEB3B
               theta_stop: 0.100 
                    nperm: 2160000 
                     p_ks: 0.00071 
        ci_ks_bounds_left: 0.00068 
       ci_ks_bounds_right: 0.00075 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.0096 
     ci_joint_bounds_left: 0.0095 
    ci_joint_bounds_right: 0.0097 

Current progress: 75 percent done.
TCERG1L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.460163e-02	ci left: 8.716295e-01	ci right 8.845493e-01	k: 8782	n:10000
Cons ci ratio: 1.471055e-02	ci left: 8.699939e-01	ci right 8.829859e-01	k: 8766	n:10000
KS ci ratio: 5.939737e-02	ci left: 2.942987e-01	ci right 3.124160e-01	k: 3033	n:10000
TCERG1L   10000 perm   2 sec   (6433 perm/sec)   p_kst 3.033000e-01   p_cons 8.766000e-01   p_joint 8.782000e-01

Outputting figure to mutsig2_images.part000000000172/TCERG1L.2_1809_10000_0.3033_0.8766_0.8782.png
                gene_name: TCERG1L
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.88 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.87 
    ci_joint_bounds_right: 0.88 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000172
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 172 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1424>
Subject: Job 4398458: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1424>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000173> was used as the working directory.
Started at Wed Oct 24 16:17:30 2012
Results reported at Wed Oct 24 16:20:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000173.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000173.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 173  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000173.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    235.48 sec.
    Max Memory :      1241 MB
    Max Swap   :      3911 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
173
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 173
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 173: processing genes 15431 - 15520
Calculating significance of each gene.
Using projection method.
15431	TCF7L2	1
15432	TCFL5	1
15433	TCHH	7.128278e-01
15434	TCHHL1	1
15435	TCHP	1.634232e-01
15436	TCIRG1	1.759108e-01
15437	TCL1A	1
15438	TCL1B	1.873622e-02
15439	TCN1	1
15440	TCN2	1
15441	TCOF1	1
15442	TCP1	2.077912e-01
15443	TCP10	1
15444	TCP10L	1
15445	TCP11	1
15446	TCP11L1	2.007207e-01
15447	TCP11L2	1
15448	TCTA	1
15449	TCTE1	1.074168e-01
15450	TCTE3	1
15451	TCTEX1D1	1
15452	TCTEX1D2	1
15453	TCTN1	1
15454	TCTN2	3.180265e-01
15455	TCTN3	1
15456	TDG	1.573686e-01
15457	TDGF1	3.697941e-03
15458	TDO2	1
15459	TDP1	1
15460	TDP2	1
15461	TDRD1	3.162462e-01
15462	TDRD10	1
15463	TDRD3	1
15464	TDRD5	1
15465	TDRD6	1.051252e-01
15466	TDRD7	1
15467	TDRD9	1
15468	TDRKH	1.586647e-01
15469	TEAD1	1.373487e-01
15470	TEAD2	4.357646e-02
15471	TEAD3	1
15472	TEAD4	1
15473	TEC	1
15474	TECPR1	1
15475	TECPR2	3.357901e-01
15476	TECR	1
15477	TECRL	1
15478	TECTA	6.880789e-01
15479	TECTB	1
15480	TEDDM1	1
15481	TEF	1
15482	TEK	2.799703e-01
15483	TEKT1	1
15484	TEKT2	2.186034e-01
15485	TEKT3	1
15486	TEKT4	1
15487	TEKT5	1.494853e-01
15488	TELO2	1
15489	TENC1	2.652914e-01
15490	TEP1	6.259665e-01
15491	TEPP	1
15492	TERF1	1
15493	TERF2	1
15494	TERF2IP	1
15495	TERT	1
15496	TES	1
15497	TESC	1
15498	TESK1	1.086332e-01
15499	TESK2	1.515056e-01
15500	TET1	1
15501	TET2	1
15502	TET3	3.202368e-01
15503	TEX10	1.517080e-01
15504	TEX101	1
15505	TEX11	1
15506	TEX12	1
15507	TEX13A	1
15508	TEX13B	1
15509	TEX14	1
15510	TEX15	6.120933e-02
15511	TEX19	1
15512	TEX2	2.052786e-01
15513	TEX261	1
15514	TEX264	1
15515	TEX9	1.333008e-01
15516	TF	1
15517	TFAM	1
15518	TFAP2A	1.129177e-01
15519	TFAP2B	1
15520	TFAP2C	1
Done

Running MutSig 2:
Scatter job 173: processing genes 15431 - 15520
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TEX15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.237715e-02	ci left: 2.185242e-01	ci right 2.350353e-01	k: 2267	n:10000
Cons ci ratio: 1.226322e-01	ci left: 8.698787e-02	ci right 9.845066e-02	k: 926	n:10000
KS ci ratio: 5.157110e-02	ci left: 3.566483e-01	ci right 3.756298e-01	k: 3661	n:10000
TEX15   10000 perm   3 sec   (3359 perm/sec)   p_kst 3.661000e-01   p_cons 9.260000e-02   p_joint 2.267000e-01

Joint ci ratio: 5.360787e-02	ci left: 2.052636e-01	ci right 2.166206e-01	k: 4218	n:20000
Cons ci ratio: 8.765693e-02	ci left: 8.690165e-02	ci right 9.491774e-02	k: 1817	n:20000
KS ci ratio: 3.586884e-02	ci left: 3.671384e-01	ci right 3.805983e-01	k: 7477	n:20000
TEX15   20000 perm   10 sec   (1944 perm/sec)   p_kst 3.738500e-01   p_cons 9.085000e-02   p_joint 2.109000e-01

Outputting figure to mutsig2_images.part000000000173/TEX15.7_8386_20000_0.37385_0.09085_0.2109.png
                gene_name: TEX15
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.091 
      ci_cons_bounds_left: 0.087 
     ci_cons_bounds_right: 0.095 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 25 percent done.
TDRD6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.680584e-02	ci left: 5.215616e-01	ci right 5.412201e-01	k: 5314	n:10000
Cons ci ratio: 4.332111e-02	ci left: 4.403148e-01	ci right 4.599142e-01	k: 4501	n:10000
KS ci ratio: 4.502334e-02	ci left: 4.213649e-01	ci right 4.408752e-01	k: 4311	n:10000
TDRD6   10000 perm   2 sec   (4073 perm/sec)   p_kst 4.311000e-01   p_cons 4.501000e-01   p_joint 5.314000e-01

Outputting figure to mutsig2_images.part000000000173/TDRD6.3_6307_10000_0.4311_0.4501_0.5314.png
                gene_name: TDRD6
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.54 

Current progress: 50 percent done.
TDGF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.089172e-02	ci left: 2.839917e-01	ci right 3.019291e-01	k: 2929	n:10000
Cons ci ratio: 1.422220e-01	ci left: 6.555836e-02	ci right 7.569349e-02	k: 705	n:10000
KS ci ratio: 3.362151e-02	ci left: 5.663433e-01	ci right 5.858123e-01	k: 5761	n:10000
TDGF1   10000 perm   1 sec   (7495 perm/sec)   p_kst 5.761000e-01   p_cons 7.050000e-02   p_joint 2.929000e-01

Joint ci ratio: 4.287597e-02	ci left: 2.883868e-01	ci right 3.010730e-01	k: 5894	n:20000
Cons ci ratio: 1.000357e-01	ci left: 6.772239e-02	ci right 7.490285e-02	k: 1425	n:20000
KS ci ratio: 2.381437e-02	ci left: 5.684140e-01	ci right 5.821641e-01	k: 11506	n:20000
TDGF1   20000 perm   3 sec   (6451 perm/sec)   p_kst 5.753000e-01   p_cons 7.125000e-02   p_joint 2.947000e-01

Joint ci ratio: 3.516171e-02	ci left: 2.877538e-01	ci right 2.980863e-01	k: 8787	n:30000
Cons ci ratio: 8.074826e-02	ci left: 6.988485e-02	ci right 7.579819e-02	k: 2184	n:30000
KS ci ratio: 1.948057e-02	ci left: 5.687814e-01	ci right 5.800042e-01	k: 17232	n:30000
TDGF1   30000 perm   5 sec   (6042 perm/sec)   p_kst 5.744000e-01   p_cons 7.280000e-02   p_joint 2.929000e-01

Outputting figure to mutsig2_images.part000000000173/TDGF1.2_591_30000_0.5744_0.0728_0.2929.png
                gene_name: TDGF1
               theta_stop: 0.081 
                    nperm: 30000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.073 
      ci_cons_bounds_left: 0.070 
     ci_cons_bounds_right: 0.076 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.30 

Current progress: 75 percent done.
TDRKH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.107859e-02	ci left: 9.207974e-01	ci right 9.311528e-01	k: 9261	n:10000
KS ci ratio: 2.729774e-02	ci left: 6.641089e-01	ci right 6.825900e-01	k: 6734	n:10000
TDRKH   10000 perm   2 sec   (6229 perm/sec)   p_kst 6.734000e-01   p_cons 9.261000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000173/TDRKH.2_1734_10000_0.6734_0.9261_1.png
                gene_name: TDRKH
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000173
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 173 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4398462: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000174> was used as the working directory.
Started at Wed Oct 24 16:17:35 2012
Results reported at Wed Oct 24 16:19:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000174.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000174.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 174  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000174.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    163.05 sec.
    Max Memory :      1506 MB
    Max Swap   :      4043 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
174
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 174
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 174: processing genes 15521 - 15610
Calculating significance of each gene.
Using projection method.
15521	TFAP2D	1
15522	TFAP2E	1
15523	TFAP4	1
15524	TFB1M	1
15525	TFB2M	1
15526	TFCP2	1.568346e-01
15527	TFCP2L1	9.755909e-02
15528	TFDP1	1
15529	TFDP2	1
15530	TFDP3	1
15531	TFE3	1
15532	TFEB	1
15533	TFEC	1
15534	TFF1	1
15535	TFF2	1
15536	TFF3	4.741640e-02
15537	TFG	1
15538	TFIP11	1
15539	TFPI	1
15540	TFPI2	1
15541	TFPT	1
15542	TFR2	1
15543	TFRC	1
15544	TG	2.825321e-01
15545	TGDS	1
15546	TGFA	1
15547	TGFB1	1
15548	TGFB1I1	1
15549	TGFB2	1
15550	TGFB3	9.395904e-03
15551	TGFBI	1
15552	TGFBR1	1
15553	TGFBR2	1
15554	TGFBR3	1.555898e-01
15555	TGFBRAP1	1
15556	TGIF1	2.095648e-01
15557	TGIF2	1
15558	TGIF2LX	1
15559	TGM1	1
15560	TGM2	1
15561	TGM3	1
15562	TGM4	1.536070e-01
15563	TGM5	1.966222e-01
15564	TGM6	9.467678e-02
15565	TGM7	1.120918e-01
15566	TGOLN2	1
15567	TGS1	1
15568	TH	1
15569	TH1L	9.012793e-02
15570	THADA	1
15571	THAP1	1
15572	THAP10	1
15573	THAP11	3.001934e-02
15574	THAP2	1
15575	THAP3	5.079646e-02
15576	THAP4	1
15577	THAP5	6.839275e-02
15578	THAP6	1
15579	THAP7	1
15580	THAP8	1
15581	THAP9	1
15582	THBD	1
15583	THBS1	1
15584	THBS2	1
15585	THBS3	2.361917e-01
15586	THBS4	1
15587	THEG	2.071200e-01
15588	THEM4	1
15589	THEM5	1
15590	THEMIS	3.044249e-01
15591	THG1L	1
15592	THNSL1	3.187420e-01
15593	THNSL2	1
15594	THOC1	2.466579e-01
15595	THOC2	3.424181e-01
15596	THOC3	1
15597	THOC4	1
15598	THOC5	1
15599	THOC6	1
15600	THOC7	1
15601	THOP1	1
15602	THPO	1
15603	THRA	7.090072e-02
15604	THRAP3	7.653579e-02
15605	THRB	1
15606	THRSP	1
15607	THSD1	1.298542e-02
15608	THSD4	3.297226e-01
15609	THSD7A	5.555952e-01
15610	THSD7B	1
Done

Running MutSig 2:
Scatter job 174: processing genes 15521 - 15610
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TG
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.787669e-02	ci left: 6.547462e-01	ci right 6.733581e-01	k: 6641	n:10000
Cons ci ratio: 1.668181e-02	ci left: 8.394879e-01	ci right 8.537096e-01	k: 8467	n:10000
KS ci ratio: 8.676772e-02	ci left: 1.620951e-01	ci right 1.768979e-01	k: 1694	n:10000
TG   10000 perm   3 sec   (3459 perm/sec)   p_kst 1.694000e-01   p_cons 8.467000e-01   p_joint 6.641000e-01

Outputting figure to mutsig2_images.part000000000174/TG.2_8499_10000_0.1694_0.8467_0.6641.png
                gene_name: TG
               theta_stop: 0.087 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 25 percent done.
TGFB3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.512284e-03	ci left: 9.778092e-01	ci right 9.833058e-01	k: 9807	n:10000
Cons ci ratio: 2.640853e-02	ci left: 6.786140e-01	ci right 6.968765e-01	k: 6878	n:10000
KS ci ratio: 4.185486e-02	ci left: 4.573820e-01	ci right 4.770371e-01	k: 4672	n:10000
TGFB3   10000 perm   1 sec   (6868 perm/sec)   p_kst 4.672000e-01   p_cons 6.878000e-01   p_joint 9.807000e-01

Outputting figure to mutsig2_images.part000000000174/TGFB3.2_1267_10000_0.4672_0.6878_0.9807.png
                gene_name: TGFB3
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 50 percent done.
THRAP3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.308130e-03	ci left: 9.421155e-01	ci right 9.510221e-01	k: 9467	n:10000
Cons ci ratio: 2.181098e-02	ci left: 7.551466e-01	ci right 7.718996e-01	k: 7636	n:10000
KS ci ratio: 1.152409e-01	ci left: 9.769325e-02	ci right 1.097387e-01	k: 1036	n:10000
THRAP3   10000 perm   2 sec   (6050 perm/sec)   p_kst 1.036000e-01   p_cons 7.636000e-01   p_joint 9.467000e-01

Joint ci ratio: 1.212274e-02	ci left: 8.342879e-01	ci right 8.445133e-01	k: 16789	n:20000
Cons ci ratio: 1.537360e-02	ci left: 7.588084e-01	ci right 7.706146e-01	k: 15295	n:20000
KS ci ratio: 8.155502e-02	ci left: 9.931124e-02	ci right 1.078044e-01	k: 2070	n:20000
THRAP3   20000 perm   4 sec   (5396 perm/sec)   p_kst 1.035000e-01   p_cons 7.647500e-01   p_joint 8.394500e-01

Outputting figure to mutsig2_images.part000000000174/THRAP3.2_2908_20000_0.1035_0.76475_0.83945.png
                gene_name: THRAP3
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.099 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.84 

Current progress: 75 percent done.
THSD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.437178e-02	ci left: 7.122978e-01	ci right 7.299732e-01	k: 7212	n:10000
KS ci ratio: 9.019158e-03	ci left: 9.453375e-01	ci right 9.539982e-01	k: 9498	n:10000
THSD1   10000 perm   2 sec   (5930 perm/sec)   p_kst 9.498000e-01   p_cons 7.212000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000174/THSD1.2_2575_10000_0.9498_0.7212_1.png
                gene_name: THSD1
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000174
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 174 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1727>
Subject: Job 4398467: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000175> was used as the working directory.
Started at Wed Oct 24 16:17:35 2012
Results reported at Wed Oct 24 16:19:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000175.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000175.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 175  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000175.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     94.06 sec.
    Max Memory :      1395 MB
    Max Swap   :      3920 MB

    Max Processes  :         7
    Max Threads    :        71

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
175
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 175
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 175: processing genes 15611 - 15699
Calculating significance of each gene.
Using projection method.
15611	THTPA	1
15612	THUMPD1	1
15613	THUMPD2	1
15614	THUMPD3	1
15615	THY1	6.038498e-03
15616	THYN1	1
15617	TIA1	1
15618	TIAF1	1
15619	TIAL1	1
15620	TIAM1	1
15621	TIAM2	1
15622	TICAM1	1
15623	TIE1	1.770727e-03
15624	TIFA	1
15625	TIFAB	1
15626	TIGD2	2.363516e-01
15627	TIGD3	1
15628	TIGD4	1.476037e-01
15629	TIGD5	1
15630	TIGD6	1
15631	TIGD7	2.107484e-01
15632	TIGIT	6.463714e-02
15633	TIMD4	1
15634	TIMELESS	3.835846e-01
15635	TIMM10	5.451751e-02
15636	TIMM13	1
15637	TIMM16	1
15638	TIMM17A	1
15639	TIMM17B	1
15640	TIMM22	1
15641	TIMM23	1
15642	TIMM44	1
15643	TIMM50	1
15644	TIMM8A	1
15645	TIMM8B	1
15646	TIMM9	1
15647	TIMP1	1
15648	TIMP2	1
15649	TIMP3	1
15650	TIMP4	1
15651	TINAG	1.113102e-01
15652	TINAGL1	1
15653	TINF2	1.241391e-01
15654	TIPARP	1
15655	TIPIN	1
15656	TIPRL	1
15657	TIRAP	1
15658	TJAP1	1
15659	TJP1	1
15660	TJP2	1
15661	TJP3	1
15662	TK1	1
15663	TK2	1
15664	TKT	1
15665	TKTL1	1
15666	TKTL2	1
15667	TLCD1	1
15668	TLE1	1
15669	TLE2	1
15670	TLE3	1
15671	TLE4	1
15672	TLE6	1
15673	TLK1	1
15674	TLK2	1
15675	TLL1	1
15676	TLL2	1
15677	TLN1	1
15678	TLN2	1
15679	TLR1	3.359469e-01
15680	TLR10	1
15681	TLR2	2.688687e-01
15682	TLR3	1
15683	TLR4	1
15684	TLR5	1
15685	TLR6	1
15686	TLR7	1
15687	TLR8	1
15688	TLR9	1
15689	TLX1	1
15690	TLX1NB	1
15691	TLX2	1
15692	TLX3	1
15693	TM2D1	1
15694	TM2D2	1
15695	TM2D3	8.096526e-02
15696	TM4SF1	1
15697	TM4SF18	1
15698	TM4SF19	1
15699	TM4SF20	1
Done

Running MutSig 2:
Scatter job 175: processing genes 15611 - 15699
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TIE1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.730584e-01	ci left: 4.456333e-02	ci right 5.310195e-02	k: 487	n:10000
Cons ci ratio: 2.669889e-01	ci left: 1.827990e-02	ci right 2.400381e-02	k: 210	n:10000
KS ci ratio: 1.749511e-01	ci left: 4.360497e-02	ci right 5.206094e-02	k: 477	n:10000
TIE1   10000 perm   2 sec   (5708 perm/sec)   p_kst 4.770000e-02   p_cons 2.100000e-02   p_joint 4.870000e-02

Joint ci ratio: 2.136671e-01	ci left: 1.478008e-02	ci right 1.836246e-02	k: 330	n:20000
Cons ci ratio: 1.881123e-01	ci left: 1.924843e-02	ci right 2.329242e-02	k: 424	n:20000
KS ci ratio: 1.218494e-01	ci left: 4.619466e-02	ci right 5.223726e-02	k: 983	n:20000
TIE1   20000 perm   5 sec   (3708 perm/sec)   p_kst 4.915000e-02   p_cons 2.120000e-02   p_joint 1.650000e-02

Joint ci ratio: 1.927416e-01	ci left: 1.228821e-02	ci right 1.494055e-02	k: 407	n:30000
Cons ci ratio: 1.530433e-01	ci left: 1.976016e-02	ci right 2.306676e-02	k: 641	n:30000
KS ci ratio: 9.991828e-02	ci left: 4.635659e-02	ci right 5.126460e-02	k: 1463	n:30000
TIE1   30000 perm   8 sec   (3955 perm/sec)   p_kst 4.876667e-02   p_cons 2.136667e-02   p_joint 1.356667e-02

Joint ci ratio: 1.684968e-01	ci left: 1.222427e-02	ci right 1.449719e-02	k: 533	n:40000
Cons ci ratio: 1.333379e-01	ci left: 1.973812e-02	ci right 2.258199e-02	k: 845	n:40000
KS ci ratio: 8.611549e-02	ci left: 4.712522e-02	ci right 5.139052e-02	k: 1969	n:40000
TIE1   40000 perm   10 sec   (4043 perm/sec)   p_kst 4.922500e-02   p_cons 2.112500e-02   p_joint 1.332500e-02

Joint ci ratio: 1.274094e-01	ci left: 1.739502e-02	ci right 1.978134e-02	k: 928	n:50000
Cons ci ratio: 1.186042e-01	ci left: 2.011056e-02	ci right 2.266543e-02	k: 1068	n:50000
KS ci ratio: 7.726376e-02	ci left: 4.706520e-02	ci right 5.086739e-02	k: 2447	n:50000
TIE1   50000 perm   12 sec   (4078 perm/sec)   p_kst 4.894000e-02   p_cons 2.136000e-02   p_joint 1.856000e-02

Joint ci ratio: 1.340591e-01	ci left: 1.310736e-02	ci right 1.500674e-02	k: 842	n:60000
Cons ci ratio: 1.078332e-01	ci left: 2.038673e-02	ci right 2.272653e-02	k: 1292	n:60000
KS ci ratio: 7.042614e-02	ci left: 4.736818e-02	ci right 5.084227e-02	k: 2945	n:60000
TIE1   60000 perm   15 sec   (4078 perm/sec)   p_kst 4.908333e-02   p_cons 2.153333e-02   p_joint 1.403333e-02

Joint ci ratio: 1.023776e-01	ci left: 1.946304e-02	ci right 2.157697e-02	k: 1435	n:70000
Cons ci ratio: 9.931407e-02	ci left: 2.068911e-02	ci right 2.286507e-02	k: 1523	n:70000
KS ci ratio: 6.512234e-02	ci left: 4.760933e-02	ci right 5.082816e-02	k: 3444	n:70000
TIE1   70000 perm   17 sec   (4059 perm/sec)   p_kst 4.920000e-02   p_cons 2.175714e-02   p_joint 2.050000e-02

Joint ci ratio: 1.045311e-01	ci left: 1.637123e-02	ci right 1.818902e-02	k: 1381	n:80000
Cons ci ratio: 9.235159e-02	ci left: 2.100688e-02	ci right 2.305298e-02	k: 1761	n:80000
KS ci ratio: 6.103998e-02	ci left: 4.752658e-02	ci right 5.053123e-02	k: 3921	n:80000
TIE1   80000 perm   20 sec   (4030 perm/sec)   p_kst 4.901250e-02   p_cons 2.201250e-02   p_joint 1.726250e-02

Joint ci ratio: 9.774830e-02	ci left: 1.669673e-02	ci right 1.842345e-02	k: 1579	n:90000
Cons ci ratio: 8.640925e-02	ci left: 2.138869e-02	ci right 2.333115e-02	k: 2011	n:90000
KS ci ratio: 5.623617e-02	ci left: 4.977993e-02	ci right 5.267130e-02	k: 4609	n:90000
TIE1   90000 perm   25 sec   (3550 perm/sec)   p_kst 5.121111e-02   p_cons 2.234444e-02   p_joint 1.754444e-02

Outputting figure to mutsig2_images.part000000000175/TIE1.4_3509_90000_0.051211_0.022344_0.017544.png
                gene_name: TIE1
               theta_stop: 0.098 
                    nperm: 90000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.050 
       ci_ks_bounds_right: 0.053 
                   p_cons: 0.022 
      ci_cons_bounds_left: 0.021 
     ci_cons_bounds_right: 0.023 
                  p_joint: 0.018 
     ci_joint_bounds_left: 0.017 
    ci_joint_bounds_right: 0.018 

Current progress: 33 percent done.
TIGD7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.131657e-02	ci left: 3.589352e-01	ci right 3.779415e-01	k: 3684	n:10000
Cons ci ratio: 4.259349e-02	ci left: 4.486973e-01	ci right 4.683269e-01	k: 4585	n:10000
KS ci ratio: 8.707717e-02	ci left: 1.611128e-01	ci right 1.758809e-01	k: 1684	n:10000
TIGD7   10000 perm   1 sec   (6810 perm/sec)   p_kst 1.684000e-01   p_cons 4.585000e-01   p_joint 3.684000e-01

Outputting figure to mutsig2_images.part000000000175/TIGD7.3_1654_10000_0.1684_0.4585_0.3684.png
                gene_name: TIGD7
               theta_stop: 0.087 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.38 

Current progress: 67 percent done.
TIMELESS
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.249072e-02	ci left: 4.498950e-01	ci right 4.695285e-01	k: 4597	n:10000
Cons ci ratio: 5.724836e-02	ci left: 3.099678e-01	ci right 3.283376e-01	k: 3191	n:10000
KS ci ratio: 5.861970e-02	ci left: 2.998509e-01	ci right 3.180605e-01	k: 3089	n:10000
TIMELESS   10000 perm   2 sec   (5475 perm/sec)   p_kst 3.089000e-01   p_cons 3.191000e-01   p_joint 4.597000e-01

Outputting figure to mutsig2_images.part000000000175/TIMELESS.3_3739_10000_0.3089_0.3191_0.4597.png
                gene_name: TIMELESS
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000175
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 175 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1646>
Subject: Job 4398470: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000176> was used as the working directory.
Started at Wed Oct 24 16:17:37 2012
Results reported at Wed Oct 24 16:19:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000176.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000176.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 176  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000176.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    125.87 sec.
    Max Memory :      1018 MB
    Max Swap   :      3906 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
176
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 176
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 176: processing genes 15700 - 15789
Calculating significance of each gene.
Using projection method.
15700	TM4SF4	1
15701	TM4SF5	1
15702	TM6SF1	1
15703	TM6SF2	1
15704	TM7SF2	1
15705	TM7SF3	1
15706	TM7SF4	1
15707	TM9SF1	1
15708	TM9SF2	1
15709	TM9SF3	1
15710	TM9SF4	1
15711	TMBIM1	9.999870e-02
15712	TMBIM4	1
15713	TMBIM6	1
15714	TMC1	1
15715	TMC2	1.637745e-01
15716	TMC3	1
15717	TMC4	1
15718	TMC5	4.115045e-01
15719	TMC6	1
15720	TMC7	1
15721	TMC8	1
15722	TMCC1	9.010364e-02
15723	TMCC2	3.190475e-01
15724	TMCC3	1
15725	TMCO1	1
15726	TMCO2	3.526599e-02
15727	TMCO3	1
15728	TMCO4	1
15729	TMCO5A	1
15730	TMCO6	1.657369e-01
15731	TMCO7	3.595169e-01
15732	TMED1	1
15733	TMED10	1
15734	TMED2	1
15735	TMED3	1
15736	TMED4	1
15737	TMED5	1
15738	TMED6	1
15739	TMED7	1
15740	TMED7-TICAM2	9.021754e-02
15741	TMED8	1
15742	TMED9	1
15743	TMEFF1	1
15744	TMEFF2	1
15745	TMEM100	1.863088e-02
15746	TMEM101	1
15747	TMEM102	1
15748	TMEM104	1
15749	TMEM105	1
15750	TMEM106A	1
15751	TMEM106B	1
15752	TMEM106C	1
15753	TMEM107	1
15754	TMEM108	1
15755	TMEM109	1
15756	TMEM11	1
15757	TMEM110	1
15758	TMEM111	1
15759	TMEM115	1
15760	TMEM116	1
15761	TMEM117	1
15762	TMEM119	1
15763	TMEM120A	1
15764	TMEM120B	1.084346e-01
15765	TMEM123	1
15766	TMEM125	1
15767	TMEM126A	1
15768	TMEM126B	1
15769	TMEM127	1
15770	TMEM128	1
15771	TMEM130	1
15772	TMEM131	3.466973e-01
15773	TMEM132A	7.046992e-02
15774	TMEM132B	1.773555e-01
15775	TMEM132D	4.911891e-02
15776	TMEM132E	1.459452e-01
15777	TMEM133	1
15778	TMEM134	1
15779	TMEM135	1
15780	TMEM136	1
15781	TMEM138	1
15782	TMEM139	1
15783	TMEM140	1
15784	TMEM141	1
15785	TMEM143	1
15786	TMEM144	1
15787	TMEM145	1
15788	TMEM146	1
15789	TMEM147	1
Done

Running MutSig 2:
Scatter job 176: processing genes 15700 - 15789
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TMEM132A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.608933e-02	ci left: 6.838544e-01	ci right 7.020331e-01	k: 6930	n:10000
Cons ci ratio: 2.092186e-02	ci left: 7.700281e-01	ci right 7.864095e-01	k: 7783	n:10000
KS ci ratio: 8.114669e-02	ci left: 1.814664e-01	ci right 1.969151e-01	k: 1891	n:10000
TMEM132A   10000 perm   2 sec   (4539 perm/sec)   p_kst 1.891000e-01   p_cons 7.783000e-01   p_joint 6.930000e-01

Outputting figure to mutsig2_images.part000000000176/TMEM132A.2_3119_10000_0.1891_0.7783_0.693.png
                gene_name: TMEM132A
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.69 
     ci_joint_bounds_left: 0.68 
    ci_joint_bounds_right: 0.70 

Current progress: 50 percent done.
TMEM132D
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.909192e-02	ci left: 6.353290e-01	ci right 6.541866e-01	k: 6448	n:10000
KS ci ratio: 4.803081e-02	ci left: 3.900798e-01	ci right 4.093787e-01	k: 3997	n:10000
TMEM132D   10000 perm   2 sec   (5436 perm/sec)   p_kst 3.997000e-01   p_cons 6.448000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000176/TMEM132D.2_3336_10000_0.3997_0.6448_1.png
                gene_name: TMEM132D
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000176
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 176 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1654>
Subject: Job 4398473: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1654>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000177> was used as the working directory.
Started at Wed Oct 24 16:17:39 2012
Results reported at Wed Oct 24 16:19:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000177.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000177.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 177  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000177.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    109.59 sec.
    Max Memory :       583 MB
    Max Swap   :      3384 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
177
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 177
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 177: processing genes 15790 - 15879
Calculating significance of each gene.
Using projection method.
15790	TMEM149	1
15791	TMEM14A	1
15792	TMEM14B	1
15793	TMEM14C	1
15794	TMEM14E	1
15795	TMEM150A	1
15796	TMEM150B	1
15797	TMEM150C	1
15798	TMEM151A	1
15799	TMEM154	1
15800	TMEM155	1
15801	TMEM156	1
15802	TMEM159	1
15803	TMEM161A	1
15804	TMEM161B	1
15805	TMEM163	4.148492e-02
15806	TMEM164	1.553515e-01
15807	TMEM165	1
15808	TMEM167A	1
15809	TMEM167B	1
15810	TMEM168	2.005416e-01
15811	TMEM169	1
15812	TMEM17	1
15813	TMEM170A	1
15814	TMEM170B	1
15815	TMEM171	1
15816	TMEM173	1
15817	TMEM174	1.670887e-02
15818	TMEM175	1
15819	TMEM176A	1
15820	TMEM176B	1.399487e-01
15821	TMEM177	1
15822	TMEM178	1
15823	TMEM179	1
15824	TMEM179B	1
15825	TMEM18	1
15826	TMEM180	1
15827	TMEM181	1
15828	TMEM182	1
15829	TMEM183A	1
15830	TMEM183B	1
15831	TMEM184A	1
15832	TMEM184B	1
15833	TMEM184C	1
15834	TMEM185A	1
15835	TMEM186	1
15836	TMEM187	1
15837	TMEM188	1
15838	TMEM189	1
15839	TMEM189-UBE2V1	1
15840	TMEM19	1
15841	TMEM190	1
15842	TMEM192	1
15843	TMEM194A	1
15844	TMEM195	1
15845	TMEM196	1
15846	TMEM198	1
15847	TMEM199	1
15848	TMEM2	1
15849	TMEM20	1
15850	TMEM200A	1
15851	TMEM200B	1
15852	TMEM200C	8.047620e-02
15853	TMEM201	1
15854	TMEM202	1.445539e-01
15855	TMEM203	1
15856	TMEM204	1
15857	TMEM205	1
15858	TMEM206	1
15859	TMEM207	2.647491e-03
15860	TMEM208	1
15861	TMEM209	1
15862	TMEM211	1
15863	TMEM213	1
15864	TMEM214	1
15865	TMEM215	1
15866	TMEM216	1
15867	TMEM217	1
15868	TMEM218	1
15869	TMEM219	1
15870	TMEM22	1
15871	TMEM220	1
15872	TMEM222	1
15873	TMEM223	1
15874	TMEM225	1
15875	TMEM229B	1
15876	TMEM231	1
15877	TMEM25	1
15878	TMEM26	1
15879	TMEM27	1
Done

Running MutSig 2:
Scatter job 177: processing genes 15790 - 15879
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000177
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 177 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1704>
Subject: Job 4398477: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1704>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000178> was used as the working directory.
Started at Wed Oct 24 16:17:39 2012
Results reported at Wed Oct 24 16:19:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000178.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000178.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 178  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000178.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    124.52 sec.
    Max Memory :      1214 MB
    Max Swap   :      4012 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
178
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 178
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 178: processing genes 15880 - 15968
Calculating significance of each gene.
Using projection method.
15880	TMEM30A	2.232076e-02
15881	TMEM30B	1
15882	TMEM31	1
15883	TMEM33	1
15884	TMEM35	1
15885	TMEM37	1
15886	TMEM38A	4.009373e-02
15887	TMEM38B	1
15888	TMEM39A	1
15889	TMEM39B	1
15890	TMEM40	1
15891	TMEM41A	1
15892	TMEM41B	1
15893	TMEM42	1
15894	TMEM43	1
15895	TMEM44	1
15896	TMEM45A	1
15897	TMEM45B	1
15898	TMEM47	3.316010e-03
15899	TMEM48	1
15900	TMEM49	1
15901	TMEM5	1
15902	TMEM50A	1
15903	TMEM50B	1
15904	TMEM51	1.955777e-04
15905	TMEM52	1
15906	TMEM53	1
15907	TMEM54	1
15908	TMEM55A	1
15909	TMEM55B	1
15910	TMEM56	1
15911	TMEM57	1
15912	TMEM59	1.036152e-01
15913	TMEM59L	1
15914	TMEM60	3.248140e-02
15915	TMEM61	1
15916	TMEM62	2.709698e-01
15917	TMEM63A	1
15918	TMEM63B	3.222866e-01
15919	TMEM63C	1
15920	TMEM64	1
15921	TMEM65	1
15922	TMEM66	1
15923	TMEM67	1
15924	TMEM68	1
15925	TMEM69	1
15926	TMEM70	1
15927	TMEM71	1
15928	TMEM72	1
15929	TMEM74	1
15930	TMEM79	1
15931	TMEM80	1
15932	TMEM81	1
15933	TMEM82	1
15934	TMEM85	1
15935	TMEM86A	1
15936	TMEM86B	1
15937	TMEM87A	1
15938	TMEM87B	1
15939	TMEM88	1
15940	TMEM89	1
15941	TMEM8A	1
15942	TMEM8B	1
15943	TMEM8C	1
15944	TMEM9	1
15945	TMEM90A	9.839965e-02
15946	TMEM90B	1
15947	TMEM91	1
15948	TMEM92	1
15949	TMEM93	1
15950	TMEM95	1
15951	TMEM97	1
15952	TMEM98	1
15953	TMEM99	6.315847e-02
15954	TMEM9B	1
15955	TMF1	4.699622e-01
15956	TMIE	1
15957	TMIGD1	1
15958	TMIGD2	2.612481e-02
15959	TMLHE	1
15960	TMOD1	1
15961	TMOD2	1
15962	TMOD3	1
15963	TMOD4	1
15964	TMPO	1
15965	TMPPE	1
15966	TMPRSS11A	1.924049e-02
15967	TMPRSS11B	1
15968	TMPRSS11D	1.927766e-01
Done

Running MutSig 2:
Scatter job 178: processing genes 15880 - 15968
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TMEM51
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.855515e-02	ci left: 3.849027e-01	ci right 4.041588e-01	k: 3945	n:10000
Cons ci ratio: 1.758489e-02	ci left: 8.250345e-01	ci right 8.397713e-01	k: 8325	n:10000
KS ci ratio: 6.521613e-02	ci left: 2.566662e-01	ci right 2.740706e-01	k: 2653	n:10000
TMEM51   10000 perm   2 sec   (6240 perm/sec)   p_kst 2.653000e-01   p_cons 8.325000e-01   p_joint 3.945000e-01

Outputting figure to mutsig2_images.part000000000178/TMEM51.3_770_10000_0.2653_0.8325_0.3945.png
                gene_name: TMEM51
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 50 percent done.
TMPRSS11A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.617512e-02	ci left: 5.301711e-01	ci right 5.498056e-01	k: 5400	n:10000
Cons ci ratio: 4.854499e-02	ci left: 3.850022e-01	ci right 4.042592e-01	k: 3946	n:10000
KS ci ratio: 1.108203e-01	ci left: 1.050046e-01	ci right 1.174229e-01	k: 1111	n:10000
TMPRSS11A   10000 perm   1 sec   (6764 perm/sec)   p_kst 1.111000e-01   p_cons 3.946000e-01   p_joint 5.400000e-01

Joint ci ratio: 5.383433e-02	ci left: 2.038776e-01	ci right 2.152070e-01	k: 4190	n:20000
Cons ci ratio: 3.596094e-02	ci left: 3.659429e-01	ci right 3.793941e-01	k: 7453	n:20000
KS ci ratio: 7.878237e-02	ci left: 1.057938e-01	ci right 1.145199e-01	k: 2202	n:20000
TMPRSS11A   20000 perm   3 sec   (5953 perm/sec)   p_kst 1.101000e-01   p_cons 3.726500e-01   p_joint 2.095000e-01

Outputting figure to mutsig2_images.part000000000178/TMPRSS11A.2_1306_20000_0.1101_0.37265_0.2095.png
                gene_name: TMPRSS11A
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000178
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 178 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1725>
Subject: Job 4398480: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000179> was used as the working directory.
Started at Wed Oct 24 16:17:42 2012
Results reported at Wed Oct 24 16:18:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000179.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000179.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 179  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000179.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     81.50 sec.
    Max Memory :      1039 MB
    Max Swap   :      3857 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
179
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 179
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 179: processing genes 15969 - 16058
Calculating significance of each gene.
Using projection method.
15969	TMPRSS11E	1
15970	TMPRSS11F	1
15971	TMPRSS12	1
15972	TMPRSS13	1
15973	TMPRSS15	1
15974	TMPRSS2	1
15975	TMPRSS3	1
15976	TMPRSS4	1
15977	TMPRSS6	1
15978	TMPRSS7	1
15979	TMPRSS9	1
15980	TMSB10	1
15981	TMSB15A	1
15982	TMSB15B	1
15983	TMSB4X	1
15984	TMSL3	1
15985	TMTC1	1
15986	TMTC2	1
15987	TMTC3	1
15988	TMTC4	1
15989	TMUB1	1
15990	TMUB2	1
15991	TMX1	1
15992	TMX2	1
15993	TMX3	1
15994	TMX4	1
15995	TNC	2.974584e-01
15996	TNF	1
15997	TNFAIP1	1
15998	TNFAIP2	1
15999	TNFAIP3	1
16000/17942 16000	TNFAIP6	1
16001	TNFAIP8	1
16002	TNFAIP8L1	1
16003	TNFAIP8L2	1
16004	TNFAIP8L3	1
16005	TNFRSF10A	1
16006	TNFRSF10B	1
16007	TNFRSF10C	1
16008	TNFRSF10D	1
16009	TNFRSF11A	1
16010	TNFRSF11B	1
16011	TNFRSF12A	1
16012	TNFRSF13B	1
16013	TNFRSF13C	1
16014	TNFRSF14	1
16015	TNFRSF17	1
16016	TNFRSF18	1
16017	TNFRSF19	1
16018	TNFRSF1A	1
16019	TNFRSF1B	1
16020	TNFRSF21	1
16021	TNFRSF25	1
16022	TNFRSF4	1
16023	TNFRSF6B	1
16024	TNFRSF8	1
16025	TNFRSF9	1
16026	TNFSF10	1
16027	TNFSF11	1
16028	TNFSF12	1
16029	TNFSF12-TNFSF13	1
16030	TNFSF13	1
16031	TNFSF13B	1
16032	TNFSF14	1
16033	TNFSF15	1
16034	TNFSF18	1
16035	TNFSF4	1
16036	TNFSF8	1
16037	TNFSF9	1
16038	TNIK	2.466528e-03
16039	TNIP1	1
16040	TNIP2	1
16041	TNIP3	1
16042	TNK1	1
16043	TNK2	1
16044	TNKS	2.235001e-01
16045	TNKS1BP1	1
16046	TNKS2	1
16047	TNMD	3.144599e-02
16048	TNN	1
16049	TNNC1	1
16050	TNNC2	1
16051	TNNI1	1
16052	TNNI2	1
16053	TNNI3	1
16054	TNNI3K	1.460825e-01
16055	TNNT1	1
16056	TNNT2	3.863679e-02
16057	TNNT3	1
16058	TNP1	1
Done

Running MutSig 2:
Scatter job 179: processing genes 15969 - 16058
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TNIK
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.977843e-02	ci left: 4.827546e-01	ci right 5.024497e-01	k: 4926	n:10000
Cons ci ratio: 3.830297e-02	ci left: 5.016506e-01	ci right 5.213427e-01	k: 5115	n:10000
KS ci ratio: 5.040300e-02	ci left: 3.672894e-01	ci right 3.863825e-01	k: 3768	n:10000
TNIK   10000 perm   2 sec   (5148 perm/sec)   p_kst 3.768000e-01   p_cons 5.115000e-01   p_joint 4.926000e-01

Outputting figure to mutsig2_images.part000000000179/TNIK.4_4215_10000_0.3768_0.5115_0.4926.png
                gene_name: TNIK
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 50 percent done.
TNC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.613873e-02	ci left: 5.306718e-01	ci right 5.503046e-01	k: 5405	n:10000
Cons ci ratio: 4.047690e-02	ci left: 4.740612e-01	ci right 4.937482e-01	k: 4839	n:10000
KS ci ratio: 3.972278e-02	ci left: 4.834542e-01	ci right 5.031497e-01	k: 4933	n:10000
TNC   10000 perm   2 sec   (4686 perm/sec)   p_kst 4.933000e-01   p_cons 4.839000e-01   p_joint 5.405000e-01

Outputting figure to mutsig2_images.part000000000179/TNC.2_6714_10000_0.4933_0.4839_0.5405.png
                gene_name: TNC
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000179
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 179 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1729>
Subject: Job 4398482: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1729>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000180> was used as the working directory.
Started at Wed Oct 24 16:17:49 2012
Results reported at Wed Oct 24 16:19:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000180.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000180.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 180  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000180.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     88.48 sec.
    Max Memory :      1590 MB
    Max Swap   :      3955 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
180
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 180
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 180: processing genes 16059 - 16148
Calculating significance of each gene.
Using projection method.
16059	TNP2	1
16060	TNPO1	1
16061	TNPO2	1
16062	TNPO3	1
16063	TNR	1
16064	TNRC18	1.974155e-01
16065	TNRC6A	1.089309e-01
16066	TNRC6B	1
16067	TNRC6C	3.475701e-01
16068	TNS1	1
16069	TNS3	1
16070	TNS4	3.392112e-01
16071	TNXB	6.844773e-01
16072	TOB1	1
16073	TOB2	1
16074	TOE1	1
16075	TOLLIP	1
16076	TOM1	1
16077	TOM1L1	2.387517e-01
16078	TOM1L2	1
16079	TOMM20	1
16080	TOMM20L	1
16081	TOMM22	1
16082	TOMM34	1
16083	TOMM40	1
16084	TOMM40L	1
16085	TOMM5	1
16086	TOMM7	1
16087	TOMM70A	1
16088	TOP1	1
16089	TOP1MT	1
16090	TOP2A	1
16091	TOP2B	1
16092	TOP3A	1
16093	TOP3B	1
16094	TOPBP1	1
16095	TOPORS	1
16096	TOR1A	8.747600e-02
16097	TOR1AIP1	1
16098	TOR1AIP2	2.870155e-01
16099	TOR1B	1
16100	TOR2A	1
16101	TOR3A	1
16102	TOX	1
16103	TOX2	1
16104	TOX3	1
16105	TOX4	1
16106	TP53	4.434705e-02
16107	TP53AIP1	1
16108	TP53BP1	2.240428e-01
16109	TP53BP2	1
16110	TP53I11	1
16111	TP53I13	1
16112	TP53I3	1
16113	TP53INP1	1
16114	TP53INP2	1
16115	TP53RK	1
16116	TP53TG5	1
16117	TP63	4.655932e-03
16118	TP73	1
16119	TPBG	1
16120	TPCN1	1
16121	TPCN2	3.224377e-01
16122	TPD52	1
16123	TPD52L1	1
16124	TPD52L2	1
16125	TPD52L3	1
16126	TPH1	1
16127	TPH2	1
16128	TPI1	1
16129	TPK1	1
16130	TPM1	1
16131	TPM2	9.412926e-02
16132	TPM3	1
16133	TPM4	1
16134	TPMT	1
16135	TPO	1
16136	TPP1	1
16137	TPP2	4.131682e-01
16138	TPPP	1
16139	TPPP2	1
16140	TPPP3	1
16141	TPR	2.363221e-01
16142	TPRA1	1
16143	TPRG1	1
16144	TPRG1L	1
16145	TPRKB	1
16146	TPRN	8.658511e-02
16147	TPRX1	1
16148	TPSAB1	1
Done

Running MutSig 2:
Scatter job 180: processing genes 16059 - 16148
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TP63
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.054346e-02	ci left: 1.837302e-01	ci right 1.992500e-01	k: 1914	n:10000
Cons ci ratio: 9.201623e-02	ci left: 1.464866e-01	ci right 1.607158e-01	k: 1535	n:10000
KS ci ratio: 6.411390e-02	ci left: 2.632958e-01	ci right 2.808372e-01	k: 2720	n:10000
TP63   10000 perm   2 sec   (6226 perm/sec)   p_kst 2.720000e-01   p_cons 1.535000e-01   p_joint 1.914000e-01

Outputting figure to mutsig2_images.part000000000180/TP63.3_2264_10000_0.272_0.1535_0.1914.png
                gene_name: TP63
               theta_stop: 0.092 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.20 

Current progress: 20 percent done.
TNRC6A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.952724e-02	ci left: 7.932406e-01	ci right 8.089836e-01	k: 8012	n:10000
KS ci ratio: 6.465934e-03	ci left: 9.702664e-01	ci right 9.766537e-01	k: 9736	n:10000
TNRC6A   10000 perm   2 sec   (5206 perm/sec)   p_kst 9.736000e-01   p_cons 8.012000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000180/TNRC6A.2_5989_10000_0.9736_0.8012_1.png
                gene_name: TNRC6A
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.98 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.81 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 40 percent done.
TNXB
Processing conservation and coverage...
67% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.201360e-02	ci left: 9.085394e-01	ci right 9.196180e-01	k: 9142	n:10000
Cons ci ratio: 1.594303e-02	ci left: 8.511065e-01	ci right 8.648842e-01	k: 8581	n:10000
KS ci ratio: 3.166431e-02	ci left: 5.954396e-01	ci right 6.146991e-01	k: 6051	n:10000
TNXB   10000 perm   3 sec   (3628 perm/sec)   p_kst 6.051000e-01   p_cons 8.581000e-01   p_joint 9.142000e-01

Outputting figure to mutsig2_images.part000000000180/TNXB.2_14886_10000_0.6051_0.8581_0.9142.png
                gene_name: TNXB
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 60 percent done.
TP53BP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.669845e-03	ci left: 9.836084e-01	ci right 9.883022e-01	k: 9861	n:10000
Cons ci ratio: 2.016861e-02	ci left: 7.825926e-01	ci right 7.986378e-01	k: 7907	n:10000
KS ci ratio: 4.860600e-02	ci left: 3.844050e-01	ci right 4.036568e-01	k: 3940	n:10000
TP53BP1   10000 perm   2 sec   (5067 perm/sec)   p_kst 3.940000e-01   p_cons 7.907000e-01   p_joint 9.861000e-01

Outputting figure to mutsig2_images.part000000000180/TP53BP1.2_6046_10000_0.394_0.7907_0.9861.png
                gene_name: TP53BP1
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 80 percent done.
TPR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.744543e-02	ci left: 3.959551e-01	ci right 4.152999e-01	k: 4056	n:10000
Cons ci ratio: 2.809562e-02	ci left: 6.512237e-01	ci right 6.698827e-01	k: 6606	n:10000
KS ci ratio: 7.154130e-02	ci left: 2.225711e-01	ci right 2.391859e-01	k: 2308	n:10000
TPR   10000 perm   2 sec   (4873 perm/sec)   p_kst 2.308000e-01   p_cons 6.606000e-01   p_joint 4.056000e-01

Outputting figure to mutsig2_images.part000000000180/TPR.2_7296_10000_0.2308_0.6606_0.4056.png
                gene_name: TPR
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.67 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000180
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 180 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1730>
Subject: Job 4398488: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1730>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000181> was used as the working directory.
Started at Wed Oct 24 16:17:49 2012
Results reported at Wed Oct 24 16:19:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000181.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000181.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 181  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000181.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     67.83 sec.
    Max Memory :       908 MB
    Max Swap   :      3778 MB

    Max Processes  :         7
    Max Threads    :        67

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
181
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 181
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 181: processing genes 16149 - 16238
Calculating significance of each gene.
Using projection method.
16149	TPSB2	1
16150	TPSD1	1
16151	TPSG1	1
16152	TPST1	1
16153	TPST2	1
16154	TPT1	1
16155	TPTE	8.039484e-03
16156	TPTE2	1
16157	TPX2	3.558088e-01
16158	TRA2A	1.318025e-02
16159	TRA2B	1
16160	TRABD	1
16161	TRADD	1
16162	TRAF1	1
16163	TRAF2	1
16164	TRAF3	2.123850e-01
16165	TRAF3IP1	8.298491e-02
16166	TRAF3IP2	1
16167	TRAF3IP3	1
16168	TRAF4	1
16169	TRAF5	1.873082e-01
16170	TRAF6	9.390948e-02
16171	TRAF7	1
16172	TRAFD1	1.048315e-01
16173	TRAIP	6.100299e-02
16174	TRAK1	1
16175	TRAK2	1
16176	TRAM1	1.503464e-01
16177	TRAM1L1	1
16178	TRAM2	1
16179	TRANK1	1
16180	TRAP1	1
16181	TRAPPC1	1
16182	TRAPPC10	1
16183	TRAPPC2	1
16184	TRAPPC2L	1
16185	TRAPPC3	1
16186	TRAPPC4	1
16187	TRAPPC5	1
16188	TRAPPC6A	1
16189	TRAPPC6B	1
16190	TRAPPC9	1
16191	TRAT1	1
16192	TRDMT1	1
16193	TRDN	1
16194	TREH	1
16195	TREM1	1
16196	TREM2	1
16197	TREML1	1
16198	TREML2	1
16199	TREML4	1
16200	TRERF1	1
16201	TREX1	1
16202	TREX2	1
16203	TRH	1.364724e-01
16204	TRHDE	1
16205	TRHR	1
16206	TRIAP1	1
16207	TRIB1	1
16208	TRIB2	1
16209	TRIB3	1
16210	TRIL	1
16211	TRIM10	1
16212	TRIM11	1
16213	TRIM13	1.980064e-02
16214	TRIM14	1.527108e-01
16215	TRIM15	1
16216	TRIM16	1
16217	TRIM16L	1
16218	TRIM17	2.394043e-01
16219	TRIM2	1
16220	TRIM21	2.321961e-01
16221	TRIM22	1
16222	TRIM23	1
16223	TRIM24	1
16224	TRIM25	1
16225	TRIM26	1
16226	TRIM27	1
16227	TRIM28	1
16228	TRIM29	1
16229	TRIM3	1
16230	TRIM31	1
16231	TRIM32	1
16232	TRIM33	1
16233	TRIM34	1
16234	TRIM35	1
16235	TRIM36	1
16236	TRIM37	1.126777e-01
16237	TRIM38	1
16238	TRIM39	1.564339e-01
Done

Running MutSig 2:
Scatter job 181: processing genes 16149 - 16238
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TPTE
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.965940e-02	ci left: 6.263806e-01	ci right 6.453402e-01	k: 6359	n:10000
Cons ci ratio: 3.696871e-02	ci left: 5.193596e-01	ci right 5.390234e-01	k: 5292	n:10000
KS ci ratio: 4.732758e-02	ci left: 3.971502e-01	ci right 4.165041e-01	k: 4068	n:10000
TPTE   10000 perm   1 sec   (6772 perm/sec)   p_kst 4.068000e-01   p_cons 5.292000e-01   p_joint 6.359000e-01

Outputting figure to mutsig2_images.part000000000181/TPTE.2_1740_10000_0.4068_0.5292_0.6359.png
                gene_name: TPTE
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000181
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 181 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 4398492: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000182> was used as the working directory.
Started at Wed Oct 24 16:17:54 2012
Results reported at Wed Oct 24 16:22:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000182.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000182.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 182  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000182.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    287.06 sec.
    Max Memory :      1507 MB
    Max Swap   :      4049 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
182
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 182
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 182: processing genes 16239 - 16327
Calculating significance of each gene.
Using projection method.
16239	TRIM4	1
16240	TRIM40	1
16241	TRIM41	1
16242	TRIM42	1
16243	TRIM43	1
16244	TRIM44	1
16245	TRIM45	2.283939e-01
16246	TRIM46	1
16247	TRIM47	1.192321e-01
16248	TRIM48	1
16249	TRIM49	1
16250	TRIM5	1
16251	TRIM50	1
16252	TRIM52	1
16253	TRIM54	5.358104e-02
16254	TRIM55	1
16255	TRIM56	1
16256	TRIM58	6.083164e-02
16257	TRIM59	8.471743e-02
16258	TRIM6	1
16259	TRIM6-TRIM34	1
16260	TRIM60	1
16261	TRIM61	1
16262	TRIM62	1
16263	TRIM63	1
16264	TRIM65	1
16265	TRIM67	1
16266	TRIM68	1
16267	TRIM69	5.150873e-02
16268	TRIM7	1.177089e-01
16269	TRIM71	1
16270	TRIM72	1
16271	TRIM73	1
16272	TRIM74	1
16273	TRIM8	1
16274	TRIM9	1.446969e-01
16275	TRIML1	1.751265e-01
16276	TRIML2	1
16277	TRIO	1
16278	TRIOBP	2.944747e-01
16279	TRIP10	1
16280	TRIP11	3.969656e-01
16281	TRIP12	3.213351e-01
16282	TRIP13	1
16283	TRIP4	1
16284	TRIP6	1.778861e-01
16285	TRIT1	1
16286	TRMT1	1
16287	TRMT11	1
16288	TRMT112	1
16289	TRMT12	1
16290	TRMT2A	7.141137e-02
16291	TRMT2B	1
16292	TRMT5	1
16293	TRMT6	1
16294	TRMT61A	1
16295	TRMT61B	1
16296	TRMU	1.993617e-01
16297	TRNAU1AP	1
16298	TRNT1	1
16299	TRO	3.842751e-01
16300	TROAP	1
16301	TROVE2	1
16302	TRPA1	1.664915e-01
16303	TRPC1	1.615187e-01
16304	TRPC3	1.582710e-01
16305	TRPC4	1
16306	TRPC4AP	1.710753e-01
16307	TRPC5	1
16308	TRPC6	1
16309	TRPC7	7.543678e-02
16310	TRPM1	1
16311	TRPM2	4.828530e-01
16312	TRPM3	3.869041e-01
16313	TRPM4	1
16314	TRPM5	1
16315	TRPM6	2.948364e-01
16316	TRPM7	3.878667e-01
16317	TRPM8	1
16318	TRPS1	2.660786e-01
16319	TRPT1	9.065692e-02
16320	TRPV1	1
16321	TRPV2	1
16322	TRPV3	1
16323	TRPV4	3.807194e-01
16324	TRPV5	1
16325	TRPV6	1.087983e-01
16326	TRRAP	1
16327	TRUB1	1
Done

Running MutSig 2:
Scatter job 182: processing genes 16239 - 16327
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TRIM42
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.049971e-02	ci left: 3.663941e-01	ci right 3.854782e-01	k: 3759	n:10000
KS ci ratio: 7.272974e-02	ci left: 2.168465e-01	ci right 2.333139e-01	k: 2250	n:10000
TRIM42   10000 perm   2 sec   (6099 perm/sec)   p_kst 2.250000e-01   p_cons 3.759000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000182/TRIM42.2_2192_10000_0.225_0.3759_1.png
                gene_name: TRIM42
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
TRPC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.614075e-01	ci left: 2.355713e-03	ci right 4.747948e-03	k: 34	n:10000
Cons ci ratio: 3.755631e-03	ci left: 9.889489e-01	ci right 9.927569e-01	k: 9910	n:10000
KS ci ratio: 6.614075e-01	ci left: 2.355713e-03	ci right 4.747948e-03	k: 34	n:10000
TRPC1   10000 perm   2 sec   (6270 perm/sec)   p_kst 3.400000e-03   p_cons 9.910000e-01   p_joint 3.400000e-03

Joint ci ratio: 4.193426e-01	ci left: 3.440841e-03	ci right 5.307780e-03	k: 86	n:20000
Cons ci ratio: 2.581317e-03	ci left: 9.900750e-01	ci right 9.926792e-01	k: 19829	n:20000
KS ci ratio: 4.487885e-01	ci left: 2.950721e-03	ci right 4.698422e-03	k: 75	n:20000
TRPC1   20000 perm   4 sec   (5347 perm/sec)   p_kst 3.750000e-03   p_cons 9.914500e-01   p_joint 4.300000e-03

Joint ci ratio: 3.404351e-01	ci left: 3.652208e-03	ci right 5.179552e-03	k: 131	n:30000
Cons ci ratio: 2.074511e-03	ci left: 9.906076e-01	ci right 9.926955e-01	k: 29751	n:30000
KS ci ratio: 3.697070e-01	ci left: 3.044727e-03	ci right 4.454070e-03	k: 111	n:30000
TRPC1   30000 perm   6 sec   (5147 perm/sec)   p_kst 3.700000e-03   p_cons 9.917000e-01   p_joint 4.366667e-03

Joint ci ratio: 2.867557e-01	ci left: 3.983757e-03	ci right 5.339698e-03	k: 185	n:40000
Cons ci ratio: 1.779325e-03	ci left: 9.909198e-01	ci right 9.927077e-01	k: 39674	n:40000
KS ci ratio: 3.142474e-01	ci left: 3.266865e-03	ci right 4.506872e-03	k: 154	n:40000
TRPC1   40000 perm   8 sec   (5003 perm/sec)   p_kst 3.850000e-03   p_cons 9.918500e-01   p_joint 4.625000e-03

Joint ci ratio: 2.567603e-01	ci left: 4.044513e-03	ci right 5.254105e-03	k: 231	n:50000
Cons ci ratio: 1.588058e-03	ci left: 9.910541e-01	ci right 9.926480e-01	k: 49594	n:50000
KS ci ratio: 2.823551e-01	ci left: 3.298269e-03	ci right 4.400568e-03	k: 191	n:50000
TRPC1   50000 perm   10 sec   (4827 perm/sec)   p_kst 3.820000e-03   p_cons 9.918800e-01   p_joint 4.620000e-03

Joint ci ratio: 2.398153e-01	ci left: 3.901834e-03	ci right 4.980298e-03	k: 265	n:60000
Cons ci ratio: 1.438590e-03	ci left: 9.912545e-01	ci right 9.926973e-01	k: 59520	n:60000
KS ci ratio: 2.631995e-01	ci left: 3.198848e-03	ci right 4.183453e-03	k: 220	n:60000
TRPC1   60000 perm   13 sec   (4734 perm/sec)   p_kst 3.666667e-03   p_cons 9.920000e-01   p_joint 4.416667e-03

Joint ci ratio: 2.207201e-01	ci left: 3.990667e-03	ci right 4.993946e-03	k: 313	n:70000
Cons ci ratio: 1.325689e-03	ci left: 9.913865e-01	ci right 9.927151e-01	k: 69445	n:70000
KS ci ratio: 2.417231e-01	ci left: 3.290604e-03	ci right 4.208431e-03	k: 261	n:70000
TRPC1   70000 perm   15 sec   (4647 perm/sec)   p_kst 3.728571e-03   p_cons 9.920714e-01   p_joint 4.471429e-03

Joint ci ratio: 2.055627e-01	ci left: 4.059855e-03	ci right 5.001632e-03	k: 361	n:80000
Cons ci ratio: 1.248477e-03	ci left: 9.913193e-01	ci right 9.925696e-01	k: 79357	n:80000
KS ci ratio: 2.258952e-01	ci left: 3.326488e-03	ci right 4.185118e-03	k: 299	n:80000
TRPC1   80000 perm   18 sec   (4528 perm/sec)   p_kst 3.737500e-03   p_cons 9.919625e-01   p_joint 4.512500e-03

Joint ci ratio: 1.924464e-01	ci left: 4.147234e-03	ci right 5.040714e-03	k: 412	n:90000
Cons ci ratio: 1.184021e-03	ci left: 9.912582e-01	ci right 9.924431e-01	k: 89268	n:90000
KS ci ratio: 2.125027e-01	ci left: 3.366447e-03	ci right 4.177165e-03	k: 338	n:90000
TRPC1   90000 perm   20 sec   (4455 perm/sec)   p_kst 3.755556e-03   p_cons 9.918667e-01   p_joint 4.577778e-03

Joint ci ratio: 1.807767e-01	ci left: 4.256859e-03	ci right 5.112261e-03	k: 467	n:100000
Cons ci ratio: 1.127120e-03	ci left: 9.912319e-01	ci right 9.923593e-01	k: 99181	n:100000
KS ci ratio: 1.983640e-01	ci left: 3.504132e-03	ci right 4.285077e-03	k: 388	n:100000
TRPC1   100000 perm   23 sec   (4381 perm/sec)   p_kst 3.880000e-03   p_cons 9.918100e-01   p_joint 4.670000e-03

Joint ci ratio: 1.743833e-01	ci left: 4.173897e-03	ci right 4.979840e-03	k: 502	n:110000
Cons ci ratio: 1.082450e-03	ci left: 9.911368e-01	ci right 9.922189e-01	k: 109086	n:110000
KS ci ratio: 1.906823e-01	ci left: 3.462312e-03	ci right 4.200592e-03	k: 420	n:110000
TRPC1   110000 perm   26 sec   (4314 perm/sec)   p_kst 3.818182e-03   p_cons 9.916909e-01   p_joint 4.563636e-03

Joint ci ratio: 1.667652e-01	ci left: 4.201028e-03	ci right 4.973214e-03	k: 549	n:120000
Cons ci ratio: 1.046175e-03	ci left: 9.909987e-01	ci right 9.920440e-01	k: 118984	n:120000
KS ci ratio: 1.822208e-01	ci left: 3.491571e-03	ci right 4.199406e-03	k: 460	n:120000
TRPC1   120000 perm   28 sec   (4243 perm/sec)   p_kst 3.833333e-03   p_cons 9.915333e-01   p_joint 4.575000e-03

Joint ci ratio: 1.593963e-01	ci left: 4.261564e-03	ci right 5.006952e-03	k: 601	n:130000
Cons ci ratio: 1.009839e-03	ci left: 9.909385e-01	ci right 9.919471e-01	k: 128889	n:130000
KS ci ratio: 1.744450e-01	ci left: 3.531655e-03	ci right 4.213846e-03	k: 502	n:130000
TRPC1   130000 perm   31 sec   (4160 perm/sec)   p_kst 3.861538e-03   p_cons 9.914538e-01   p_joint 4.623077e-03

Joint ci ratio: 1.529251e-01	ci left: 4.314093e-03	ci right 5.035229e-03	k: 653	n:140000
Cons ci ratio: 9.732957e-04	ci left: 9.909538e-01	ci right 9.919257e-01	k: 138803	n:140000
KS ci ratio: 1.671255e-01	ci left: 3.587096e-03	ci right 4.247997e-03	k: 547	n:140000
TRPC1   140000 perm   34 sec   (4095 perm/sec)   p_kst 3.907143e-03   p_cons 9.914500e-01   p_joint 4.664286e-03

Joint ci ratio: 1.474983e-01	ci left: 4.340882e-03	ci right 5.038476e-03	k: 702	n:150000
Cons ci ratio: 9.356386e-04	ci left: 9.910567e-01	ci right 9.919908e-01	k: 148730	n:150000
KS ci ratio: 1.617552e-01	ci left: 3.584473e-03	ci right 4.221606e-03	k: 584	n:150000
TRPC1   150000 perm   37 sec   (4019 perm/sec)   p_kst 3.893333e-03   p_cons 9.915333e-01   p_joint 4.680000e-03

Joint ci ratio: 1.421369e-01	ci left: 4.394859e-03	ci right 5.073279e-03	k: 756	n:160000
Cons ci ratio: 9.070292e-04	ci left: 9.910509e-01	ci right 9.919562e-01	k: 158642	n:160000
KS ci ratio: 1.563674e-01	ci left: 3.606498e-03	ci right 4.224192e-03	k: 625	n:160000
TRPC1   160000 perm   40 sec   (3960 perm/sec)   p_kst 3.906250e-03   p_cons 9.915125e-01   p_joint 4.725000e-03

Joint ci ratio: 1.380063e-01	ci left: 4.397445e-03	ci right 5.054915e-03	k: 802	n:170000
Cons ci ratio: 8.805820e-04	ci left: 9.910522e-01	ci right 9.919309e-01	k: 168555	n:170000
KS ci ratio: 1.518277e-01	ci left: 3.609263e-03	ci right 4.207851e-03	k: 663	n:170000
TRPC1   170000 perm   44 sec   (3905 perm/sec)   p_kst 3.900000e-03   p_cons 9.915000e-01   p_joint 4.717647e-03

Joint ci ratio: 1.345348e-01	ci left: 4.378518e-03	ci right 5.015373e-03	k: 844	n:180000
Cons ci ratio: 8.591321e-04	ci left: 9.909968e-01	ci right 9.918539e-01	k: 178458	n:180000
KS ci ratio: 1.479794e-01	ci left: 3.595898e-03	ci right 4.175816e-03	k: 698	n:180000
TRPC1   180000 perm   47 sec   (3852 perm/sec)   p_kst 3.877778e-03   p_cons 9.914333e-01   p_joint 4.688889e-03

Joint ci ratio: 1.305753e-01	ci left: 4.412684e-03	ci right 5.034154e-03	k: 896	n:190000
Cons ci ratio: 8.352540e-04	ci left: 9.910285e-01	ci right 9.918617e-01	k: 188376	n:190000
KS ci ratio: 1.442126e-01	ci left: 3.594258e-03	ci right 4.157887e-03	k: 735	n:190000
TRPC1   190000 perm   50 sec   (3792 perm/sec)   p_kst 3.868421e-03   p_cons 9.914526e-01   p_joint 4.715789e-03

Joint ci ratio: 1.269460e-01	ci left: 4.443680e-03	ci right 5.050811e-03	k: 948	n:200000
Cons ci ratio: 8.149388e-04	ci left: 9.910214e-01	ci right 9.918342e-01	k: 198287	n:200000
KS ci ratio: 1.401744e-01	ci left: 3.621901e-03	ci right 4.172632e-03	k: 778	n:200000
TRPC1   200000 perm   54 sec   (3734 perm/sec)   p_kst 3.890000e-03   p_cons 9.914350e-01   p_joint 4.740000e-03

Joint ci ratio: 1.234177e-01	ci left: 4.485786e-03	ci right 5.080391e-03	k: 1003	n:210000
Cons ci ratio: 7.922404e-04	ci left: 9.910981e-01	ci right 9.918882e-01	k: 208215	n:210000
KS ci ratio: 1.362082e-01	ci left: 3.660910e-03	ci right 4.200544e-03	k: 824	n:210000
TRPC1   210000 perm   57 sec   (3686 perm/sec)   p_kst 3.923810e-03   p_cons 9.915000e-01   p_joint 4.776190e-03

Joint ci ratio: 1.199407e-01	ci left: 4.541914e-03	ci right 5.125795e-03	k: 1062	n:220000
Cons ci ratio: 7.733899e-04	ci left: 9.911215e-01	ci right 9.918927e-01	k: 218133	n:220000
KS ci ratio: 1.323320e-01	ci left: 3.709757e-03	ci right 4.239807e-03	k: 873	n:220000
TRPC1   220000 perm   61 sec   (3632 perm/sec)   p_kst 3.968182e-03   p_cons 9.915136e-01   p_joint 4.827273e-03

Joint ci ratio: 1.173212e-01	ci left: 4.546943e-03	ci right 5.117819e-03	k: 1110	n:230000
Cons ci ratio: 7.544529e-04	ci left: 9.911741e-01	ci right 9.919264e-01	k: 228058	n:230000
KS ci ratio: 1.296176e-01	ci left: 3.704061e-03	ci right 4.221606e-03	k: 910	n:230000
TRPC1   230000 perm   64 sec   (3583 perm/sec)   p_kst 3.956522e-03   p_cons 9.915565e-01   p_joint 4.826087e-03

Joint ci ratio: 1.146675e-01	ci left: 4.567871e-03	ci right 5.127524e-03	k: 1162	n:240000
Cons ci ratio: 7.371933e-04	ci left: 9.912140e-01	ci right 9.919490e-01	k: 237981	n:240000
KS ci ratio: 1.264625e-01	ci left: 3.735257e-03	ci right 4.243504e-03	k: 956	n:240000
TRPC1   240000 perm   68 sec   (3533 perm/sec)   p_kst 3.983333e-03   p_cons 9.915875e-01   p_joint 4.841667e-03

Joint ci ratio: 1.121861e-01	ci left: 4.587257e-03	ci right 5.136319e-03	k: 1214	n:250000
Cons ci ratio: 7.265854e-04	ci left: 9.911201e-01	ci right 9.918444e-01	k: 247872	n:250000
KS ci ratio: 1.235888e-01	ci left: 3.760220e-03	ci right 4.259387e-03	k: 1001	n:250000
TRPC1   250000 perm   72 sec   (3482 perm/sec)   p_kst 4.004000e-03   p_cons 9.914880e-01   p_joint 4.856000e-03

Joint ci ratio: 1.101215e-01	ci left: 4.582828e-03	ci right 5.120609e-03	k: 1260	n:260000
Cons ci ratio: 7.109880e-04	ci left: 9.911632e-01	ci right 9.918719e-01	k: 257796	n:260000
KS ci ratio: 1.213691e-01	ci left: 3.753543e-03	ci right 4.242231e-03	k: 1038	n:260000
TRPC1   260000 perm   76 sec   (3441 perm/sec)   p_kst 3.992308e-03   p_cons 9.915231e-01   p_joint 4.846154e-03

Joint ci ratio: 1.081667e-01	ci left: 4.578812e-03	ci right 5.105977e-03	k: 1306	n:270000
Cons ci ratio: 6.955729e-04	ci left: 9.912221e-01	ci right 9.919154e-01	k: 267725	n:270000
KS ci ratio: 1.192091e-01	ci left: 3.751029e-03	ci right 4.230085e-03	k: 1076	n:270000
TRPC1   270000 perm   80 sec   (3394 perm/sec)   p_kst 3.985185e-03   p_cons 9.915741e-01   p_joint 4.837037e-03

Joint ci ratio: 1.060765e-01	ci left: 4.596024e-03	ci right 5.114306e-03	k: 1358	n:280000
Cons ci ratio: 6.816814e-04	ci left: 9.912623e-01	ci right 9.919417e-01	k: 277650	n:280000
KS ci ratio: 1.167930e-01	ci left: 3.773037e-03	ci right 4.244464e-03	k: 1121	n:280000
TRPC1   280000 perm   84 sec   (3350 perm/sec)   p_kst 4.003571e-03   p_cons 9.916071e-01   p_joint 4.850000e-03

Joint ci ratio: 1.047011e-01	ci left: 4.558401e-03	ci right 5.065366e-03	k: 1394	n:290000
Cons ci ratio: 6.695528e-04	ci left: 9.912752e-01	ci right 9.919425e-01	k: 287568	n:290000
KS ci ratio: 1.151139e-01	ci left: 3.753422e-03	ci right 4.215198e-03	k: 1154	n:290000
TRPC1   290000 perm   88 sec   (3307 perm/sec)   p_kst 3.979310e-03   p_cons 9.916138e-01   p_joint 4.806897e-03

Joint ci ratio: 1.028376e-01	ci left: 4.572044e-03	ci right 5.070929e-03	k: 1445	n:300000
Cons ci ratio: 6.608140e-04	ci left: 9.912160e-01	ci right 9.918745e-01	k: 297465	n:300000
KS ci ratio: 1.129812e-01	ci left: 3.770793e-03	ci right 4.225538e-03	k: 1198	n:300000
TRPC1   300000 perm   92 sec   (3268 perm/sec)   p_kst 3.993333e-03   p_cons 9.915500e-01   p_joint 4.816667e-03

Joint ci ratio: 1.015141e-01	ci left: 4.544004e-03	ci right 5.033067e-03	k: 1483	n:310000
Cons ci ratio: 6.484989e-04	ci left: 9.912626e-01	ci right 9.919088e-01	k: 307393	n:310000
KS ci ratio: 1.115045e-01	ci left: 3.749480e-03	ci right 4.195356e-03	k: 1230	n:310000
TRPC1   310000 perm   96 sec   (3231 perm/sec)   p_kst 3.967742e-03   p_cons 9.915903e-01   p_joint 4.783871e-03

Joint ci ratio: 9.965004e-02	ci left: 4.572605e-03	ci right 5.055180e-03	k: 1539	n:320000
Cons ci ratio: 6.381508e-04	ci left: 9.912714e-01	ci right 9.919072e-01	k: 317310	n:320000
KS ci ratio: 1.094767e-01	ci left: 3.772088e-03	ci right 4.211969e-03	k: 1276	n:320000
TRPC1   320000 perm   100 sec   (3196 perm/sec)   p_kst 3.987500e-03   p_cons 9.915938e-01   p_joint 4.809375e-03

Joint ci ratio: 9.819462e-02	ci left: 4.569986e-03	ci right 5.044835e-03	k: 1585	n:330000
Cons ci ratio: 6.297657e-04	ci left: 9.912395e-01	ci right 9.918669e-01	k: 327214	n:330000
KS ci ratio: 1.079248e-01	ci left: 3.766855e-03	ci right 4.199503e-03	k: 1313	n:330000
TRPC1   330000 perm   104 sec   (3161 perm/sec)   p_kst 3.978788e-03   p_cons 9.915576e-01   p_joint 4.803030e-03

Joint ci ratio: 9.689068e-02	ci left: 4.558958e-03	ci right 5.026014e-03	k: 1628	n:340000
Cons ci ratio: 6.218009e-04	ci left: 9.912067e-01	ci right 9.918261e-01	k: 337117	n:340000
KS ci ratio: 1.064767e-01	ci left: 3.759107e-03	ci right 4.184709e-03	k: 1349	n:340000
TRPC1   340000 perm   109 sec   (3126 perm/sec)   p_kst 3.967647e-03   p_cons 9.915206e-01   p_joint 4.788235e-03

Joint ci ratio: 9.555124e-02	ci left: 4.556968e-03	ci right 5.017004e-03	k: 1674	n:350000
Cons ci ratio: 6.146393e-04	ci left: 9.911613e-01	ci right 9.917734e-01	k: 347015	n:350000
KS ci ratio: 1.051234e-01	ci left: 3.749057e-03	ci right 4.167793e-03	k: 1384	n:350000
TRPC1   350000 perm   113 sec   (3091 perm/sec)   p_kst 3.954286e-03   p_cons 9.914714e-01   p_joint 4.782857e-03

Joint ci ratio: 9.407382e-02	ci left: 4.574119e-03	ci right 5.028353e-03	k: 1727	n:360000
Cons ci ratio: 6.069064e-04	ci left: 9.911410e-01	ci right 9.917455e-01	k: 356921	n:360000
KS ci ratio: 1.033828e-01	ci left: 3.772070e-03	ci right 4.185977e-03	k: 1431	n:360000
TRPC1   360000 perm   118 sec   (3052 perm/sec)   p_kst 3.975000e-03   p_cons 9.914472e-01   p_joint 4.797222e-03

Joint ci ratio: 9.271520e-02	ci left: 4.585113e-03	ci right 5.033507e-03	k: 1778	n:370000
Cons ci ratio: 5.979279e-04	ci left: 9.911660e-01	ci right 9.917614e-01	k: 366843	n:370000
KS ci ratio: 1.018643e-01	ci left: 3.783357e-03	ci right 4.192039e-03	k: 1474	n:370000
TRPC1   370000 perm   123 sec   (3016 perm/sec)   p_kst 3.983784e-03   p_cons 9.914676e-01   p_joint 4.805405e-03

Joint ci ratio: 9.179257e-02	ci left: 4.557000e-03	ci right 4.997972e-03	k: 1814	n:380000
Cons ci ratio: 5.890577e-04	ci left: 9.911977e-01	ci right 9.917843e-01	k: 376768	n:380000
KS ci ratio: 1.008789e-01	ci left: 3.758173e-03	ci right 4.159975e-03	k: 1503	n:380000
TRPC1   380000 perm   127 sec   (2982 perm/sec)   p_kst 3.955263e-03   p_cons 9.914947e-01   p_joint 4.773684e-03

Joint ci ratio: 9.055349e-02	ci left: 4.565437e-03	ci right 5.000945e-03	k: 1864	n:390000
Cons ci ratio: 5.818914e-04	ci left: 9.911887e-01	ci right 9.917681e-01	k: 386678	n:390000
KS ci ratio: 9.946660e-02	ci left: 3.769305e-03	ci right 4.166326e-03	k: 1546	n:390000
TRPC1   390000 perm   132 sec   (2950 perm/sec)   p_kst 3.964103e-03   p_cons 9.914821e-01   p_joint 4.779487e-03

Outputting figure to mutsig2_images.part000000000182/TRPC1.2_2328_390000_0.0039641_0.99148_0.0047795.png
                gene_name: TRPC1
               theta_stop: 0.099 
                    nperm: 390000 
                     p_ks: 0.0040 
        ci_ks_bounds_left: 0.0038 
       ci_ks_bounds_right: 0.0042 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.0048 
     ci_joint_bounds_left: 0.0046 
    ci_joint_bounds_right: 0.0050 

Current progress: 50 percent done.
TRPM7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.660958e-02	ci left: 4.045217e-01	ci right 4.239283e-01	k: 4142	n:10000
Cons ci ratio: 1.120715e-01	ci left: 1.028590e-01	ci right 1.151698e-01	k: 1089	n:10000
KS ci ratio: 5.207474e-02	ci left: 3.521745e-01	ci right 3.711061e-01	k: 3616	n:10000
TRPM7   10000 perm   2 sec   (4763 perm/sec)   p_kst 3.616000e-01   p_cons 1.089000e-01   p_joint 4.142000e-01

Joint ci ratio: 3.580763e-02	ci left: 3.679354e-01	ci right 3.814011e-01	k: 7493	n:20000
Cons ci ratio: 1.006066e-01	ci left: 6.698988e-02	ci right 7.413558e-02	k: 1410	n:20000
KS ci ratio: 3.629784e-02	ci left: 3.616097e-01	ci right 3.750286e-01	k: 7366	n:20000
TRPM7   20000 perm   5 sec   (4314 perm/sec)   p_kst 3.683000e-01   p_cons 7.050000e-02   p_joint 3.746500e-01

Joint ci ratio: 7.709795e-02	ci left: 7.626656e-02	ci right 8.241520e-02	k: 2379	n:30000
Cons ci ratio: 8.151533e-02	ci left: 6.864201e-02	ci right 7.450795e-02	k: 2146	n:30000
KS ci ratio: 2.964021e-02	ci left: 3.628049e-01	ci right 3.737539e-01	k: 11048	n:30000
TRPM7   30000 perm   7 sec   (4147 perm/sec)   p_kst 3.682667e-01   p_cons 7.153333e-02   p_joint 7.930000e-02

Outputting figure to mutsig2_images.part000000000182/TRPM7.2_5754_30000_0.36827_0.071533_0.0793.png
                gene_name: TRPM7
               theta_stop: 0.082 
                    nperm: 30000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.072 
      ci_cons_bounds_left: 0.069 
     ci_cons_bounds_right: 0.075 
                  p_joint: 0.079 
     ci_joint_bounds_left: 0.076 
    ci_joint_bounds_right: 0.082 

Current progress: 75 percent done.
TRPV4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.669787e-02	ci left: 6.738786e-01	ci right 6.922147e-01	k: 6831	n:10000
Cons ci ratio: 1.273034e-01	ci left: 8.106153e-02	ci right 9.218067e-02	k: 865	n:10000
KS ci ratio: 1.137175e-01	ci left: 1.001293e-01	ci right 1.123011e-01	k: 1061	n:10000
TRPV4   10000 perm   2 sec   (6021 perm/sec)   p_kst 1.061000e-01   p_cons 8.650000e-02   p_joint 6.831000e-01

Joint ci ratio: 4.752799e-02	ci left: 2.477303e-01	ci right 2.598414e-01	k: 5075	n:20000
Cons ci ratio: 1.079048e-01	ci left: 5.855047e-02	ci right 6.527759e-02	k: 1237	n:20000
KS ci ratio: 8.103225e-02	ci left: 1.004895e-01	ci right 1.090258e-01	k: 2094	n:20000
TRPV4   20000 perm   4 sec   (5369 perm/sec)   p_kst 1.047000e-01   p_cons 6.185000e-02   p_joint 2.537500e-01

Joint ci ratio: 3.618431e-02	ci left: 2.760841e-01	ci right 2.862916e-01	k: 8435	n:30000
Cons ci ratio: 8.777750e-02	ci left: 5.959078e-02	ci right 6.509435e-02	k: 1869	n:30000
KS ci ratio: 6.592305e-02	ci left: 1.019469e-01	ci right 1.089297e-01	k: 3162	n:30000
TRPV4   30000 perm   6 sec   (5011 perm/sec)   p_kst 1.054000e-01   p_cons 6.230000e-02   p_joint 2.811667e-01

Outputting figure to mutsig2_images.part000000000182/TRPV4.2_2676_30000_0.1054_0.0623_0.28117.png
                gene_name: TRPV4
               theta_stop: 0.088 
                    nperm: 30000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.062 
      ci_cons_bounds_left: 0.060 
     ci_cons_bounds_right: 0.065 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000182
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 182 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1540>
Subject: Job 4398496: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000183> was used as the working directory.
Started at Wed Oct 24 16:17:54 2012
Results reported at Wed Oct 24 16:20:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000183.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000183.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 183  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000183.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    187.85 sec.
    Max Memory :       945 MB
    Max Swap   :      3742 MB

    Max Processes  :         7
    Max Threads    :        55

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
183
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 183
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 183: processing genes 16328 - 16417
Calculating significance of each gene.
Using projection method.
16328	TRUB2	1
16329	TRYX3	1
16330	TSC1	1.961421e-01
16331	TSC2	1
16332	TSC22D1	1
16333	TSC22D2	2.822676e-01
16334	TSC22D3	1
16335	TSC22D4	1
16336	TSEN15	1
16337	TSEN2	1
16338	TSEN34	1
16339	TSEN54	1
16340	TSFM	1
16341	TSG101	1
16342	TSGA10	1.642014e-01
16343	TSGA10IP	1
16344	TSGA13	1
16345	TSGA14	1
16346	TSHB	1
16347	TSHR	1.915488e-01
16348	TSHZ1	1
16349	TSHZ2	4.379148e-01
16350	TSHZ3	1
16351	TSKS	9.353627e-02
16352	TSKU	1
16353	TSLP	1
16354	TSN	1
16355	TSNARE1	1
16356	TSNAX	1
16357	TSNAXIP1	1
16358	TSPAN1	1
16359	TSPAN10	1
16360	TSPAN11	1
16361	TSPAN12	1
16362	TSPAN13	1
16363	TSPAN14	1
16364	TSPAN15	1
16365	TSPAN16	1
16366	TSPAN17	1
16367	TSPAN18	1
16368	TSPAN19	1
16369	TSPAN2	1
16370	TSPAN3	1
16371	TSPAN31	1
16372	TSPAN32	1
16373	TSPAN33	1
16374	TSPAN4	1
16375	TSPAN5	1
16376	TSPAN6	1
16377	TSPAN7	1
16378	TSPAN8	6.803514e-03
16379	TSPAN9	1
16380	TSPO	1
16381	TSPO2	1
16382	TSPYL1	1
16383	TSPYL2	1
16384	TSPYL4	1
16385	TSPYL5	8.042828e-03
16386	TSPYL6	1.563133e-01
16387	TSR1	1
16388	TSR2	1
16389	TSSC1	1
16390	TSSC4	1
16391	TSSK1B	1
16392	TSSK2	1
16393	TSSK3	1
16394	TSSK4	1
16395	TSSK6	1.070148e-01
16396	TST	9.234171e-02
16397	TSTA3	1
16398	TSTD2	1
16399	TTBK1	3.948274e-01
16400	TTBK2	5.202358e-01
16401	TTC1	1
16402	TTC12	1
16403	TTC13	1
16404	TTC14	1
16405	TTC15	1
16406	TTC16	1
16407	TTC17	1.976930e-01
16408	TTC18	1
16409	TTC19	1
16410	TTC21A	1
16411	TTC21B	1.282212e-01
16412	TTC22	1
16413	TTC23	1
16414	TTC23L	1.421140e-01
16415	TTC24	1
16416	TTC25	1
16417	TTC26	1
Done

Running MutSig 2:
Scatter job 183: processing genes 16328 - 16417
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TSPAN8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.384084e-02	ci left: 8.828843e-01	ci right 8.952880e-01	k: 8892	n:10000
KS ci ratio: 1.722442e-02	ci left: 8.308338e-01	ci right 8.453686e-01	k: 8382	n:10000
TSPAN8   10000 perm   1 sec   (6748 perm/sec)   p_kst 8.382000e-01   p_cons 8.892000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000183/TSPAN8.2_746_10000_0.8382_0.8892_1.png
                gene_name: TSPAN8
               theta_stop: 0.017 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.90 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
TSPYL5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.340890e-02	ci left: 8.891337e-01	ci right 9.012350e-01	k: 8953	n:10000
KS ci ratio: 1.045149e-02	ci left: 9.286459e-01	ci right 9.384997e-01	k: 9337	n:10000
TSPYL5   10000 perm   2 sec   (6227 perm/sec)   p_kst 9.337000e-01   p_cons 8.953000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000183/TSPYL5.2_1258_10000_0.9337_0.8953_1.png
                gene_name: TSPYL5
               theta_stop: 0.013 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
TTBK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.333015e-02	ci left: 8.902613e-01	ci right 9.023067e-01	k: 8964	n:10000
Cons ci ratio: 2.284895e-02	ci left: 7.377518e-01	ci right 7.549045e-01	k: 7464	n:10000
KS ci ratio: 6.328272e-02	ci left: 2.684428e-01	ci right 2.860871e-01	k: 2772	n:10000
TTBK2   10000 perm   2 sec   (5115 perm/sec)   p_kst 2.772000e-01   p_cons 7.464000e-01   p_joint 8.964000e-01

Outputting figure to mutsig2_images.part000000000183/TTBK2.2_3791_10000_0.2772_0.7464_0.8964.png
                gene_name: TTBK2
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.89 
    ci_joint_bounds_right: 0.90 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000183
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 183 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1655>
Subject: Job 4398501: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000184> was used as the working directory.
Started at Wed Oct 24 16:17:56 2012
Results reported at Wed Oct 24 16:22:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000184.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000184.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 184  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000184.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    311.21 sec.
    Max Memory :      1327 MB
    Max Swap   :      4162 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
184
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 184
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 184: processing genes 16418 - 16507
Calculating significance of each gene.
Using projection method.
16418	TTC27	1
16419	TTC29	1.937369e-01
16420	TTC3	4.323156e-01
16421	TTC30A	1.133943e-01
16422	TTC30B	2.728664e-01
16423	TTC31	1
16424	TTC32	1
16425	TTC33	1
16426	TTC35	1
16427	TTC36	1
16428	TTC37	1
16429	TTC38	1
16430	TTC39A	1
16431	TTC39B	1
16432	TTC39C	1.922828e-01
16433	TTC4	1
16434	TTC5	1
16435	TTC7A	1
16436	TTC7B	1
16437	TTC8	1
16438	TTC9	1
16439	TTC9B	1
16440	TTC9C	1
16441	TTF1	1
16442	TTF2	1
16443	TTK	2.407883e-01
16444	TTL	1
16445	TTLL1	1.223741e-01
16446	TTLL10	1
16447	TTLL11	1
16448	TTLL12	2.678240e-02
16449	TTLL13	1
16450	TTLL2	1
16451	TTLL3	1
16452	TTLL4	1
16453	TTLL5	1
16454	TTLL6	1
16455	TTLL7	1
16456	TTLL8	1
16457	TTLL9	1
16458	TTN	9.999221e-01
16459	TTPA	1
16460	TTPAL	1
16461	TTR	4.894467e-02
16462	TTYH1	1
16463	TTYH2	1
16464	TTYH3	1
16465	TUB	3.435535e-03
16466	TUBA1A	1
16467	TUBA1B	2.105978e-01
16468	TUBA1C	9.414860e-02
16469	TUBA3C	6.793934e-02
16470	TUBA3D	1
16471	TUBA3E	1
16472	TUBA4A	1
16473	TUBA8	4.038442e-02
16474	TUBAL3	1
16475	TUBB	1
16476	TUBB1	1
16477	TUBB2A	1
16478	TUBB2B	1
16479	TUBB2C	1
16480	TUBB3	1
16481	TUBB4	1.791034e-01
16482	TUBB4Q	1
16483	TUBB6	1
16484	TUBB8	1
16485	TUBD1	5.441201e-02
16486	TUBE1	1
16487	TUBG1	1
16488	TUBG2	1
16489	TUBGCP2	1
16490	TUBGCP3	1
16491	TUBGCP4	3.195242e-01
16492	TUBGCP5	2.122633e-01
16493	TUBGCP6	4.573965e-01
16494	TUFM	1
16495	TUFT1	7.386448e-02
16496	TULP1	1
16497	TULP2	1
16498	TULP3	1
16499	TULP4	1
16500	TUSC2	1
16501	TUSC3	1
16502	TUSC5	1
16503	TUT1	1
16504	TWF1	1
16505	TWF2	1
16506	TWIST1	1
16507	TWISTNB	8.271290e-02
Done

Running MutSig 2:
Scatter job 184: processing genes 16418 - 16507
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TTN
Processing conservation and coverage...
8% 17% 26% 35% 44% 53% 62% 71% 80% 89% 98% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.489098e-02	ci left: 5.481004e-01	ci right 5.676658e-01	k: 5579	n:10000
Cons ci ratio: 7.221246e-02	ci left: 2.193138e-01	ci right 2.358452e-01	k: 2275	n:10000
KS ci ratio: 2.391782e-02	ci left: 7.198696e-01	ci right 7.373970e-01	k: 7287	n:10000
TTN   10000 perm   15 sec   (667 perm/sec)   p_kst 7.287000e-01   p_cons 2.275000e-01   p_joint 5.579000e-01

Outputting figure to mutsig2_images.part000000000184/TTN.29_111433_10000_0.7287_0.2275_0.5579.png
                gene_name: TTN
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.57 

Current progress: 20 percent done.
TUB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.047660e-01	ci left: 1.163301e-01	ci right 1.292906e-01	k: 1227	n:10000
Cons ci ratio: 4.219262e-02	ci left: 4.533887e-01	ci right 4.730328e-01	k: 4632	n:10000
KS ci ratio: 9.096898e-02	ci left: 1.494297e-01	ci right 1.637710e-01	k: 1565	n:10000
TUB   10000 perm   2 sec   (6057 perm/sec)   p_kst 1.565000e-01   p_cons 4.632000e-01   p_joint 1.227000e-01

Joint ci ratio: 3.886143e-02	ci left: 3.305974e-01	ci right 3.437500e-01	k: 6743	n:20000
Cons ci ratio: 2.964289e-02	ci left: 4.595164e-01	ci right 4.733934e-01	k: 9329	n:20000
KS ci ratio: 6.312323e-02	ci left: 1.565232e-01	ci right 1.667754e-01	k: 3232	n:20000
TUB   20000 perm   4 sec   (5391 perm/sec)   p_kst 1.616000e-01   p_cons 4.664500e-01   p_joint 3.371500e-01

Outputting figure to mutsig2_images.part000000000184/TUB.3_1780_20000_0.1616_0.46645_0.33715.png
                gene_name: TUB
               theta_stop: 0.063 
                    nperm: 20000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.34 

Current progress: 40 percent done.
TTC30A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.750894e-02	ci left: 6.606855e-01	ci right 6.792154e-01	k: 6700	n:10000
Cons ci ratio: 5.173814e-02	ci left: 3.551569e-01	ci right 3.741220e-01	k: 3646	n:10000
KS ci ratio: 3.111722e-02	ci left: 6.037736e-01	ci right 6.229603e-01	k: 6134	n:10000
TTC30A   10000 perm   2 sec   (6136 perm/sec)   p_kst 6.134000e-01   p_cons 3.646000e-01   p_joint 6.700000e-01

Outputting figure to mutsig2_images.part000000000184/TTC30A.2_2002_10000_0.6134_0.3646_0.67.png
                gene_name: TTC30A
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    ci_joint_bounds_right: 0.68 

Current progress: 60 percent done.
TTLL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.870215e-02	ci left: 2.992559e-01	ci right 3.174558e-01	k: 3083	n:10000
Cons ci ratio: 1.726883e-02	ci left: 8.301215e-01	ci right 8.446814e-01	k: 8375	n:10000
KS ci ratio: 8.655262e-02	ci left: 1.627829e-01	ci right 1.776098e-01	k: 1701	n:10000
TTLL1   10000 perm   1 sec   (6809 perm/sec)   p_kst 1.701000e-01   p_cons 8.375000e-01   p_joint 3.083000e-01

Outputting figure to mutsig2_images.part000000000184/TTLL1.2_1308_10000_0.1701_0.8375_0.3083.png
                gene_name: TTLL1
               theta_stop: 0.087 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.32 

Current progress: 80 percent done.
TTLL12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.188359e-02	ci left: 3.538645e-01	ci right 3.728152e-01	k: 3633	n:10000
KS ci ratio: 4.736681e-02	ci left: 3.967519e-01	ci right 4.161027e-01	k: 4064	n:10000
TTLL12   10000 perm   2 sec   (6469 perm/sec)   p_kst 4.064000e-01   p_cons 3.633000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000184/TTLL12.2_1991_10000_0.4064_0.3633_1.png
                gene_name: TTLL12
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000184
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 184 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1723>
Subject: Job 4398508: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000185> was used as the working directory.
Started at Wed Oct 24 16:17:56 2012
Results reported at Wed Oct 24 16:19:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000185.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000185.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 185  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000185.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    126.22 sec.
    Max Memory :      1338 MB
    Max Swap   :      4154 MB

    Max Processes  :         7
    Max Threads    :        70

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
185
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 185
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 185: processing genes 16508 - 16596
Calculating significance of each gene.
Using projection method.
16508	TWSG1	1
16509	TXK	1
16510	TXLNA	1
16511	TXLNB	1.974877e-01
16512	TXLNG	1
16513	TXN	1
16514	TXN2	1
16515	TXNDC11	1
16516	TXNDC12	1
16517	TXNDC15	1
16518	TXNDC16	3.501261e-01
16519	TXNDC17	1
16520	TXNDC2	2.769183e-01
16521	TXNDC3	1
16522	TXNDC5	1
16523	TXNDC6	1
16524	TXNDC8	1
16525	TXNDC9	1
16526	TXNIP	2.069780e-01
16527	TXNL1	1
16528	TXNL4A	1
16529	TXNL4B	1.964405e-02
16530	TXNRD1	1.073334e-01
16531	TXNRD2	1
16532	TXNRD3IT1	1
16533	TYK2	1.148706e-02
16534	TYMP	1
16535	TYMS	1
16536	TYR	1
16537	TYRO3	1.479575e-01
16538	TYROBP	1
16539	TYRP1	1.250085e-01
16540	TYSND1	6.934672e-02
16541	TYW1	1
16542	TYW3	1
16543	U2AF1	1
16544	U2AF1L4	1
16545	U2AF2	1.005264e-01
16546	UACA	1.536628e-01
16547	UAP1	1.626388e-01
16548	UAP1L1	1
16549	UBA1	4.252672e-01
16550	UBA2	1
16551	UBA3	1
16552	UBA5	1
16553	UBA52	1.794932e-02
16554	UBA6	1
16555	UBA7	1
16556	UBAC1	1
16557	UBAC2	1
16558	UBAP1	1
16559	UBAP2	1
16560	UBAP2L	1
16561	UBASH3A	1.653446e-01
16562	UBASH3B	1
16563	UBB	1
16564	UBC	1
16565	UBD	1
16566	UBE2A	1
16567	UBE2B	1
16568	UBE2C	1
16569	UBE2CBP	8.804017e-02
16570	UBE2D1	1
16571	UBE2D2	1
16572	UBE2D3	7.073232e-02
16573	UBE2D4	1
16574	UBE2E1	1
16575	UBE2E2	1
16576	UBE2E3	1
16577	UBE2F	1
16578	UBE2G1	1
16579	UBE2G2	1
16580	UBE2H	5.272459e-02
16581	UBE2I	1
16582	UBE2J1	1
16583	UBE2J2	1.376825e-01
16584	UBE2K	1
16585	UBE2L3	1
16586	UBE2L6	1
16587	UBE2M	1
16588	UBE2N	1
16589	UBE2NL	2.055289e-02
16590	UBE2O	1
16591	UBE2Q1	1
16592	UBE2Q2	1
16593	UBE2R2	1
16594	UBE2S	1
16595	UBE2T	1
16596	UBE2U	1
Done

Running MutSig 2:
Scatter job 185: processing genes 16508 - 16596
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TYK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.020604e-02	ci left: 6.178376e-01	ci right 6.368881e-01	k: 6274	n:10000
Cons ci ratio: 5.410874e-02	ci left: 3.347852e-01	ci right 3.535056e-01	k: 3441	n:10000
KS ci ratio: 3.948518e-02	ci left: 4.864527e-01	ci right 5.061494e-01	k: 4963	n:10000
TYK2   10000 perm   2 sec   (5657 perm/sec)   p_kst 4.963000e-01   p_cons 3.441000e-01   p_joint 6.274000e-01

Outputting figure to mutsig2_images.part000000000185/TYK2.3_3656_10000_0.4963_0.3441_0.6274.png
                gene_name: TYK2
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 33 percent done.
UACA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.638133e-01	ci left: 1.874721e-02	ci right 2.453613e-02	k: 215	n:10000
Cons ci ratio: 7.032931e-03	ci left: 9.653082e-01	ci right 9.722151e-01	k: 9689	n:10000
KS ci ratio: 4.337666e-01	ci left: 6.348452e-03	ci right 9.946939e-03	k: 80	n:10000
UACA   10000 perm   2 sec   (5616 perm/sec)   p_kst 8.000000e-03   p_cons 9.689000e-01   p_joint 2.150000e-02

Joint ci ratio: 1.560097e-01	ci left: 2.820837e-02	ci right 3.302937e-02	k: 611	n:20000
Cons ci ratio: 4.819354e-03	ci left: 9.682682e-01	ci right 9.729936e-01	k: 19414	n:20000
KS ci ratio: 2.750958e-01	ci left: 8.667639e-03	ci right 1.147755e-02	k: 200	n:20000
UACA   20000 perm   4 sec   (5011 perm/sec)   p_kst 1.000000e-02   p_cons 9.707000e-01   p_joint 3.055000e-02

Joint ci ratio: 5.000166e-02	ci left: 1.657648e-01	ci right 1.742992e-01	k: 5100	n:30000
Cons ci ratio: 3.829139e-03	ci left: 9.702767e-01	ci right 9.740311e-01	k: 29166	n:30000
KS ci ratio: 2.259452e-01	ci left: 8.810667e-03	ci right 1.108575e-02	k: 297	n:30000
UACA   30000 perm   6 sec   (4790 perm/sec)   p_kst 9.900000e-03   p_cons 9.722000e-01   p_joint 1.700000e-01

Joint ci ratio: 3.360971e-02	ci left: 2.494910e-01	ci right 2.580447e-01	k: 10150	n:40000
Cons ci ratio: 3.311091e-03	ci left: 9.706188e-01	ci right 9.738621e-01	k: 38891	n:40000
KS ci ratio: 1.972692e-01	ci left: 8.810294e-03	ci right 1.076186e-02	k: 390	n:40000
UACA   40000 perm   9 sec   (4645 perm/sec)   p_kst 9.750000e-03   p_cons 9.722750e-01   p_joint 2.537500e-01

Joint ci ratio: 3.677085e-02	ci left: 1.817836e-01	ci right 1.886130e-01	k: 9259	n:50000
Cons ci ratio: 2.947818e-03	ci left: 9.710494e-01	ci right 9.739354e-01	k: 48626	n:50000
KS ci ratio: 1.763978e-01	ci left: 8.916851e-03	ci right 1.066077e-02	k: 488	n:50000
UACA   50000 perm   11 sec   (4532 perm/sec)   p_kst 9.760000e-03   p_cons 9.725200e-01   p_joint 1.851800e-01

Joint ci ratio: 2.901787e-02	ci left: 2.298210e-01	ci right 2.366048e-01	k: 13992	n:60000
Cons ci ratio: 2.683444e-03	ci left: 9.713306e-01	ci right 9.739568e-01	k: 58360	n:60000
KS ci ratio: 1.607247e-01	ci left: 9.027228e-03	ci right 1.062072e-02	k: 588	n:60000
UACA   60000 perm   14 sec   (4429 perm/sec)   p_kst 9.800000e-03   p_cons 9.726667e-01   p_joint 2.332000e-01

Joint ci ratio: 1.952314e-02	ci left: 3.618740e-01	ci right 3.690229e-01	k: 25581	n:70000
Cons ci ratio: 2.488734e-03	ci left: 9.713346e-01	ci right 9.737689e-01	k: 68080	n:70000
KS ci ratio: 1.477385e-01	ci left: 9.221087e-03	ci right 1.070567e-02	k: 696	n:70000
UACA   70000 perm   16 sec   (4339 perm/sec)   p_kst 9.942857e-03   p_cons 9.725714e-01   p_joint 3.654429e-01

Joint ci ratio: 1.835392e-02	ci left: 3.597914e-01	ci right 3.664686e-01	k: 29050	n:80000
Cons ci ratio: 2.327774e-03	ci left: 9.714198e-01	ci right 9.736958e-01	k: 77806	n:80000
KS ci ratio: 1.366943e-01	ci left: 9.479057e-03	ci right 1.088181e-02	k: 813	n:80000
UACA   80000 perm   19 sec   (4256 perm/sec)   p_kst 1.016250e-02   p_cons 9.725750e-01   p_joint 3.631250e-01

Joint ci ratio: 2.242807e-02	ci left: 2.505608e-01	ci right 2.562551e-01	k: 22806	n:90000
Cons ci ratio: 2.198592e-03	ci left: 9.713880e-01	ci right 9.735369e-01	k: 87523	n:90000
KS ci ratio: 1.281541e-01	ci left: 9.629123e-03	ci right 1.095828e-02	k: 925	n:90000
UACA   90000 perm   22 sec   (4174 perm/sec)   p_kst 1.027778e-02   p_cons 9.724778e-01   p_joint 2.534000e-01

Joint ci ratio: 1.664830e-02	ci left: 3.536903e-01	ci right 3.596380e-01	k: 35666	n:100000
Cons ci ratio: 2.076667e-03	ci left: 9.716814e-01	ci right 9.737111e-01	k: 97271	n:100000
KS ci ratio: 1.207439e-01	ci left: 9.799859e-03	ci right 1.106878e-02	k: 1042	n:100000
UACA   100000 perm   24 sec   (4101 perm/sec)   p_kst 1.042000e-02   p_cons 9.727100e-01   p_joint 3.566600e-01

Joint ci ratio: 1.588382e-02	ci left: 3.535327e-01	ci right 3.592021e-01	k: 39200	n:110000
Cons ci ratio: 1.985107e-03	ci left: 9.715905e-01	ci right 9.735300e-01	k: 106983	n:110000
KS ci ratio: 1.158050e-01	ci left: 9.711739e-03	ci right 1.091429e-02	k: 1133	n:110000
UACA   110000 perm   27 sec   (4031 perm/sec)   p_kst 1.030000e-02   p_cons 9.725727e-01   p_joint 3.563636e-01

Joint ci ratio: 2.184780e-02	ci left: 2.092089e-01	ci right 2.138384e-01	k: 25382	n:120000
Cons ci ratio: 1.783596e-03	ci left: 9.748809e-01	ci right 9.766294e-01	k: 117092	n:120000
KS ci ratio: 1.100727e-01	ci left: 9.882334e-03	ci right 1.104151e-02	k: 1254	n:120000
UACA   120000 perm   30 sec   (3964 perm/sec)   p_kst 1.045000e-02   p_cons 9.757667e-01   p_joint 2.115167e-01

Joint ci ratio: 2.165730e-02	ci left: 1.991002e-01	ci right 2.034670e-01	k: 26166	n:130000
Cons ci ratio: 1.713231e-03	ci left: 9.749267e-01	ci right 9.766059e-01	k: 126851	n:130000
KS ci ratio: 1.053085e-01	ci left: 9.990463e-03	ci right 1.110845e-02	k: 1370	n:130000
UACA   130000 perm   33 sec   (3900 perm/sec)   p_kst 1.053846e-02   p_cons 9.757769e-01   p_joint 2.012769e-01

Joint ci ratio: 2.158544e-02	ci left: 1.885952e-01	ci right 1.927176e-01	k: 26691	n:140000
Cons ci ratio: 1.646592e-03	ci left: 9.750832e-01	ci right 9.766970e-01	k: 136626	n:140000
KS ci ratio: 1.013552e-01	ci left: 1.003532e-02	ci right 1.111366e-02	k: 1479	n:140000
UACA   140000 perm   36 sec   (3838 perm/sec)   p_kst 1.056429e-02   p_cons 9.759000e-01   p_joint 1.906500e-01

Joint ci ratio: 2.264785e-02	ci left: 1.645847e-01	ci right 1.683615e-01	k: 24970	n:150000
Cons ci ratio: 1.588490e-03	ci left: 9.751790e-01	ci right 9.767358e-01	k: 146395	n:150000
KS ci ratio: 9.803453e-02	ci left: 1.002935e-02	ci right 1.106970e-02	k: 1581	n:150000
UACA   150000 perm   40 sec   (3779 perm/sec)   p_kst 1.054000e-02   p_cons 9.759667e-01   p_joint 1.664667e-01

Outputting figure to mutsig2_images.part000000000185/UACA.2_4370_150000_0.01054_0.97597_0.16647.png
                gene_name: UACA
               theta_stop: 0.098 
                    nperm: 150000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.16 
    ci_joint_bounds_right: 0.17 

Current progress: 67 percent done.
UAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.437554e-03	ci left: 9.515867e-01	ci right 9.597452e-01	k: 9558	n:10000
Cons ci ratio: 3.513206e-02	ci left: 5.446939e-01	ci right 5.642744e-01	k: 5545	n:10000
KS ci ratio: 1.377760e-02	ci left: 8.838059e-01	ci right 8.961658e-01	k: 8901	n:10000
UAP1   10000 perm   1 sec   (6669 perm/sec)   p_kst 8.901000e-01   p_cons 5.545000e-01   p_joint 9.558000e-01

Outputting figure to mutsig2_images.part000000000185/UAP1.2_1554_10000_0.8901_0.5545_0.9558.png
                gene_name: UAP1
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000185
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 185 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1554>
Subject: Job 4398511: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000186> was used as the working directory.
Started at Wed Oct 24 16:17:59 2012
Results reported at Wed Oct 24 16:20:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000186.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000186.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 186  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000186.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    226.64 sec.
    Max Memory :      1480 MB
    Max Swap   :      4007 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
186
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 186
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 186: processing genes 16597 - 16686
Calculating significance of each gene.
Using projection method.
16597	UBE2V1	1
16598	UBE2V2	1
16599	UBE2W	1
16600	UBE2Z	1
16601	UBE3A	2.755998e-01
16602	UBE3B	1.670711e-01
16603	UBE3C	9.931825e-02
16604	UBE4A	1
16605	UBE4B	1
16606	UBFD1	4.652187e-02
16607	UBIAD1	1
16608	UBL3	1
16609	UBL4A	1
16610	UBL4B	1
16611	UBL5	1
16612	UBL7	1
16613	UBLCP1	1
16614	UBN1	1
16615	UBN2	4.821736e-01
16616	UBOX5	1
16617	UBP1	1
16618	UBQLN1	1
16619	UBQLN2	1
16620	UBQLN3	1
16621	UBQLN4	2.642926e-01
16622	UBQLNL	1
16623	UBR1	1
16624	UBR2	1
16625	UBR3	1.858208e-01
16626	UBR4	1
16627	UBR5	5.556506e-01
16628	UBR7	1
16629	UBTD1	1
16630	UBTD2	1.075571e-01
16631	UBTF	1
16632	UBXN1	1
16633	UBXN10	1
16634	UBXN11	1
16635	UBXN2A	1
16636	UBXN2B	1
16637	UBXN4	1
16638	UBXN6	1
16639	UBXN7	1
16640	UBXN8	1
16641	UCHL1	1
16642	UCHL3	1
16643	UCHL5	1.610428e-01
16644	UCK1	1
16645	UCK2	1
16646	UCKL1	1.959511e-01
16647	UCMA	1
16648	UCN	1
16649	UCN2	1
16650	UCN3	1
16651	UCP1	1
16652	UCP2	1
16653	UCP3	1
16654	UEVLD	1.568369e-01
16655	UFC1	2.418700e-02
16656	UFD1L	1
16657	UFM1	1
16658	UFSP1	1
16659	UFSP2	1
16660	UGCG	1
16661	UGDH	1
16662	UGGT1	5.895007e-01
16663	UGGT2	1
16664	UGP2	1
16665	UGT1A1	1
16666	UGT1A10	1
16667	UGT1A3	3.683955e-02
16668	UGT1A4	1.480684e-01
16669	UGT1A5	1.799210e-01
16670	UGT1A6	1
16671	UGT1A7	1
16672	UGT1A8	1
16673	UGT1A9	1
16674	UGT2A1	1
16675	UGT2A2	1
16676	UGT2A3	1
16677	UGT2B10	1
16678	UGT2B11	1
16679	UGT2B15	2.636268e-01
16680	UGT2B17	1
16681	UGT2B28	1
16682	UGT2B4	1
16683	UGT2B7	1
16684	UGT3A1	1
16685	UGT3A2	1.843263e-01
16686	UGT8	1
Done

Running MutSig 2:
Scatter job 186: processing genes 16597 - 16686
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
UBR4
Processing conservation and coverage...
62% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.315853e-02	ci left: 1.741859e-01	ci right 1.893999e-01	k: 1817	n:10000
Cons ci ratio: 4.544803e-02	ci left: 4.167792e-01	ci right 4.362636e-01	k: 4265	n:10000
KS ci ratio: 8.394965e-02	ci left: 1.714324e-01	ci right 1.865551e-01	k: 1789	n:10000
UBR4   10000 perm   5 sec   (1992 perm/sec)   p_kst 1.789000e-01   p_cons 4.265000e-01   p_joint 1.817000e-01

Outputting figure to mutsig2_images.part000000000186/UBR4.5_15976_10000_0.1789_0.4265_0.1817.png
                gene_name: UBR4
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.19 

Current progress: 33 percent done.
UBE3C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.245959e-02	ci left: 9.024739e-01	ci right 9.138870e-01	k: 9083	n:10000
Cons ci ratio: 5.357377e-02	ci left: 3.392554e-01	ci right 3.580328e-01	k: 3486	n:10000
KS ci ratio: 3.108443e-02	ci left: 6.042758e-01	ci right 6.234578e-01	k: 6139	n:10000
UBE3C   10000 perm   2 sec   (5657 perm/sec)   p_kst 6.139000e-01   p_cons 3.486000e-01   p_joint 9.083000e-01

Outputting figure to mutsig2_images.part000000000186/UBE3C.2_3344_10000_0.6139_0.3486_0.9083.png
                gene_name: UBE3C
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.91 

Current progress: 67 percent done.
UBR5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.753719e-03	ci left: 9.759962e-01	ci right 9.817201e-01	k: 9790	n:10000
Cons ci ratio: 7.066629e-02	ci left: 2.269154e-01	ci right 2.436391e-01	k: 2352	n:10000
KS ci ratio: 4.347894e-02	ci left: 4.385190e-01	ci right 4.581112e-01	k: 4483	n:10000
UBR5   10000 perm   3 sec   (3253 perm/sec)   p_kst 4.483000e-01   p_cons 2.352000e-01   p_joint 9.790000e-01

Outputting figure to mutsig2_images.part000000000186/UBR5.2_8636_10000_0.4483_0.2352_0.979.png
                gene_name: UBR5
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000186
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 186 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 4398516: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000187> was used as the working directory.
Started at Wed Oct 24 16:18:03 2012
Results reported at Wed Oct 24 16:23:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000187.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000187.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 187  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000187.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    405.81 sec.
    Max Memory :      1601 MB
    Max Swap   :      4027 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
187
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 187
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 187: processing genes 16687 - 16776
Calculating significance of each gene.
Using projection method.
16687	UHMK1	1
16688	UHRF1	1
16689	UHRF1BP1	8.571121e-02
16690	UHRF1BP1L	3.825010e-01
16691	UHRF2	4.703515e-02
16692	UIMC1	1
16693	ULBP1	1
16694	ULBP2	1.174410e-01
16695	ULBP3	1
16696	ULK1	1
16697	ULK2	9.519968e-02
16698	ULK3	1
16699	ULK4	1
16700	UMOD	1
16701	UMODL1	2.537663e-01
16702	UMPS	1.417086e-01
16703	UNC119	1
16704	UNC119B	1
16705	UNC13A	1
16706	UNC13B	5.233786e-01
16707	UNC13C	1
16708	UNC13D	1
16709	UNC45A	1
16710	UNC45B	1
16711	UNC50	1
16712	UNC5A	1
16713	UNC5B	1
16714	UNC5C	1
16715	UNC5CL	1
16716	UNC5D	1
16717	UNC93A	1
16718	UNC93B1	1
16719	UNG	1.021786e-01
16720	UNK	2.167824e-02
16721	UPB1	1
16722	UPF1	1
16723	UPF2	2.809233e-01
16724	UPF3A	1.561040e-01
16725	UPF3B	5.036009e-02
16726	UPK1A	1
16727	UPK1B	1
16728	UPK2	1
16729	UPK3A	1.028637e-01
16730	UPK3B	1
16731	UPP1	1
16732	UPP2	1.290774e-01
16733	UPRT	1
16734	UQCC	1
16735	UQCR10	1
16736	UQCR11	1
16737	UQCRB	1
16738	UQCRC1	1
16739	UQCRC2	1.625647e-01
16740	UQCRFS1	1
16741	UQCRH	1
16742	UQCRHL	1
16743	UQCRQ	1
16744	URB2	1.498109e-01
16745	URGCP	1
16746	URM1	3.187555e-02
16747	UROC1	1
16748	UROD	1
16749	UROS	1.041780e-01
16750	USE1	1
16751	USF1	1
16752	USF2	1
16753	USH1C	1
16754	USH1G	1
16755	USH2A	2.878732e-01
16756	USHBP1	1
16757	USMG5	1
16758	USO1	1
16759	USP1	1.259821e-01
16760	USP10	1
16761	USP11	1.425820e-02
16762	USP12	1
16763	USP13	1
16764	USP14	1
16765	USP15	1
16766	USP16	1
16767	USP17L2	1
16768	USP18	2.718946e-02
16769	USP19	1
16770	USP2	1.183991e-01
16771	USP20	1.352063e-01
16772	USP21	2.793967e-01
16773	USP22	1
16774	USP24	1
16775	USP25	1
16776	USP26	1.998071e-02
Done

Running MutSig 2:
Scatter job 187: processing genes 16687 - 16776
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
UNK
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.357268e-02	ci left: 8.867766e-01	ci right 8.989934e-01	k: 8930	n:10000
Cons ci ratio: 4.546661e-02	ci left: 4.165799e-01	ci right 4.360631e-01	k: 4263	n:10000
KS ci ratio: 5.437344e-02	ci left: 3.326001e-01	ci right 3.512920e-01	k: 3419	n:10000
UNK   10000 perm   2 sec   (4818 perm/sec)   p_kst 3.419000e-01   p_cons 4.263000e-01   p_joint 8.930000e-01

Outputting figure to mutsig2_images.part000000000187/UNK.4_2729_10000_0.3419_0.4263_0.893.png
                gene_name: UNK
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.89 
    ci_joint_bounds_right: 0.90 

Current progress: 17 percent done.
USH2A
Processing conservation and coverage...
62% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.510603e-02	ci left: 4.204677e-01	ci right 4.399730e-01	k: 4302	n:10000
Cons ci ratio: 6.388808e-02	ci left: 2.646814e-01	ci right 2.822508e-01	k: 2734	n:10000
KS ci ratio: 3.580541e-02	ci left: 5.352782e-01	ci right 5.548955e-01	k: 5451	n:10000
USH2A   10000 perm   5 sec   (2212 perm/sec)   p_kst 5.451000e-01   p_cons 2.734000e-01   p_joint 4.302000e-01

Outputting figure to mutsig2_images.part000000000187/USH2A.4_15907_10000_0.5451_0.2734_0.4302.png
                gene_name: USH2A
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 33 percent done.
UHRF1BP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.173737e-02	ci left: 4.587799e-01	ci right 4.784384e-01	k: 4686	n:10000
Cons ci ratio: 1.137175e-01	ci left: 1.001293e-01	ci right 1.123011e-01	k: 1061	n:10000
KS ci ratio: 6.590188e-03	ci left: 9.692095e-01	ci right 9.757113e-01	k: 9726	n:10000
UHRF1BP1   10000 perm   2 sec   (4925 perm/sec)   p_kst 9.726000e-01   p_cons 1.061000e-01   p_joint 4.686000e-01

Joint ci ratio: 3.647006e-02	ci left: 3.594184e-01	ci right 3.728205e-01	k: 7322	n:20000
Cons ci ratio: 7.818539e-02	ci left: 1.072678e-01	ci right 1.160454e-01	k: 2232	n:20000
KS ci ratio: 4.919931e-03	ci left: 9.670225e-01	ci right 9.718397e-01	k: 19390	n:20000
UHRF1BP1   20000 perm   5 sec   (4407 perm/sec)   p_kst 9.695000e-01   p_cons 1.116000e-01   p_joint 3.661000e-01

Outputting figure to mutsig2_images.part000000000187/UHRF1BP1.3_4407_20000_0.9695_0.1116_0.3661.png
                gene_name: UHRF1BP1
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 50 percent done.
USP11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.077899e-01	ci left: 1.104696e-01	ci right 1.231546e-01	k: 1167	n:10000
Cons ci ratio: 4.841319e-02	ci left: 3.862964e-01	ci right 4.055643e-01	k: 3959	n:10000
KS ci ratio: 1.629514e-01	ci left: 5.022725e-02	ci right 5.923435e-02	k: 546	n:10000
USP11   10000 perm   2 sec   (5682 perm/sec)   p_kst 5.460000e-02   p_cons 3.959000e-01   p_joint 1.167000e-01

Joint ci ratio: 6.386703e-02	ci left: 1.534141e-01	ci right 1.635854e-01	k: 3169	n:20000
Cons ci ratio: 3.459713e-02	ci left: 3.841287e-01	ci right 3.977030e-01	k: 7818	n:20000
KS ci ratio: 1.174580e-01	ci left: 4.964363e-02	ci right 5.588721e-02	k: 1054	n:20000
USP11   20000 perm   4 sec   (5007 perm/sec)   p_kst 5.270000e-02   p_cons 3.909000e-01   p_joint 1.584500e-01

Joint ci ratio: 5.721426e-02	ci left: 1.314153e-01	ci right 1.391888e-01	k: 4058	n:30000
Cons ci ratio: 2.834648e-02	ci left: 3.837435e-01	ci right 3.948113e-01	k: 11678	n:30000
KS ci ratio: 9.475660e-02	ci left: 5.140387e-02	ci right 5.654961e-02	k: 1618	n:30000
USP11   30000 perm   6 sec   (4754 perm/sec)   p_kst 5.393333e-02   p_cons 3.892667e-01   p_joint 1.352667e-01

Outputting figure to mutsig2_images.part000000000187/USP11.3_2976_30000_0.053933_0.38927_0.13527.png
                gene_name: USP11
               theta_stop: 0.095 
                    nperm: 30000 
                     p_ks: 0.054 
        ci_ks_bounds_left: 0.051 
       ci_ks_bounds_right: 0.057 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 67 percent done.
UHRF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 6.163475e-02	ci left: 2.790384e-01	ci right 2.968853e-01	k: 2879	n:10000
KS ci ratio: 6.682605e-02	ci left: 2.473694e-01	ci right 2.645729e-01	k: 2559	n:10000
UHRF2   10000 perm   2 sec   (5747 perm/sec)   p_kst 2.559000e-01   p_cons 2.879000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000187/UHRF2.2_2473_10000_0.2559_0.2879_1.png
                gene_name: UHRF2
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
USP26
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.884054e-01	ci left: 4.844389e-03	ci right 8.053335e-03	k: 63	n:10000
Cons ci ratio: 5.319759e-01	ci left: 3.972510e-03	ci right 6.926868e-03	k: 53	n:10000
KS ci ratio: 2.079888e-01	ci left: 3.072413e-02	ci right 3.795045e-02	k: 342	n:10000
USP26   10000 perm   2 sec   (5614 perm/sec)   p_kst 3.420000e-02   p_cons 5.300000e-03   p_joint 6.300000e-03

Joint ci ratio: 3.929888e-01	ci left: 3.979794e-03	ci right 5.968329e-03	k: 98	n:20000
Cons ci ratio: 3.628969e-01	ci left: 4.749480e-03	ci right 6.898025e-03	k: 115	n:20000
KS ci ratio: 1.467418e-01	ci left: 3.191701e-02	ci right 3.701950e-02	k: 688	n:20000
USP26   20000 perm   4 sec   (4937 perm/sec)   p_kst 3.440000e-02   p_cons 5.750000e-03   p_joint 4.900000e-03

Joint ci ratio: 3.404351e-01	ci left: 3.652208e-03	ci right 5.179552e-03	k: 131	n:30000
Cons ci ratio: 2.971666e-01	ci left: 4.910451e-03	ci right 6.654022e-03	k: 172	n:30000
KS ci ratio: 1.203285e-01	ci left: 3.210725e-02	ci right 3.625027e-02	k: 1024	n:30000
USP26   30000 perm   6 sec   (4703 perm/sec)   p_kst 3.413333e-02   p_cons 5.733333e-03   p_joint 4.366667e-03

Joint ci ratio: 3.634302e-01	ci left: 2.374173e-03	ci right 3.450008e-03	k: 115	n:40000
Cons ci ratio: 2.617666e-01	ci left: 4.845542e-03	ci right 6.327624e-03	k: 222	n:40000
KS ci ratio: 1.029917e-01	ci left: 3.314718e-02	ci right 3.677074e-02	k: 1397	n:40000
USP26   40000 perm   9 sec   (4499 perm/sec)   p_kst 3.492500e-02   p_cons 5.550000e-03   p_joint 2.875000e-03

Joint ci ratio: 3.153926e-01	ci left: 2.594922e-03	ci right 3.584166e-03	k: 153	n:50000
Cons ci ratio: 2.311283e-01	ci left: 5.058959e-03	ci right 6.399407e-03	k: 285	n:50000
KS ci ratio: 9.276711e-02	ci left: 3.287823e-02	ci right 3.609611e-02	k: 1723	n:50000
USP26   50000 perm   12 sec   (4312 perm/sec)   p_kst 3.446000e-02   p_cons 5.700000e-03   p_joint 3.060000e-03

Joint ci ratio: 3.196637e-01	ci left: 2.100991e-03	ci right 2.914990e-03	k: 149	n:60000
Cons ci ratio: 2.083212e-01	ci left: 5.255462e-03	ci right 6.493069e-03	k: 351	n:60000
KS ci ratio: 8.470149e-02	ci left: 3.300489e-02	ci right 3.594037e-02	k: 2067	n:60000
USP26   60000 perm   14 sec   (4194 perm/sec)   p_kst 3.445000e-02   p_cons 5.850000e-03   p_joint 2.483333e-03

Joint ci ratio: 2.985276e-01	ci left: 2.090783e-03	ci right 2.837130e-03	k: 171	n:70000
Cons ci ratio: 1.997525e-01	ci left: 4.924832e-03	ci right 6.031054e-03	k: 382	n:70000
KS ci ratio: 7.839600e-02	ci left: 3.313213e-02	ci right 3.584950e-02	k: 2413	n:70000
USP26   70000 perm   17 sec   (4120 perm/sec)   p_kst 3.447143e-02   p_cons 5.457143e-03   p_joint 2.442857e-03

Joint ci ratio: 2.727658e-01	ci left: 2.224068e-03	ci right 2.937768e-03	k: 205	n:80000
Cons ci ratio: 1.889716e-01	ci left: 4.844352e-03	ci right 5.867024e-03	k: 427	n:80000
KS ci ratio: 7.342737e-02	ci left: 3.313544e-02	ci right 3.567347e-02	k: 2751	n:80000
USP26   80000 perm   20 sec   (4048 perm/sec)   p_kst 3.438750e-02   p_cons 5.337500e-03   p_joint 2.562500e-03

Joint ci ratio: 2.140933e-01	ci left: 3.313849e-03	ci right 4.118660e-03	k: 333	n:90000
Cons ci ratio: 1.778859e-01	ci left: 4.889171e-03	ci right 5.854243e-03	k: 482	n:90000
KS ci ratio: 6.939068e-02	ci left: 3.305489e-02	ci right 3.544192e-02	k: 3081	n:90000
USP26   90000 perm   23 sec   (3976 perm/sec)   p_kst 3.423333e-02   p_cons 5.355556e-03   p_joint 3.700000e-03

Joint ci ratio: 1.960995e-01	ci left: 3.589702e-03	ci right 4.379496e-03	k: 397	n:100000
Cons ci ratio: 1.688630e-01	ci left: 4.907269e-03	ci right 5.821781e-03	k: 535	n:100000
KS ci ratio: 6.575473e-02	ci left: 3.319035e-02	ci right 3.545677e-02	k: 3431	n:100000
USP26   100000 perm   26 sec   (3897 perm/sec)   p_kst 3.431000e-02   p_cons 5.350000e-03   p_joint 3.970000e-03

Joint ci ratio: 2.054060e-01	ci left: 2.961068e-03	ci right 3.647351e-03	k: 362	n:110000
Cons ci ratio: 1.619183e-01	ci left: 4.870738e-03	ci right 5.737477e-03	k: 582	n:110000
KS ci ratio: 6.273946e-02	ci left: 3.319641e-02	ci right 3.535551e-02	k: 3769	n:110000
USP26   110000 perm   29 sec   (3835 perm/sec)   p_kst 3.426364e-02   p_cons 5.290909e-03   p_joint 3.290909e-03

Joint ci ratio: 2.098283e-01	ci left: 2.595758e-03	ci right 3.211988e-03	k: 347	n:120000
Cons ci ratio: 1.560145e-01	ci left: 4.824919e-03	ci right 5.649269e-03	k: 627	n:120000
KS ci ratio: 6.011184e-02	ci left: 3.319524e-02	ci right 3.526068e-02	k: 4106	n:120000
USP26   120000 perm   32 sec   (3774 perm/sec)   p_kst 3.421667e-02   p_cons 5.225000e-03   p_joint 2.891667e-03

Joint ci ratio: 1.765721e-01	ci left: 3.443389e-03	ci right 4.117505e-03	k: 490	n:130000
Cons ci ratio: 1.507127e-01	ci left: 4.786636e-03	ci right 5.574146e-03	k: 672	n:130000
KS ci ratio: 5.786310e-02	ci left: 3.311242e-02	ci right 3.509305e-02	k: 4432	n:130000
USP26   130000 perm   35 sec   (3715 perm/sec)   p_kst 3.409231e-02   p_cons 5.169231e-03   p_joint 3.769231e-03

Joint ci ratio: 1.622906e-01	ci left: 3.813131e-03	ci right 4.493372e-03	k: 580	n:140000
Cons ci ratio: 1.452072e-01	ci left: 4.802416e-03	ci right 5.561157e-03	k: 724	n:140000
KS ci ratio: 5.606910e-02	ci left: 3.278901e-02	ci right 3.468751e-02	k: 4722	n:140000
USP26   140000 perm   38 sec   (3656 perm/sec)   p_kst 3.372857e-02   p_cons 5.171429e-03   p_joint 4.142857e-03

Joint ci ratio: 1.580029e-01	ci left: 3.763699e-03	ci right 4.415700e-03	k: 612	n:150000
Cons ci ratio: 1.407199e-01	ci left: 4.784379e-03	ci right 5.514950e-03	k: 771	n:150000
KS ci ratio: 5.419206e-02	ci left: 3.279247e-02	ci right 3.462561e-02	k: 5055	n:150000
USP26   150000 perm   42 sec   (3601 perm/sec)   p_kst 3.370000e-02   p_cons 5.140000e-03   p_joint 4.080000e-03

Joint ci ratio: 1.527357e-01	ci left: 3.786774e-03	ci right 4.418904e-03	k: 655	n:160000
Cons ci ratio: 1.357114e-01	ci left: 4.835331e-03	ci right 5.545281e-03	k: 829	n:160000
KS ci ratio: 5.257255e-02	ci left: 3.269770e-02	ci right 3.446925e-02	k: 5372	n:160000
USP26   160000 perm   45 sec   (3546 perm/sec)   p_kst 3.357500e-02   p_cons 5.181250e-03   p_joint 4.093750e-03

Joint ci ratio: 1.322543e-01	ci left: 4.801042e-03	ci right 5.486589e-03	k: 873	n:170000
Cons ci ratio: 1.312765e-01	ci left: 4.875004e-03	ci right 5.565564e-03	k: 886	n:170000
KS ci ratio: 5.103439e-02	ci left: 3.268452e-02	ci right 3.440202e-02	k: 5701	n:170000
USP26   170000 perm   49 sec   (3493 perm/sec)   p_kst 3.353529e-02   p_cons 5.211765e-03   p_joint 5.135294e-03

Joint ci ratio: 1.486212e-01	ci left: 3.563797e-03	ci right 4.141252e-03	k: 692	n:180000
Cons ci ratio: 1.273855e-01	ci left: 4.899845e-03	ci right 5.571797e-03	k: 941	n:180000
KS ci ratio: 4.965788e-02	ci left: 3.262957e-02	ci right 3.429661e-02	k: 6022	n:180000
USP26   180000 perm   52 sec   (3440 perm/sec)   p_kst 3.345556e-02   p_cons 5.227778e-03   p_joint 3.844444e-03

Joint ci ratio: 1.450059e-01	ci left: 3.553671e-03	ci right 4.114266e-03	k: 727	n:190000
Cons ci ratio: 1.242605e-01	ci left: 4.886636e-03	ci right 5.539127e-03	k: 989	n:190000
KS ci ratio: 4.828479e-02	ci left: 3.271621e-02	ci right 3.434017e-02	k: 6369	n:190000
USP26   190000 perm   56 sec   (3381 perm/sec)   p_kst 3.352105e-02   p_cons 5.205263e-03   p_joint 3.826316e-03

Joint ci ratio: 1.414562e-01	ci left: 3.554358e-03	ci right 4.100178e-03	k: 764	n:200000
Cons ci ratio: 1.218275e-01	ci left: 4.836141e-03	ci right 5.468333e-03	k: 1029	n:200000
KS ci ratio: 4.702688e-02	ci left: 3.278487e-02	ci right 3.436868e-02	k: 6714	n:200000
USP26   200000 perm   60 sec   (3334 perm/sec)   p_kst 3.357000e-02   p_cons 5.145000e-03   p_joint 3.820000e-03

Joint ci ratio: 1.202685e-01	ci left: 4.730511e-03	ci right 5.340418e-03	k: 1056	n:210000
Cons ci ratio: 1.188086e-01	ci left: 4.850636e-03	ci right 5.467906e-03	k: 1082	n:210000
KS ci ratio: 4.579868e-02	ci left: 3.293696e-02	ci right 3.448547e-02	k: 7078	n:210000
USP26   210000 perm   64 sec   (3289 perm/sec)   p_kst 3.370476e-02   p_cons 5.152381e-03   p_joint 5.028571e-03

Joint ci ratio: 1.173083e-01	ci left: 4.753652e-03	ci right 5.350412e-03	k: 1110	n:220000
Cons ci ratio: 1.158500e-01	ci left: 4.877232e-03	ci right 5.481373e-03	k: 1138	n:220000
KS ci ratio: 4.470547e-02	ci left: 3.301276e-02	ci right 3.452683e-02	k: 7428	n:220000
USP26   220000 perm   68 sec   (3243 perm/sec)   p_kst 3.376364e-02   p_cons 5.172727e-03   p_joint 5.045455e-03

Joint ci ratio: 1.198402e-01	ci left: 4.352849e-03	ci right 4.911921e-03	k: 1064	n:230000
Cons ci ratio: 1.135325e-01	ci left: 4.863662e-03	ci right 5.453263e-03	k: 1185	n:230000
KS ci ratio: 4.365794e-02	ci left: 3.312539e-02	ci right 3.460813e-02	k: 7788	n:230000
USP26   230000 perm   72 sec   (3199 perm/sec)   p_kst 3.386087e-02   p_cons 5.152174e-03   p_joint 4.626087e-03

Joint ci ratio: 1.228420e-01	ci left: 3.965381e-03	ci right 4.488371e-03	k: 1013	n:240000
Cons ci ratio: 1.113033e-01	ci left: 4.855384e-03	ci right 5.431667e-03	k: 1233	n:240000
KS ci ratio: 4.279230e-02	ci left: 3.305994e-02	ci right 3.450968e-02	k: 8107	n:240000
USP26   240000 perm   76 sec   (3156 perm/sec)   p_kst 3.377917e-02   p_cons 5.137500e-03   p_joint 4.220833e-03

Joint ci ratio: 1.081457e-01	ci left: 4.945168e-03	ci right 5.514395e-03	k: 1306	n:250000
Cons ci ratio: 1.089446e-01	ci left: 4.871221e-03	ci right 5.436345e-03	k: 1287	n:250000
KS ci ratio: 4.196073e-02	ci left: 3.302375e-02	ci right 3.444308e-02	k: 8432	n:250000
USP26   250000 perm   80 sec   (3112 perm/sec)   p_kst 3.372800e-02   p_cons 5.148000e-03   p_joint 5.224000e-03

Joint ci ratio: 1.342347e-01	ci left: 3.049725e-03	ci right 3.492232e-03	k: 849	n:260000
Cons ci ratio: 1.070509e-01	ci left: 4.856008e-03	ci right 5.408957e-03	k: 1333	n:260000
KS ci ratio: 4.110060e-02	ci left: 3.310865e-02	ci right 3.450177e-02	k: 8788	n:260000
USP26   260000 perm   85 sec   (3069 perm/sec)   p_kst 3.380000e-02   p_cons 5.126923e-03   p_joint 3.265385e-03

Joint ci ratio: 1.162137e-01	ci left: 3.952353e-03	ci right 4.443568e-03	k: 1132	n:270000
Cons ci ratio: 1.050234e-01	ci left: 4.863642e-03	ci right 5.406323e-03	k: 1385	n:270000
KS ci ratio: 4.032553e-02	ci left: 3.313251e-02	ci right 3.449974e-02	k: 9129	n:270000
USP26   270000 perm   89 sec   (3027 perm/sec)   p_kst 3.381111e-02   p_cons 5.129630e-03   p_joint 4.192593e-03

Joint ci ratio: 1.140203e-01	ci left: 3.963817e-03	ci right 4.446534e-03	k: 1176	n:280000
Cons ci ratio: 1.034692e-01	ci left: 4.836026e-03	ci right 5.367154e-03	k: 1427	n:280000
KS ci ratio: 3.956894e-02	ci left: 3.319381e-02	ci right 3.453728e-02	k: 9481	n:280000
USP26   280000 perm   94 sec   (2986 perm/sec)   p_kst 3.386071e-02   p_cons 5.096429e-03   p_joint 4.200000e-03

Joint ci ratio: 1.116715e-01	ci left: 3.994685e-03	ci right 4.470479e-03	k: 1226	n:290000
Cons ci ratio: 1.010194e-01	ci left: 4.904482e-03	ci right 5.429619e-03	k: 1497	n:290000
KS ci ratio: 3.883296e-02	ci left: 3.328527e-02	ci right 3.460682e-02	k: 9843	n:290000
USP26   290000 perm   98 sec   (2948 perm/sec)   p_kst 3.394138e-02   p_cons 5.162069e-03   p_joint 4.227586e-03

Joint ci ratio: 1.234450e-01	ci left: 3.143146e-03	ci right 3.559873e-03	k: 1004	n:300000
Cons ci ratio: 9.911773e-02	ci left: 4.929497e-03	ci right 5.446799e-03	k: 1555	n:300000
KS ci ratio: 3.819861e-02	ci left: 3.326516e-02	ci right 3.456386e-02	k: 10173	n:300000
USP26   300000 perm   103 sec   (2912 perm/sec)   p_kst 3.391000e-02   p_cons 5.183333e-03   p_joint 3.346667e-03

Joint ci ratio: 1.217025e-01	ci left: 3.132433e-03	ci right 3.541455e-03	k: 1033	n:310000
Cons ci ratio: 9.734987e-02	ci left: 4.949837e-03	ci right 5.459480e-03	k: 1612	n:310000
KS ci ratio: 3.760548e-02	ci left: 3.322733e-02	ci right 3.450398e-02	k: 10497	n:310000
USP26   310000 perm   108 sec   (2876 perm/sec)   p_kst 3.386129e-02   p_cons 5.200000e-03   p_joint 3.332258e-03

Joint ci ratio: 1.199186e-01	ci left: 3.128492e-03	ci right 3.530586e-03	k: 1064	n:320000
Cons ci ratio: 9.578873e-02	ci left: 4.956781e-03	ci right 5.458494e-03	k: 1665	n:320000
KS ci ratio: 3.702322e-02	ci left: 3.321989e-02	ci right 3.447607e-02	k: 10830	n:320000
USP26   320000 perm   113 sec   (2840 perm/sec)   p_kst 3.384375e-02   p_cons 5.203125e-03   p_joint 3.325000e-03

Joint ci ratio: 1.248420e-01	ci left: 2.792777e-03	ci right 3.167550e-03	k: 982	n:330000
Cons ci ratio: 9.430037e-02	ci left: 4.963364e-03	ci right 5.457507e-03	k: 1718	n:330000
KS ci ratio: 3.645874e-02	ci left: 3.322806e-02	ci right 3.446499e-02	k: 11168	n:330000
USP26   330000 perm   118 sec   (2806 perm/sec)   p_kst 3.384242e-02   p_cons 5.206061e-03   p_joint 2.975758e-03

Joint ci ratio: 1.161100e-01	ci left: 3.147125e-03	ci right 3.537886e-03	k: 1135	n:340000
Cons ci ratio: 9.293203e-02	ci left: 4.963871e-03	ci right 5.450503e-03	k: 1769	n:340000
KS ci ratio: 3.596138e-02	ci left: 3.316008e-02	ci right 3.437729e-02	k: 11480	n:340000
USP26   340000 perm   123 sec   (2772 perm/sec)   p_kst 3.376471e-02   p_cons 5.202941e-03   p_joint 3.338235e-03

Joint ci ratio: 1.016797e-01	ci left: 4.013495e-03	ci right 4.446205e-03	k: 1479	n:350000
Cons ci ratio: 9.162157e-02	ci left: 4.964398e-03	ci right 5.443851e-03	k: 1820	n:350000
KS ci ratio: 3.539078e-02	ci left: 3.326606e-02	ci right 3.446739e-02	k: 11852	n:350000
USP26   350000 perm   128 sec   (2740 perm/sec)   p_kst 3.386286e-02   p_cons 5.200000e-03   p_joint 4.225714e-03

Joint ci ratio: 1.000034e-01	ci left: 4.037397e-03	ci right 4.465087e-03	k: 1529	n:360000
Cons ci ratio: 9.048659e-02	ci left: 4.951364e-03	ci right 5.423321e-03	k: 1866	n:360000
KS ci ratio: 3.490564e-02	ci left: 3.325611e-02	ci right 3.444029e-02	k: 12184	n:360000
USP26   360000 perm   133 sec   (2708 perm/sec)   p_kst 3.384444e-02   p_cons 5.183333e-03   p_joint 4.247222e-03

Joint ci ratio: 9.865854e-02	ci left: 4.038972e-03	ci right 4.460742e-03	k: 1571	n:370000
Cons ci ratio: 8.915882e-02	ci left: 4.965497e-03	ci right 5.431493e-03	k: 1922	n:370000
KS ci ratio: 3.444990e-02	ci left: 3.322805e-02	ci right 3.439548e-02	k: 12509	n:370000
USP26   370000 perm   138 sec   (2673 perm/sec)   p_kst 3.380811e-02   p_cons 5.194595e-03   p_joint 4.245946e-03

Outputting figure to mutsig2_images.part000000000187/USP26.2_2745_370000_0.033808_0.0051946_0.0042459.png
                gene_name: USP26
               theta_stop: 0.099 
                    nperm: 370000 
                     p_ks: 0.034 
        ci_ks_bounds_left: 0.033 
       ci_ks_bounds_right: 0.034 
                   p_cons: 0.0052 
      ci_cons_bounds_left: 0.0050 
     ci_cons_bounds_right: 0.0054 
                  p_joint: 0.0042 
     ci_joint_bounds_left: 0.0040 
    ci_joint_bounds_right: 0.0045 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000187
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 187 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 4398523: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000188> was used as the working directory.
Started at Wed Oct 24 16:18:03 2012
Results reported at Wed Oct 24 16:21:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000188.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000188.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 188  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000188.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    294.24 sec.
    Max Memory :      1626 MB
    Max Swap   :      4017 MB

    Max Processes  :         7
    Max Threads    :        59

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
188
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 188
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 188: processing genes 16777 - 16865
Calculating significance of each gene.
Using projection method.
16777	USP28	3.493054e-01
16778	USP29	2.644330e-01
16779	USP3	1
16780	USP30	1
16781	USP31	1
16782	USP32	1
16783	USP33	1
16784	USP34	6.023313e-01
16785	USP35	1
16786	USP36	4.733407e-01
16787	USP37	6.000034e-03
16788	USP38	2.568774e-01
16789	USP39	1
16790	USP4	4.100735e-01
16791	USP40	1
16792	USP42	1
16793	USP43	1
16794	USP44	1
16795	USP45	1
16796	USP46	1
16797	USP47	1
16798	USP48	2.120508e-01
16799	USP49	1
16800	USP5	1
16801	USP50	1
16802	USP51	1
16803	USP53	5.925333e-02
16804	USP54	1.786424e-01
16805	USP6	1
16806	USP6NL	1
16807	USP7	1.715824e-01
16808	USP8	1.392938e-01
16809	USP9X	5.797245e-01
16810	USPL1	1
16811	UST	1
16812	UTP11L	1
16813	UTP14A	1
16814	UTP14C	8.143674e-03
16815	UTP15	1
16816	UTP18	1
16817	UTP20	5.645339e-01
16818	UTP23	1
16819	UTP3	1
16820	UTP6	1
16821	UTRN	5.047374e-01
16822	UTS2	1
16823	UTS2D	2.171397e-02
16824	UVRAG	4.454397e-02
16825	UXS1	1.542320e-01
16826	UXT	1
16827	VAC14	1
16828	VAMP1	1
16829	VAMP2	1
16830	VAMP3	1
16831	VAMP4	1
16832	VAMP5	1
16833	VAMP7	1
16834	VAMP8	1
16835	VANGL1	1
16836	VANGL2	1
16837	VAPA	1
16838	VAPB	1
16839	VARS	1
16840	VARS2	4.353056e-01
16841	VASH1	1
16842	VASH2	1
16843	VASN	1
16844	VASP	1
16845	VAT1	1
16846	VAT1L	1
16847	VAV1	1
16848	VAV2	1
16849	VAV3	1
16850	VAX1	1
16851	VAX2	1
16852	VBP1	1
16853	VCAM1	1
16854	VCAN	1
16855	VCL	1
16856	VCP	1
16857	VCPIP1	4.710066e-01
16858	VCX	1
16859	VCX2	1
16860	VCX3A	1
16861	VCX3B	1
16862	VDAC1	1
16863	VDAC2	9.952323e-02
16864	VDAC3	1
16865	VDR	1
Done

Running MutSig 2:
Scatter job 188: processing genes 16777 - 16865
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
USP37
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.701956e-02	ci left: 2.462819e-01	ci right 2.634612e-01	k: 2548	n:10000
Cons ci ratio: 2.148972e-01	ci left: 2.873209e-02	ci right 3.574387e-02	k: 321	n:10000
KS ci ratio: 3.235097e-02	ci left: 5.851015e-01	ci right 6.044433e-01	k: 5948	n:10000
USP37   10000 perm   2 sec   (4847 perm/sec)   p_kst 5.948000e-01   p_cons 3.210000e-02   p_joint 2.548000e-01

Joint ci ratio: 7.019251e-02	ci left: 1.301446e-01	ci right 1.396618e-01	k: 2697	n:20000
Cons ci ratio: 1.492271e-01	ci left: 3.085647e-02	ci right 3.588039e-02	k: 666	n:20000
KS ci ratio: 2.296951e-02	ci left: 5.860029e-01	ci right 5.996701e-01	k: 11857	n:20000
USP37   20000 perm   7 sec   (2718 perm/sec)   p_kst 5.928500e-01   p_cons 3.330000e-02   p_joint 1.348500e-01

Joint ci ratio: 5.422957e-02	ci left: 1.442959e-01	ci right 1.523723e-01	k: 4449	n:30000
Cons ci ratio: 1.228966e-01	ci left: 3.078084e-02	ci right 3.484363e-02	k: 983	n:30000
KS ci ratio: 1.866243e-02	ci left: 5.896533e-01	ci right 6.007949e-01	k: 17857	n:30000
USP37   30000 perm   10 sec   (3018 perm/sec)   p_kst 5.952333e-01   p_cons 3.276667e-02   p_joint 1.483000e-01

Joint ci ratio: 4.723257e-02	ci left: 1.434193e-01	ci right 1.503821e-01	k: 5875	n:40000
Cons ci ratio: 1.074093e-01	ci left: 3.049156e-02	ci right 3.397679e-02	k: 1288	n:40000
KS ci ratio: 1.617011e-02	ci left: 5.901701e-01	ci right 5.998161e-01	k: 23800	n:40000
USP37   40000 perm   13 sec   (3182 perm/sec)   p_kst 5.950000e-01   p_cons 3.220000e-02   p_joint 1.468750e-01

Joint ci ratio: 4.639022e-02	ci left: 1.220536e-01	ci right 1.278700e-01	k: 6247	n:50000
Cons ci ratio: 9.641835e-02	ci left: 3.045501e-02	ci right 3.355964e-02	k: 1599	n:50000
KS ci ratio: 1.452858e-02	ci left: 5.884983e-01	ci right 5.971309e-01	k: 29641	n:50000
USP37   50000 perm   15 sec   (3249 perm/sec)   p_kst 5.928200e-01   p_cons 3.198000e-02   p_joint 1.249400e-01

Outputting figure to mutsig2_images.part000000000188/USP37.3_3032_50000_0.59282_0.03198_0.12494.png
                gene_name: USP37
               theta_stop: 0.096 
                    nperm: 50000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.032 
      ci_cons_bounds_left: 0.030 
     ci_cons_bounds_right: 0.034 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 17 percent done.
UTP14C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.846546e-02	ci left: 1.300234e-01	ci right 1.435889e-01	k: 1367	n:10000
Cons ci ratio: 3.619696e-02	ci left: 5.298707e-01	ci right 5.495061e-01	k: 5397	n:10000
KS ci ratio: 2.098973e-01	ci left: 3.015459e-02	ci right 3.732038e-02	k: 336	n:10000
UTP14C   10000 perm   2 sec   (5594 perm/sec)   p_kst 3.360000e-02   p_cons 5.397000e-01   p_joint 1.367000e-01

Joint ci ratio: 8.049680e-02	ci left: 1.017171e-01	ci right 1.102979e-01	k: 2119	n:20000
Cons ci ratio: 2.547089e-02	ci left: 5.352144e-01	ci right 5.490733e-01	k: 10843	n:20000
KS ci ratio: 1.480826e-01	ci left: 3.133844e-02	ci right 3.639826e-02	k: 676	n:20000
UTP14C   20000 perm   4 sec   (4998 perm/sec)   p_kst 3.380000e-02   p_cons 5.421500e-01   p_joint 1.059500e-01

Joint ci ratio: 6.479514e-02	ci left: 1.051991e-01	ci right 1.122768e-01	k: 3261	n:30000
Cons ci ratio: 2.071302e-02	ci left: 5.385101e-01	ci right 5.498146e-01	k: 16325	n:30000
KS ci ratio: 1.213745e-01	ci left: 3.155716e-02	ci right 3.566714e-02	k: 1007	n:30000
UTP14C   30000 perm   6 sec   (4778 perm/sec)   p_kst 3.356667e-02   p_cons 5.441667e-01   p_joint 1.087000e-01

Joint ci ratio: 7.718549e-02	ci left: 5.823218e-02	ci right 6.293187e-02	k: 2422	n:40000
Cons ci ratio: 1.874289e-02	ci left: 5.174160e-01	ci right 5.272308e-01	k: 20893	n:40000
KS ci ratio: 1.053982e-01	ci left: 3.166062e-02	ci right 3.520754e-02	k: 1336	n:40000
UTP14C   40000 perm   9 sec   (4622 perm/sec)   p_kst 3.340000e-02   p_cons 5.223250e-01   p_joint 6.055000e-02

Joint ci ratio: 5.778520e-02	ci left: 8.183940e-02	ci right 8.672899e-02	k: 4213	n:50000
Cons ci ratio: 1.675033e-02	ci left: 5.183507e-01	ci right 5.271267e-01	k: 26137	n:50000
KS ci ratio: 9.492693e-02	ci left: 3.141229e-02	ci right 3.456224e-02	k: 1648	n:50000
UTP14C   50000 perm   11 sec   (4493 perm/sec)   p_kst 3.296000e-02   p_cons 5.227400e-01   p_joint 8.426000e-02

Outputting figure to mutsig2_images.part000000000188/UTP14C.3_2305_50000_0.03296_0.52274_0.08426.png
                gene_name: UTP14C
               theta_stop: 0.095 
                    nperm: 50000 
                     p_ks: 0.033 
        ci_ks_bounds_left: 0.031 
       ci_ks_bounds_right: 0.035 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.084 
     ci_joint_bounds_left: 0.082 
    ci_joint_bounds_right: 0.087 

Current progress: 33 percent done.
USP53
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.462034e-02	ci left: 7.081598e-01	ci right 7.259136e-01	k: 7171	n:10000
Cons ci ratio: 1.140784e-01	ci left: 9.954457e-02	ci right 1.116863e-01	k: 1055	n:10000
KS ci ratio: 2.113385e-02	ci left: 7.664836e-01	ci right 7.829561e-01	k: 7748	n:10000
USP53   10000 perm   2 sec   (5392 perm/sec)   p_kst 7.748000e-01   p_cons 1.055000e-01   p_joint 7.171000e-01

Joint ci ratio: 3.903156e-02	ci left: 3.286570e-01	ci right 3.417909e-01	k: 6704	n:20000
Cons ci ratio: 7.840294e-02	ci left: 1.067273e-01	ci right 1.154861e-01	k: 2221	n:20000
KS ci ratio: 1.493313e-02	ci left: 7.691984e-01	ci right 7.808215e-01	k: 15501	n:20000
USP53   20000 perm   4 sec   (4898 perm/sec)   p_kst 7.750500e-01   p_cons 1.110500e-01   p_joint 3.352000e-01

Outputting figure to mutsig2_images.part000000000188/USP53.2_3282_20000_0.77505_0.11105_0.3352.png
                gene_name: USP53
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.34 

Current progress: 50 percent done.
USP54
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.527067e-02	ci left: 6.973649e-01	ci right 7.153147e-01	k: 7064	n:10000
KS ci ratio: 6.224134e-02	ci left: 2.750767e-01	ci right 2.928493e-01	k: 2839	n:10000
USP54   10000 perm   2 sec   (4578 perm/sec)   p_kst 2.839000e-01   p_cons 7.064000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000188/USP54.2_5143_10000_0.2839_0.7064_1.png
                gene_name: USP54
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
UVRAG
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.020373e-01	ci left: 1.219999e-01	ci right 1.352172e-01	k: 1285	n:10000
Cons ci ratio: 1.267434e-01	ci left: 8.174120e-02	ci right 9.290058e-02	k: 872	n:10000
KS ci ratio: 3.004477e-02	ci left: 6.203499e-01	ci right 6.393743e-01	k: 6299	n:10000
UVRAG   10000 perm   2 sec   (6288 perm/sec)   p_kst 6.299000e-01   p_cons 8.720000e-02   p_joint 1.285000e-01

Joint ci ratio: 1.099110e-02	ci left: 8.593235e-01	ci right 8.688703e-01	k: 17283	n:20000
Cons ci ratio: 8.973561e-02	ci left: 8.317825e-02	ci right 9.104227e-02	k: 1741	n:20000
KS ci ratio: 2.083991e-02	ci left: 6.321482e-01	ci right 6.455114e-01	k: 12777	n:20000
UVRAG   20000 perm   4 sec   (5482 perm/sec)   p_kst 6.388500e-01   p_cons 8.705000e-02   p_joint 8.641500e-01

Outputting figure to mutsig2_images.part000000000188/UVRAG.2_2160_20000_0.63885_0.08705_0.86415.png
                gene_name: UVRAG
               theta_stop: 0.090 
                    nperm: 20000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.087 
      ci_cons_bounds_left: 0.083 
     ci_cons_bounds_right: 0.091 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 83 percent done.
VCPIP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.769094e-01	ci left: 8.686342e-03	ci right 1.280614e-02	k: 106	n:10000
Cons ci ratio: 9.995174e-02	ci left: 1.265977e-01	ci right 1.400167e-01	k: 1332	n:10000
KS ci ratio: 3.769094e-01	ci left: 8.686342e-03	ci right 1.280614e-02	k: 106	n:10000
VCPIP1   10000 perm   2 sec   (5055 perm/sec)   p_kst 1.060000e-02   p_cons 1.332000e-01   p_joint 1.060000e-02

Joint ci ratio: 2.536541e-01	ci left: 1.030287e-02	ci right 1.334154e-02	k: 235	n:20000
Cons ci ratio: 7.123371e-02	ci left: 1.267960e-01	ci right 1.362115e-01	k: 2629	n:20000
KS ci ratio: 2.536541e-01	ci left: 1.030287e-02	ci right 1.334154e-02	k: 235	n:20000
VCPIP1   20000 perm   4 sec   (4623 perm/sec)   p_kst 1.175000e-02   p_cons 1.314500e-01   p_joint 1.175000e-02

Joint ci ratio: 2.083036e-01	ci left: 1.045075e-02	ci right 1.291184e-02	k: 349	n:30000
Cons ci ratio: 5.812001e-02	ci left: 1.278267e-01	ci right 1.355115e-01	k: 3949	n:30000
KS ci ratio: 2.083036e-01	ci left: 1.045075e-02	ci right 1.291184e-02	k: 349	n:30000
VCPIP1   30000 perm   7 sec   (4430 perm/sec)   p_kst 1.163333e-02   p_cons 1.316333e-01   p_joint 1.163333e-02

Joint ci ratio: 1.839528e-01	ci left: 1.019181e-02	ci right 1.228005e-02	k: 448	n:40000
Cons ci ratio: 4.987469e-02	ci left: 1.304285e-01	ci right 1.371248e-01	k: 5350	n:40000
KS ci ratio: 1.839528e-01	ci left: 1.019181e-02	ci right 1.228005e-02	k: 448	n:40000
VCPIP1   40000 perm   9 sec   (4299 perm/sec)   p_kst 1.120000e-02   p_cons 1.337500e-01   p_joint 1.120000e-02

Joint ci ratio: 1.625310e-01	ci left: 1.056470e-02	ci right 1.245265e-02	k: 574	n:50000
Cons ci ratio: 4.446270e-02	ci left: 1.315405e-01	ci right 1.375420e-01	k: 6726	n:50000
KS ci ratio: 1.625310e-01	ci left: 1.056470e-02	ci right 1.245265e-02	k: 574	n:50000
VCPIP1   50000 perm   12 sec   (4208 perm/sec)   p_kst 1.148000e-02   p_cons 1.345200e-01   p_joint 1.148000e-02

Joint ci ratio: 1.490269e-01	ci left: 1.054987e-02	ci right 1.226455e-02	k: 683	n:60000
Cons ci ratio: 4.067730e-02	ci left: 1.313002e-01	ci right 1.367686e-01	k: 8041	n:60000
KS ci ratio: 1.490269e-01	ci left: 1.054987e-02	ci right 1.226455e-02	k: 683	n:60000
VCPIP1   60000 perm   15 sec   (4124 perm/sec)   p_kst 1.138333e-02   p_cons 1.340167e-01   p_joint 1.138333e-02

Joint ci ratio: 1.381475e-01	ci left: 1.058533e-02	ci right 1.216984e-02	k: 795	n:70000
Cons ci ratio: 3.779802e-02	ci left: 1.306626e-01	ci right 1.357107e-01	k: 9322	n:70000
KS ci ratio: 1.381475e-01	ci left: 1.058533e-02	ci right 1.216984e-02	k: 795	n:70000
VCPIP1   70000 perm   17 sec   (4048 perm/sec)   p_kst 1.135714e-02   p_cons 1.331714e-01   p_joint 1.135714e-02

Joint ci ratio: 1.300750e-01	ci left: 1.049438e-02	ci right 1.196639e-02	k: 897	n:80000
Cons ci ratio: 3.529735e-02	ci left: 1.312123e-01	ci right 1.359393e-01	k: 10685	n:80000
KS ci ratio: 1.300750e-01	ci left: 1.049438e-02	ci right 1.196639e-02	k: 897	n:80000
VCPIP1   80000 perm   20 sec   (3976 perm/sec)   p_kst 1.121250e-02   p_cons 1.335625e-01   p_joint 1.121250e-02

Joint ci ratio: 1.225287e-01	ci left: 1.055503e-02	ci right 1.194341e-02	k: 1011	n:90000
Cons ci ratio: 3.333912e-02	ci left: 1.309312e-01	ci right 1.353814e-01	k: 11983	n:90000
KS ci ratio: 1.225287e-01	ci left: 1.055503e-02	ci right 1.194341e-02	k: 1011	n:90000
VCPIP1   90000 perm   23 sec   (3902 perm/sec)   p_kst 1.123333e-02   p_cons 1.331444e-01   p_joint 1.123333e-02

Joint ci ratio: 1.157446e-01	ci left: 1.068323e-02	ci right 1.200535e-02	k: 1133	n:100000
Cons ci ratio: 3.173083e-02	ci left: 1.303050e-01	ci right 1.345163e-01	k: 13240	n:100000
KS ci ratio: 1.157446e-01	ci left: 1.068323e-02	ci right 1.200535e-02	k: 1133	n:100000
VCPIP1   100000 perm   26 sec   (3830 perm/sec)   p_kst 1.133000e-02   p_cons 1.324000e-01   p_joint 1.133000e-02

Joint ci ratio: 1.106908e-01	ci left: 1.064837e-02	ci right 1.190487e-02	k: 1239	n:110000
Cons ci ratio: 3.026387e-02	ci left: 1.303300e-01	ci right 1.343439e-01	k: 14556	n:110000
KS ci ratio: 1.106908e-01	ci left: 1.064837e-02	ci right 1.190487e-02	k: 1239	n:110000
VCPIP1   110000 perm   29 sec   (3765 perm/sec)   p_kst 1.126364e-02   p_cons 1.323273e-01   p_joint 1.126364e-02

Joint ci ratio: 1.065667e-01	ci left: 1.055546e-02	ci right 1.175168e-02	k: 1337	n:120000
Cons ci ratio: 2.897689e-02	ci left: 1.304043e-01	ci right 1.342468e-01	k: 15878	n:120000
KS ci ratio: 1.065667e-01	ci left: 1.055546e-02	ci right 1.175168e-02	k: 1337	n:120000
VCPIP1   120000 perm   32 sec   (3700 perm/sec)   p_kst 1.114167e-02   p_cons 1.323167e-01   p_joint 1.114167e-02

Joint ci ratio: 1.017665e-01	ci left: 1.071000e-02	ci right 1.186580e-02	k: 1466	n:130000
Cons ci ratio: 2.786367e-02	ci left: 1.302867e-01	ci right 1.339759e-01	k: 17176	n:130000
KS ci ratio: 1.017665e-01	ci left: 1.071000e-02	ci right 1.186580e-02	k: 1466	n:130000
VCPIP1   130000 perm   36 sec   (3638 perm/sec)   p_kst 1.127692e-02   p_cons 1.321231e-01   p_joint 1.127692e-02

Joint ci ratio: 9.856590e-02	ci left: 1.062048e-02	ci right 1.172848e-02	k: 1563	n:140000
Cons ci ratio: 2.685121e-02	ci left: 1.303446e-01	ci right 1.338992e-01	k: 18496	n:140000
KS ci ratio: 9.856590e-02	ci left: 1.062048e-02	ci right 1.172848e-02	k: 1563	n:140000
VCPIP1   140000 perm   39 sec   (3581 perm/sec)   p_kst 1.116429e-02   p_cons 1.321143e-01   p_joint 1.116429e-02

Outputting figure to mutsig2_images.part000000000188/VCPIP1.2_3681_140000_0.011164_0.13211_0.011164.png
                gene_name: VCPIP1
               theta_stop: 0.099 
                    nperm: 140000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.011 
       ci_ks_bounds_right: 0.012 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.011 
     ci_joint_bounds_left: 0.011 
    ci_joint_bounds_right: 0.012 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000188
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 188 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1652>
Subject: Job 4398529: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1652>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000189> was used as the working directory.
Started at Wed Oct 24 16:18:05 2012
Results reported at Wed Oct 24 16:20:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000189.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000189.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 189  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000189.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    137.60 sec.
    Max Memory :      1556 MB
    Max Swap   :      3989 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
189
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 189
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 189: processing genes 16866 - 16955
Calculating significance of each gene.
Using projection method.
16866	VEGFA	1
16867	VEGFB	1
16868	VEGFC	1.918097e-01
16869	VENTX	1
16870	VEPH1	3.769756e-01
16871	VEZF1	1
16872	VEZT	1
16873	VGF	2.028907e-01
16874	VGLL1	1
16875	VGLL2	1
16876	VGLL3	1
16877	VGLL4	1
16878	VHL	1
16879	VHLL	1
16880	VIL1	1
16881	VILL	2.781440e-01
16882	VIM	1
16883	VIP	1
16884	VIPAR	1
16885	VIPR1	1
16886	VIPR2	1
16887	VIT	1
16888	VKORC1	1
16889	VKORC1L1	1
16890	VLDLR	1
16891	VMA21	1
16892	VMAC	1
16893	VMO1	1
16894	VN1R1	1
16895	VN1R2	1
16896	VN1R4	1.511266e-02
16897	VN1R5	1
16898	VNN1	1.960324e-01
16899	VNN2	1
16900	VOPP1	1
16901	VPRBP	4.118144e-01
16902	VPREB1	1
16903	VPREB3	1
16904	VPS11	1
16905	VPS13A	2.096956e-01
16906	VPS13B	7.030164e-01
16907	VPS13C	5.376100e-01
16908	VPS13D	7.082989e-01
16909	VPS16	1
16910	VPS18	1
16911	VPS24	1
16912	VPS25	7.805360e-02
16913	VPS26A	1
16914	VPS26B	1
16915	VPS28	1
16916	VPS29	1
16917	VPS33A	1
16918	VPS33B	1
16919	VPS35	1
16920	VPS36	1
16921	VPS37A	1
16922	VPS37B	1
16923	VPS37C	1
16924	VPS39	1
16925	VPS41	1
16926	VPS45	1.902586e-01
16927	VPS4A	1
16928	VPS4B	1
16929	VPS52	2.741787e-01
16930	VPS53	1.084905e-01
16931	VPS54	1
16932	VPS72	1.960985e-01
16933	VPS8	1
16934	VRK1	1
16935	VRK2	1
16936	VRK3	1
16937	VSIG1	1
16938	VSIG10	1
16939	VSIG2	1.650198e-01
16940	VSIG4	1
16941	VSIG8	1
16942	VSNL1	1
16943	VSTM1	1
16944	VSTM2A	1
16945	VSTM2L	1
16946	VSX1	1
16947	VSX2	1
16948	VTA1	1
16949	VTCN1	1
16950	VTI1A	1
16951	VTI1B	1
16952	VTN	1
16953	VWA1	1
16954	VWA2	1
16955	VWA3A	1.526028e-03
Done

Running MutSig 2:
Scatter job 189: processing genes 16866 - 16955
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
VPS13A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.142636e-02	ci left: 5.990540e-01	ci right 6.182826e-01	k: 6087	n:10000
Cons ci ratio: 4.445889e-02	ci left: 4.275470e-01	ci right 4.470895e-01	k: 4373	n:10000
KS ci ratio: 3.375935e-02	ci left: 5.643380e-01	ci right 5.838188e-01	k: 5741	n:10000
VPS13A   10000 perm   3 sec   (3659 perm/sec)   p_kst 5.741000e-01   p_cons 4.373000e-01   p_joint 6.087000e-01

Outputting figure to mutsig2_images.part000000000189/VPS13A.3_9941_10000_0.5741_0.4373_0.6087.png
                gene_name: VPS13A
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 33 percent done.
VWA3A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.138375e-01	ci left: 9.993440e-02	ci right 1.120962e-01	k: 1059	n:10000
Cons ci ratio: 2.019297e-02	ci left: 7.821871e-01	ci right 7.982435e-01	k: 7903	n:10000
KS ci ratio: 1.509149e-01	ci left: 5.841227e-02	ci right 6.804410e-02	k: 631	n:10000
VWA3A   10000 perm   2 sec   (4501 perm/sec)   p_kst 6.310000e-02   p_cons 7.903000e-01   p_joint 1.059000e-01

Joint ci ratio: 7.409931e-02	ci left: 1.181830e-01	ci right 1.273270e-01	k: 2454	n:20000
Cons ci ratio: 1.428056e-02	ci left: 7.845406e-01	ci right 7.958749e-01	k: 15805	n:20000
KS ci ratio: 1.099059e-01	ci left: 5.650427e-02	ci right 6.312442e-02	k: 1195	n:20000
VWA3A   20000 perm   5 sec   (4416 perm/sec)   p_kst 5.975000e-02   p_cons 7.902500e-01   p_joint 1.227000e-01

Joint ci ratio: 6.817359e-02	ci left: 9.587243e-02	ci right 1.026721e-01	k: 2977	n:30000
Cons ci ratio: 1.164064e-02	ci left: 7.861527e-01	ci right 7.953909e-01	k: 23724	n:30000
KS ci ratio: 9.093044e-02	ci left: 5.567479e-02	ci right 6.101114e-02	k: 1749	n:30000
VWA3A   30000 perm   7 sec   (4304 perm/sec)   p_kst 5.830000e-02   p_cons 7.908000e-01   p_joint 9.923333e-02

Outputting figure to mutsig2_images.part000000000189/VWA3A.3_3687_30000_0.0583_0.7908_0.099233.png
                gene_name: VWA3A
               theta_stop: 0.091 
                    nperm: 30000 
                     p_ks: 0.058 
        ci_ks_bounds_left: 0.056 
       ci_ks_bounds_right: 0.061 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.099 
     ci_joint_bounds_left: 0.096 
    ci_joint_bounds_right: 0.10 

Current progress: 67 percent done.
VPS13B
Processing conservation and coverage...
79% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.019175e-03	ci left: 9.925085e-01	ci right 9.955930e-01	k: 9942	n:10000
Cons ci ratio: 3.934331e-02	ci left: 4.882520e-01	ci right 5.079491e-01	k: 4981	n:10000
KS ci ratio: 2.991605e-02	ci left: 6.223600e-01	ci right 6.413631e-01	k: 6319	n:10000
VPS13B   10000 perm   3 sec   (3378 perm/sec)   p_kst 6.319000e-01   p_cons 4.981000e-01   p_joint 9.942000e-01

Outputting figure to mutsig2_images.part000000000189/VPS13B.2_12507_10000_0.6319_0.4981_0.9942.png
                gene_name: VPS13B
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 1.00 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000189
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 189 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1547>
Subject: Job 4398534: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000190> was used as the working directory.
Started at Wed Oct 24 16:18:08 2012
Results reported at Wed Oct 24 16:20:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000190.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000190.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 190  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000190.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    265.90 sec.
    Max Memory :      1445 MB
    Max Swap   :      3889 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
190
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 190
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 190: processing genes 16956 - 17045
Calculating significance of each gene.
Using projection method.
16956	VWA3B	1
16957	VWA5A	1
16958	VWC2	2.893603e-03
16959	VWC2L	1
16960	VWCE	1
16961	VWF	1.543497e-01
16962	WAC	9.532573e-02
16963	WAPAL	1
16964	WARS	1.460514e-01
16965	WARS2	1
16966	WAS	1
16967	WASF1	1
16968	WASF2	2.529477e-01
16969	WASF3	1
16970	WASL	1
16971	WBP1	1
16972	WBP11	1
16973	WBP2	1
16974	WBP2NL	1
16975	WBP4	1
16976	WBP5	1
16977	WBSCR16	1
16978	WBSCR17	1
16979	WBSCR22	1
16980	WBSCR27	1
16981	WBSCR28	1
16982	WDFY1	1
16983	WDFY2	1
16984	WDFY3	7.462048e-01
16985	WDHD1	1
16986	WDR1	1
16987	WDR11	1
16988	WDR12	1
16989	WDR13	1
16990	WDR16	1
16991	WDR17	9.355855e-02
16992	WDR18	1
16993	WDR19	3.126176e-01
16994	WDR20	1
16995	WDR24	1
16996	WDR25	1
16997	WDR26	1
16998	WDR27	1
16999	WDR3	1.241254e-01
17000/17942 17000	WDR31	1
17001	WDR33	1
17002	WDR34	1
17003	WDR35	3.295961e-01
17004	WDR36	3.902538e-01
17005	WDR37	1
17006	WDR38	1
17007	WDR4	8.390510e-02
17008	WDR41	1
17009	WDR43	1
17010	WDR44	1
17011	WDR45	1
17012	WDR45L	1
17013	WDR46	1
17014	WDR47	1
17015	WDR48	2.504020e-01
17016	WDR49	6.906026e-03
17017	WDR5	1
17018	WDR52	1
17019	WDR53	1
17020	WDR54	1
17021	WDR55	1.402007e-01
17022	WDR59	1.551392e-01
17023	WDR5B	1
17024	WDR6	1
17025	WDR60	8.833366e-02
17026	WDR61	1
17027	WDR62	5.523365e-01
17028	WDR63	1
17029	WDR64	1
17030	WDR65	3.170171e-02
17031	WDR66	1
17032	WDR67	4.311310e-01
17033	WDR69	1
17034	WDR7	7.891870e-02
17035	WDR70	1
17036	WDR72	1
17037	WDR73	9.158363e-02
17038	WDR74	3.462300e-02
17039	WDR75	3.302736e-01
17040	WDR76	1
17041	WDR77	1
17042	WDR78	1.671227e-01
17043	WDR8	1
17044	WDR81	8.889125e-02
17045	WDR82	1
Done

Running MutSig 2:
Scatter job 190: processing genes 16956 - 17045
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
WDR65
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.357136e-01	ci left: 7.175179e-02	ci right 8.229618e-02	k: 769	n:10000
Cons ci ratio: 5.740679e-02	ci left: 3.087773e-01	ci right 3.271288e-01	k: 3179	n:10000
KS ci ratio: 2.252227e-01	ci left: 2.608227e-02	ci right 3.279558e-02	k: 293	n:10000
WDR65   10000 perm   2 sec   (5789 perm/sec)   p_kst 2.930000e-02   p_cons 3.179000e-01   p_joint 7.690000e-02

Joint ci ratio: 1.302882e-01	ci left: 4.047238e-02	ci right 4.616135e-02	k: 865	n:20000
Cons ci ratio: 4.051339e-02	ci left: 3.123432e-01	ci right 3.253095e-01	k: 6376	n:20000
KS ci ratio: 1.560097e-01	ci left: 2.820837e-02	ci right 3.302937e-02	k: 611	n:20000
WDR65   20000 perm   7 sec   (2818 perm/sec)   p_kst 3.055000e-02   p_cons 3.188000e-01   p_joint 4.325000e-02

Joint ci ratio: 8.992521e-02	ci left: 5.688186e-02	ci right 6.227049e-02	k: 1786	n:30000
Cons ci ratio: 3.288836e-02	ci left: 3.160498e-01	ci right 3.266515e-01	k: 9640	n:30000
KS ci ratio: 1.283959e-01	ci left: 2.819549e-02	ci right 3.209621e-02	k: 903	n:30000
WDR65   30000 perm   9 sec   (3243 perm/sec)   p_kst 3.010000e-02   p_cons 3.213333e-01   p_joint 5.953333e-02

Joint ci ratio: 9.168694e-02	ci left: 4.169289e-02	ci right 4.572369e-02	k: 1747	n:40000
Cons ci ratio: 2.853394e-02	ci left: 3.159772e-01	ci right 3.251489e-01	k: 12822	n:40000
KS ci ratio: 1.119792e-01	ci left: 2.805811e-02	ci right 3.141062e-02	k: 1188	n:40000
WDR65   40000 perm   11 sec   (3484 perm/sec)   p_kst 2.970000e-02   p_cons 3.205500e-01   p_joint 4.367500e-02

Joint ci ratio: 6.623816e-02	ci left: 6.328763e-02	ci right 6.764299e-02	k: 3272	n:50000
Cons ci ratio: 2.555996e-02	ci left: 3.158121e-01	ci right 3.240088e-01	k: 15995	n:50000
KS ci ratio: 1.034786e-01	ci left: 2.645445e-02	ci right 2.936071e-02	k: 1394	n:50000
WDR65   50000 perm   14 sec   (3631 perm/sec)   p_kst 2.788000e-02   p_cons 3.199000e-01   p_joint 6.544000e-02

Joint ci ratio: 6.020985e-02	ci left: 6.399319e-02	ci right 6.798225e-02	k: 3958	n:60000
Cons ci ratio: 2.337519e-02	ci left: 3.153874e-01	ci right 3.228635e-01	k: 19147	n:60000
KS ci ratio: 9.452081e-02	ci left: 2.654795e-02	ci right 2.919798e-02	k: 1671	n:60000
WDR65   60000 perm   16 sec   (3718 perm/sec)   p_kst 2.785000e-02   p_cons 3.191167e-01   p_joint 6.596667e-02

Outputting figure to mutsig2_images.part000000000190/WDR65.3_2137_60000_0.02785_0.31912_0.065967.png
                gene_name: WDR65
               theta_stop: 0.095 
                    nperm: 60000 
                     p_ks: 0.028 
        ci_ks_bounds_left: 0.027 
       ci_ks_bounds_right: 0.029 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.066 
     ci_joint_bounds_left: 0.064 
    ci_joint_bounds_right: 0.068 

Current progress: 17 percent done.
VWF
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.283688e-02	ci left: 7.379539e-01	ci right 7.551022e-01	k: 7466	n:10000
KS ci ratio: 2.502117e-02	ci left: 7.015006e-01	ci right 7.193767e-01	k: 7105	n:10000
VWF   10000 perm   3 sec   (3419 perm/sec)   p_kst 7.105000e-01   p_cons 7.466000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000190/VWF.2_8646_10000_0.7105_0.7466_1.png
                gene_name: VWF
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.76 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 33 percent done.
WDR17
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.880677e-02	ci left: 6.398548e-01	ci right 6.586581e-01	k: 6493	n:10000
Cons ci ratio: 2.873724e-02	ci left: 6.409613e-01	ci right 6.597510e-01	k: 6504	n:10000
KS ci ratio: 8.386407e-02	ci left: 1.717274e-01	ci right 1.868599e-01	k: 1792	n:10000
WDR17   10000 perm   2 sec   (4867 perm/sec)   p_kst 1.792000e-01   p_cons 6.504000e-01   p_joint 6.493000e-01

Outputting figure to mutsig2_images.part000000000190/WDR17.2_4089_10000_0.1792_0.6504_0.6493.png
                gene_name: WDR17
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 50 percent done.
WDR49
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.688109e-03	ci left: 9.683648e-01	ci right 9.749566e-01	k: 9718	n:10000
Cons ci ratio: 2.747785e-02	ci left: 6.611889e-01	ci right 6.797117e-01	k: 6705	n:10000
KS ci ratio: 8.838341e-03	ci left: 9.473144e-01	ci right 9.558201e-01	k: 9517	n:10000
WDR49   10000 perm   2 sec   (6280 perm/sec)   p_kst 9.517000e-01   p_cons 6.705000e-01   p_joint 9.718000e-01

Outputting figure to mutsig2_images.part000000000190/WDR49.2_2150_10000_0.9517_0.6705_0.9718.png
                gene_name: WDR49
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.97 

Current progress: 67 percent done.
WDR67
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.936231e-03	ci left: 9.348550e-01	ci right 9.442869e-01	k: 9397	n:10000
Cons ci ratio: 2.252919e-02	ci left: 7.431099e-01	ci right 7.601433e-01	k: 7517	n:10000
KS ci ratio: 6.298409e-02	ci left: 2.703238e-01	ci right 2.880050e-01	k: 2791	n:10000
WDR67   10000 perm   2 sec   (5551 perm/sec)   p_kst 2.791000e-01   p_cons 7.517000e-01   p_joint 9.397000e-01

Outputting figure to mutsig2_images.part000000000190/WDR67.2_3289_10000_0.2791_0.7517_0.9397.png
                gene_name: WDR67
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 83 percent done.
WDR7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.194384e-03	ci left: 9.917226e-01	ci right 9.949800e-01	k: 9935	n:10000
Cons ci ratio: 1.240382e-01	ci left: 8.514113e-02	ci right 9.649855e-02	k: 907	n:10000
KS ci ratio: 3.593554e-02	ci left: 5.334756e-01	ci right 5.530992e-01	k: 5433	n:10000
WDR7   10000 perm   2 sec   (4817 perm/sec)   p_kst 5.433000e-01   p_cons 9.070000e-02   p_joint 9.935000e-01

Joint ci ratio: 2.284753e-03	ci left: 9.920697e-01	ci right 9.943834e-01	k: 19866	n:20000
Cons ci ratio: 8.832658e-02	ci left: 8.567661e-02	ci right 9.364316e-02	k: 1792	n:20000
KS ci ratio: 2.507837e-02	ci left: 5.429232e-01	ci right 5.567623e-01	k: 10997	n:20000
WDR7   20000 perm   5 sec   (4320 perm/sec)   p_kst 5.498500e-01   p_cons 8.960000e-02   p_joint 9.933000e-01

Outputting figure to mutsig2_images.part000000000190/WDR7.2_4581_20000_0.54985_0.0896_0.9933.png
                gene_name: WDR7
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.090 
      ci_cons_bounds_left: 0.086 
     ci_cons_bounds_right: 0.094 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000190
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 190 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 4398539: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000191> was used as the working directory.
Started at Wed Oct 24 16:18:10 2012
Results reported at Wed Oct 24 16:20:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000191.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000191.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 191  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000191.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    154.15 sec.
    Max Memory :      1321 MB
    Max Swap   :      3970 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
191
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 191
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 191: processing genes 17046 - 17135
Calculating significance of each gene.
Using projection method.
17046	WDR83	9.382198e-02
17047	WDR85	1
17048	WDR86	1
17049	WDR88	1
17050	WDR89	1
17051	WDR90	1
17052	WDR91	1
17053	WDR92	1
17054	WDR93	1
17055	WDSUB1	1
17056	WDTC1	7.191940e-02
17057	WDYHV1	1
17058	WEE1	1
17059	WEE2	1
17060	WFDC1	1
17061	WFDC10A	1
17062	WFDC10B	1
17063	WFDC11	1
17064	WFDC12	1
17065	WFDC13	1
17066	WFDC2	1
17067	WFDC3	1
17068	WFDC5	1
17069	WFDC6	1
17070	WFDC8	1
17071	WFDC9	1
17072	WFIKKN1	1
17073	WFIKKN2	2.498156e-01
17074	WFS1	1
17075	WHAMM	1
17076	WHSC1	1
17077	WHSC1L1	4.506024e-01
17078	WHSC2	1
17079	WIBG	1
17080	WIF1	1.536999e-01
17081	WIPF1	1
17082	WIPF2	1
17083	WIPF3	1
17084	WIPI1	1
17085	WIPI2	1
17086	WISP1	1
17087	WISP2	1
17088	WISP3	1
17089	WIZ	1
17090	WLS	1
17091	WNK1	7.053915e-01
17092	WNK2	1
17093	WNK3	3.746076e-01
17094	WNK4	1.171152e-01
17095	WNT1	1
17096	WNT10A	3.213609e-02
17097	WNT10B	1
17098	WNT11	1
17099	WNT16	1
17100	WNT2	1
17101	WNT2B	1
17102	WNT3	1
17103	WNT3A	1
17104	WNT4	1
17105	WNT5A	4.662766e-02
17106	WNT5B	1
17107	WNT6	1
17108	WNT7A	1
17109	WNT7B	1
17110	WNT8A	1
17111	WNT8B	1
17112	WNT9A	1
17113	WNT9B	1
17114	WRAP53	1
17115	WRB	1
17116	WRN	1
17117	WRNIP1	1
17118	WSB1	1
17119	WSB2	1
17120	WSCD1	1
17121	WSCD2	1
17122	WT1	1
17123	WTAP	1
17124	WTIP	1
17125	WWC1	1
17126	WWC2	1
17127	WWC3	2.388889e-01
17128	WWOX	1
17129	WWP1	1
17130	WWP2	3.926445e-02
17131	WWTR1	1
17132	XAB2	3.580304e-01
17133	XAF1	1
17134	XAGE3	1
17135	XAGE5	1
Done

Running MutSig 2:
Scatter job 191: processing genes 17046 - 17135
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
WNK4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.060498e-01	ci left: 1.137899e-01	ci right 1.266323e-01	k: 1201	n:10000
Cons ci ratio: 1.129536e-02	ci left: 9.180131e-01	ci right 9.285388e-01	k: 9234	n:10000
KS ci ratio: 1.910384e-01	ci left: 3.652992e-02	ci right 4.434069e-02	k: 403	n:10000
WNK4   10000 perm   2 sec   (5326 perm/sec)   p_kst 4.030000e-02   p_cons 9.234000e-01   p_joint 1.201000e-01

Joint ci ratio: 9.925096e-02	ci left: 6.874809e-02	ci right 7.597683e-02	k: 1446	n:20000
Cons ci ratio: 8.128209e-03	ci left: 9.170219e-01	ci right 9.245552e-01	k: 18417	n:20000
KS ci ratio: 1.365920e-01	ci left: 3.684265e-02	ci right 4.229226e-02	k: 790	n:20000
WNK4   20000 perm   6 sec   (3309 perm/sec)   p_kst 3.950000e-02   p_cons 9.208500e-01   p_joint 7.230000e-02

Joint ci ratio: 6.974443e-02	ci left: 9.193435e-02	ci right 9.861093e-02	k: 2857	n:30000
Cons ci ratio: 6.661179e-03	ci left: 9.171778e-01	ci right 9.233405e-01	k: 27609	n:30000
KS ci ratio: 1.099689e-01	ci left: 3.839460e-02	ci right 4.289491e-02	k: 1218	n:30000
WNK4   30000 perm   8 sec   (3602 perm/sec)   p_kst 4.060000e-02   p_cons 9.203000e-01   p_joint 9.523333e-02

Joint ci ratio: 5.103140e-02	ci left: 1.252598e-01	ci right 1.318442e-01	k: 5141	n:40000
Cons ci ratio: 5.784257e-03	ci left: 9.171968e-01	ci right 9.225421e-01	k: 36796	n:40000
KS ci ratio: 9.583188e-02	ci left: 3.822271e-02	ci right 4.209441e-02	k: 1605	n:40000
WNK4   40000 perm   11 sec   (3728 perm/sec)   p_kst 4.012500e-02   p_cons 9.199000e-01   p_joint 1.285250e-01

Outputting figure to mutsig2_images.part000000000191/WNK4.3_3808_40000_0.040125_0.9199_0.12853.png
                gene_name: WNK4
               theta_stop: 0.096 
                    nperm: 40000 
                     p_ks: 0.040 
        ci_ks_bounds_left: 0.038 
       ci_ks_bounds_right: 0.042 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.13 

Current progress: 50 percent done.
WWP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.336559e-01	ci left: 7.388330e-02	ci right 8.456334e-02	k: 791	n:10000
Cons ci ratio: 3.953258e-02	ci left: 4.858530e-01	ci right 5.055495e-01	k: 4957	n:10000
KS ci ratio: 2.669889e-01	ci left: 1.827990e-02	ci right 2.400381e-02	k: 210	n:10000
WWP2   10000 perm   2 sec   (6047 perm/sec)   p_kst 2.100000e-02   p_cons 4.957000e-01   p_joint 7.910000e-02

Joint ci ratio: 9.393256e-02	ci left: 7.632531e-02	ci right 8.389730e-02	k: 1601	n:20000
Cons ci ratio: 2.807916e-02	ci left: 4.865474e-01	ci right 5.004545e-01	k: 9870	n:20000
KS ci ratio: 1.887942e-01	ci left: 1.910538e-02	ci right 2.313553e-02	k: 421	n:20000
WWP2   20000 perm   4 sec   (5397 perm/sec)   p_kst 2.105000e-02   p_cons 4.935000e-01   p_joint 8.005000e-02

Joint ci ratio: 4.549145e-02	ci left: 1.938669e-01	ci right 2.029249e-01	k: 5951	n:30000
Cons ci ratio: 2.285082e-02	ci left: 4.894930e-01	ci right 5.008412e-01	k: 14855	n:30000
KS ci ratio: 1.570918e-01	ci left: 1.873410e-02	ci right 2.195973e-02	k: 609	n:30000
WWP2   30000 perm   6 sec   (5159 perm/sec)   p_kst 2.030000e-02   p_cons 4.951667e-01   p_joint 1.983667e-01

Joint ci ratio: 5.904576e-02	ci left: 9.631187e-02	ci right 1.021964e-01	k: 3969	n:40000
Cons ci ratio: 1.966700e-02	ci left: 4.933629e-01	ci right 5.031874e-01	k: 19931	n:40000
KS ci ratio: 1.352280e-01	ci left: 1.918207e-02	ci right 2.198814e-02	k: 822	n:40000
WWP2   40000 perm   8 sec   (4989 perm/sec)   p_kst 2.055000e-02   p_cons 4.982750e-01   p_joint 9.922500e-02

Joint ci ratio: 9.934239e-02	ci left: 2.869775e-02	ci right 3.171712e-02	k: 1509	n:50000
Cons ci ratio: 1.761177e-02	ci left: 4.932877e-01	ci right 5.020726e-01	k: 24884	n:50000
KS ci ratio: 1.213590e-01	ci left: 1.919822e-02	ci right 2.169789e-02	k: 1021	n:50000
WWP2   50000 perm   10 sec   (4846 perm/sec)   p_kst 2.042000e-02   p_cons 4.976800e-01   p_joint 3.018000e-02

Joint ci ratio: 9.053248e-02	ci left: 2.892657e-02	ci right 3.168578e-02	k: 1817	n:60000
Cons ci ratio: 1.607618e-02	ci left: 4.937078e-01	ci right 5.017257e-01	k: 29863	n:60000
KS ci ratio: 1.107116e-01	ci left: 1.933242e-02	ci right 2.161429e-02	k: 1227	n:60000
WWP2   60000 perm   13 sec   (4736 perm/sec)   p_kst 2.045000e-02   p_cons 4.977167e-01   p_joint 3.028333e-02

Joint ci ratio: 7.204940e-02	ci left: 3.910776e-02	ci right 4.204476e-02	k: 2839	n:70000
Cons ci ratio: 1.493020e-02	ci left: 4.924463e-01	ci right 4.998683e-01	k: 34731	n:70000
KS ci ratio: 1.027802e-01	ci left: 1.930985e-02	ci right 2.141589e-02	k: 1424	n:70000
WWP2   70000 perm   15 sec   (4637 perm/sec)   p_kst 2.034286e-02   p_cons 4.961571e-01   p_joint 4.055714e-02

Joint ci ratio: 6.777475e-02	ci left: 3.877551e-02	ci right 4.150796e-02	k: 3210	n:80000
Cons ci ratio: 1.396721e-02	ci left: 4.926418e-01	ci right 4.995835e-01	k: 39689	n:80000
KS ci ratio: 9.704542e-02	ci left: 1.901665e-02	ci right 2.096838e-02	k: 1598	n:80000
WWP2   80000 perm   18 sec   (4518 perm/sec)   p_kst 1.997500e-02   p_cons 4.961125e-01   p_joint 4.012500e-02

Outputting figure to mutsig2_images.part000000000191/WWP2.2_2709_80000_0.019975_0.49611_0.040125.png
                gene_name: WWP2
               theta_stop: 0.097 
                    nperm: 80000 
                     p_ks: 0.020 
        ci_ks_bounds_left: 0.019 
       ci_ks_bounds_right: 0.021 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.040 
     ci_joint_bounds_left: 0.039 
    ci_joint_bounds_right: 0.042 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000191
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 191 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 4398542: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000192> was used as the working directory.
Started at Wed Oct 24 16:18:12 2012
Results reported at Wed Oct 24 16:20:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000192.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000192.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 192  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000192.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    146.85 sec.
    Max Memory :      1613 MB
    Max Swap   :      4006 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
192
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 192
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 192: processing genes 17136 - 17224
Calculating significance of each gene.
Using projection method.
17136	XBP1	1
17137	XCL1	1
17138	XCL2	1
17139	XCR1	1
17140	XDH	1
17141	XG	1
17142	XIAP	1
17143	XIRP1	1
17144	XIRP2	3.585577e-01
17145	XK	3.539165e-02
17146	XKR3	6.710251e-02
17147	XKR4	1
17148	XKR6	1.596997e-01
17149	XKR7	1
17150	XKR8	1
17151	XKR9	1
17152	XKRX	1
17153	XPA	1
17154	XPC	1
17155	XPNPEP1	1.194682e-01
17156	XPNPEP2	1
17157	XPNPEP3	1
17158	XPO1	2.031617e-01
17159	XPO4	1
17160	XPO5	1
17161	XPO6	1
17162	XPO7	1
17163	XPOT	3.770434e-03
17164	XPR1	1
17165	XRCC1	1
17166	XRCC2	1
17167	XRCC3	1
17168	XRCC4	1
17169	XRCC5	1
17170	XRCC6	1
17171	XRCC6BP1	1
17172	XRN1	1
17173	XRN2	1.466114e-01
17174	XRRA1	1
17175	XYLB	1
17176	XYLT1	1
17177	XYLT2	1
17178	YAF2	7.632506e-02
17179	YAP1	1
17180	YARS	1
17181	YARS2	1
17182	YBX1	1
17183	YBX2	1
17184	YDJC	1
17185	YEATS2	1
17186	YEATS4	1
17187	YES1	1
17188	YIF1A	1
17189	YIF1B	1
17190	YIPF1	1
17191	YIPF2	1
17192	YIPF3	1.077168e-01
17193	YIPF4	1
17194	YIPF5	1
17195	YIPF6	1.124809e-01
17196	YIPF7	1
17197	YJEFN3	1
17198	YKT6	1
17199	YLPM1	5.377294e-02
17200	YME1L1	1
17201	YOD1	1
17202	YPEL1	1
17203	YPEL2	1
17204	YPEL3	1
17205	YPEL4	1
17206	YPEL5	1
17207	YRDC	1
17208	YSK4	4.447358e-01
17209	YTHDC1	2.895706e-01
17210	YTHDC2	3.448683e-01
17211	YTHDF1	1
17212	YTHDF2	1
17213	YTHDF3	1
17214	YWHAB	1
17215	YWHAE	1
17216	YWHAG	1
17217	YWHAH	1
17218	YWHAQ	1
17219	YWHAZ	5.048011e-02
17220	YY1	1.082636e-02
17221	YY1AP1	1
17222	YY2	1
17223	ZACN	1
17224	ZADH2	1
Done

Running MutSig 2:
Scatter job 192: processing genes 17136 - 17224
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
YTHDC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.892670e-02	ci left: 1.289466e-01	ci right 1.424664e-01	k: 1356	n:10000
Cons ci ratio: 6.589183e-02	ci left: 2.527095e-01	ci right 2.700297e-01	k: 2613	n:10000
KS ci ratio: 1.453474e-01	ci left: 6.285242e-02	ci right 7.280114e-02	k: 677	n:10000
YTHDC1   10000 perm   2 sec   (5912 perm/sec)   p_kst 6.770000e-02   p_cons 2.613000e-01   p_joint 1.356000e-01

Joint ci ratio: 8.166503e-02	ci left: 9.906579e-02	ci right 1.075499e-01	k: 2065	n:20000
Cons ci ratio: 4.684764e-02	ci left: 2.531870e-01	ci right 2.653831e-01	k: 5185	n:20000
KS ci ratio: 1.026971e-01	ci left: 6.440262e-02	ci right 7.142363e-02	k: 1357	n:20000
YTHDC1   20000 perm   6 sec   (3517 perm/sec)   p_kst 6.785000e-02   p_cons 2.592500e-01   p_joint 1.032500e-01

Joint ci ratio: 6.366213e-02	ci left: 1.086167e-01	ci right 1.157919e-01	k: 3365	n:30000
Cons ci ratio: 3.826764e-02	ci left: 2.541489e-01	ci right 2.640978e-01	k: 7773	n:30000
KS ci ratio: 8.458987e-02	ci left: 6.396742e-02	ci right 6.965016e-02	k: 2003	n:30000
YTHDC1   30000 perm   8 sec   (3864 perm/sec)   p_kst 6.676667e-02   p_cons 2.591000e-01   p_joint 1.121667e-01

Outputting figure to mutsig2_images.part000000000192/YTHDC1.4_2252_30000_0.066767_0.2591_0.11217.png
                gene_name: YTHDC1
               theta_stop: 0.085 
                    nperm: 30000 
                     p_ks: 0.067 
        ci_ks_bounds_left: 0.064 
       ci_ks_bounds_right: 0.070 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

Current progress: 17 percent done.
XIRP2
Processing conservation and coverage...
81% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.099875e-01	ci left: 1.064680e-01	ci right 1.189587e-01	k: 1126	n:10000
Cons ci ratio: 7.221246e-02	ci left: 2.193138e-01	ci right 2.358452e-01	k: 2275	n:10000
KS ci ratio: 1.025412e-01	ci left: 1.209243e-01	ci right 1.340936e-01	k: 1274	n:10000
XIRP2   10000 perm   3 sec   (3458 perm/sec)   p_kst 1.274000e-01   p_cons 2.275000e-01   p_joint 1.126000e-01

Joint ci ratio: 6.040261e-02	ci left: 1.686698e-01	ci right 1.792252e-01	k: 3478	n:20000
Cons ci ratio: 5.117890e-02	ci left: 2.209619e-01	ci right 2.326177e-01	k: 4535	n:20000
KS ci ratio: 7.488375e-02	ci left: 1.159695e-01	ci right 1.250412e-01	k: 2409	n:20000
XIRP2   20000 perm   6 sec   (3196 perm/sec)   p_kst 1.204500e-01   p_cons 2.267500e-01   p_joint 1.739000e-01

Outputting figure to mutsig2_images.part000000000192/XIRP2.3_12236_20000_0.12045_0.22675_0.1739.png
                gene_name: XIRP2
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 33 percent done.
XPOT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.949312e-02	ci left: 6.289944e-01	ci right 6.479249e-01	k: 6385	n:10000
Cons ci ratio: 9.495584e-02	ci left: 1.386431e-01	ci right 1.525641e-01	k: 1455	n:10000
KS ci ratio: 2.448693e-02	ci left: 7.103801e-01	ci right 7.280920e-01	k: 7193	n:10000
XPOT   10000 perm   2 sec   (5307 perm/sec)   p_kst 7.193000e-01   p_cons 1.455000e-01   p_joint 6.385000e-01

Outputting figure to mutsig2_images.part000000000192/XPOT.3_2985_10000_0.7193_0.1455_0.6385.png
                gene_name: XPOT
               theta_stop: 0.095 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 50 percent done.
YLPM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.960716e-02	ci left: 1.273806e-01	ci right 1.408333e-01	k: 1340	n:10000
Cons ci ratio: 8.805305e-02	ci left: 1.580679e-01	ci right 1.727275e-01	k: 1653	n:10000
KS ci ratio: 7.387413e-02	ci left: 2.115188e-01	ci right 2.278448e-01	k: 2196	n:10000
YLPM1   10000 perm   3 sec   (3821 perm/sec)   p_kst 2.196000e-01   p_cons 1.653000e-01   p_joint 1.340000e-01

Outputting figure to mutsig2_images.part000000000192/YLPM1.3_6521_10000_0.2196_0.1653_0.134.png
                gene_name: YLPM1
               theta_stop: 0.100 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 67 percent done.
YAF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.981450e-03	ci left: 9.815599e-01	ci right 9.865523e-01	k: 9842	n:10000
Cons ci ratio: 9.309272e-02	ci left: 1.435445e-01	ci right 1.576597e-01	k: 1505	n:10000
KS ci ratio: 7.066629e-02	ci left: 2.269154e-01	ci right 2.436391e-01	k: 2352	n:10000
YAF2   10000 perm   1 sec   (6832 perm/sec)   p_kst 2.352000e-01   p_cons 1.505000e-01   p_joint 9.842000e-01

Outputting figure to mutsig2_images.part000000000192/YAF2.2_559_10000_0.2352_0.1505_0.9842.png
                gene_name: YAF2
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 83 percent done.
YY1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.634004e-02	ci left: 8.448877e-01	ci right 8.589066e-01	k: 8520	n:10000
KS ci ratio: 4.267076e-02	ci left: 4.477990e-01	ci right 4.674257e-01	k: 4576	n:10000
YY1   10000 perm   1 sec   (6828 perm/sec)   p_kst 4.576000e-01   p_cons 8.520000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000192/YY1.2_1265_10000_0.4576_0.852_1.png
                gene_name: YY1
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.86 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000192
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 192 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1703>
Subject: Job 4398548: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1703>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000193> was used as the working directory.
Started at Wed Oct 24 16:18:12 2012
Results reported at Wed Oct 24 16:20:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000193.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000193.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 193  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000193.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    184.63 sec.
    Max Memory :      1597 MB
    Max Swap   :      3979 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
193
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 193
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 193: processing genes 17225 - 17314
Calculating significance of each gene.
Using projection method.
17225	ZAK	2.697127e-01
17226	ZAN	1
17227	ZAP70	1
17228	ZAR1	1
17229	ZBBX	1.084849e-01
17230	ZBED1	1
17231	ZBED2	1
17232	ZBED4	1
17233	ZBP1	1
17234	ZBTB1	1
17235	ZBTB10	1
17236	ZBTB11	1
17237	ZBTB12	1.458183e-01
17238	ZBTB16	1
17239	ZBTB17	1
17240	ZBTB2	1
17241	ZBTB20	1
17242	ZBTB22	1
17243	ZBTB24	1
17244	ZBTB25	1
17245	ZBTB26	1
17246	ZBTB3	1
17247	ZBTB32	1
17248	ZBTB33	1
17249	ZBTB34	1
17250	ZBTB37	7.731982e-03
17251	ZBTB38	5.679231e-02
17252	ZBTB39	3.219804e-01
17253	ZBTB4	6.834002e-02
17254	ZBTB40	4.357507e-01
17255	ZBTB41	1
17256	ZBTB43	1
17257	ZBTB44	1
17258	ZBTB45	1
17259	ZBTB46	1
17260	ZBTB47	1
17261	ZBTB48	1
17262	ZBTB49	1
17263	ZBTB5	1
17264	ZBTB6	1
17265	ZBTB7A	1
17266	ZBTB7B	1
17267	ZBTB7C	1
17268	ZBTB8A	1
17269	ZBTB8OS	1
17270	ZBTB9	1
17271	ZC3H10	1
17272	ZC3H11A	2.925672e-01
17273	ZC3H12A	2.178800e-02
17274	ZC3H12B	7.367904e-03
17275	ZC3H12C	1
17276	ZC3H12D	1
17277	ZC3H13	6.520371e-01
17278	ZC3H14	5.246421e-02
17279	ZC3H15	1
17280	ZC3H18	1
17281	ZC3H3	1
17282	ZC3H4	1.504341e-01
17283	ZC3H6	1
17284	ZC3H7A	1.325555e-01
17285	ZC3H7B	1
17286	ZC3H8	1
17287	ZC3HAV1	3.980613e-01
17288	ZC3HAV1L	1
17289	ZC3HC1	1
17290	ZC4H2	1
17291	ZCCHC10	1
17292	ZCCHC11	1.280180e-01
17293	ZCCHC12	1
17294	ZCCHC13	1
17295	ZCCHC14	1
17296	ZCCHC16	7.270466e-02
17297	ZCCHC17	1
17298	ZCCHC2	3.154508e-01
17299	ZCCHC24	1
17300	ZCCHC3	1
17301	ZCCHC4	1
17302	ZCCHC5	1
17303	ZCCHC6	3.670628e-01
17304	ZCCHC7	1
17305	ZCCHC8	1
17306	ZCCHC9	1
17307	ZCRB1	1
17308	ZCWPW1	1
17309	ZCWPW2	5.734582e-02
17310	ZDBF2	1.792609e-01
17311	ZDHHC1	1
17312	ZDHHC11	1
17313	ZDHHC12	1
17314	ZDHHC13	1
Done

Running MutSig 2:
Scatter job 193: processing genes 17225 - 17314
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZBTB38
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.643869e-01	ci left: 4.936226e-02	ci right 5.829990e-02	k: 537	n:10000
Cons ci ratio: 1.588454e-01	ci left: 5.282421e-02	ci right 6.203572e-02	k: 573	n:10000
KS ci ratio: 8.310267e-02	ci left: 1.743827e-01	ci right 1.896031e-01	k: 1819	n:10000
ZBTB38   10000 perm   2 sec   (5358 perm/sec)   p_kst 1.819000e-01   p_cons 5.730000e-02   p_joint 5.370000e-02

Joint ci ratio: 1.310014e-01	ci left: 4.003650e-02	ci right 4.569738e-02	k: 856	n:20000
Cons ci ratio: 1.140188e-01	ci left: 5.260997e-02	ci right 5.901994e-02	k: 1115	n:20000
KS ci ratio: 5.845918e-02	ci left: 1.781568e-01	ci right 1.889354e-01	k: 3670	n:20000
ZBTB38   20000 perm   6 sec   (3281 perm/sec)   p_kst 1.835000e-01   p_cons 5.575000e-02   p_joint 4.280000e-02

Joint ci ratio: 8.278910e-02	ci left: 6.664747e-02	ci right 7.243623e-02	k: 2085	n:30000
Cons ci ratio: 8.740425e-02	ci left: 6.008051e-02	ci right 6.560452e-02	k: 1884	n:30000
KS ci ratio: 4.802325e-02	ci left: 1.773509e-01	ci right 1.861108e-01	k: 5451	n:30000
ZBTB38   30000 perm   8 sec   (3586 perm/sec)   p_kst 1.817000e-01   p_cons 6.280000e-02   p_joint 6.950000e-02

Outputting figure to mutsig2_images.part000000000193/ZBTB38.5_3592_30000_0.1817_0.0628_0.0695.png
                gene_name: ZBTB38
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.063 
      ci_cons_bounds_left: 0.060 
     ci_cons_bounds_right: 0.066 
                  p_joint: 0.070 
     ci_joint_bounds_left: 0.067 
    ci_joint_bounds_right: 0.072 

Current progress: 11 percent done.
ZBTB37
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.470120e-02	ci left: 3.299187e-01	ci right 3.485750e-01	k: 3392	n:10000
Cons ci ratio: 5.840080e-02	ci left: 3.014375e-01	ci right 3.196729e-01	k: 3105	n:10000
KS ci ratio: 8.484586e-02	ci left: 1.683846e-01	ci right 1.834047e-01	k: 1758	n:10000
ZBTB37   10000 perm   2 sec   (6208 perm/sec)   p_kst 1.758000e-01   p_cons 3.105000e-01   p_joint 3.392000e-01

Outputting figure to mutsig2_images.part000000000193/ZBTB37.2_1587_10000_0.1758_0.3105_0.3392.png
                gene_name: ZBTB37
               theta_stop: 0.085 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.35 

Current progress: 22 percent done.
ZBTB4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.430680e-02	ci left: 8.760270e-01	ci right 8.887493e-01	k: 8825	n:10000
Cons ci ratio: 9.445442e-03	ci left: 9.405580e-01	ci right 9.495805e-01	k: 9452	n:10000
KS ci ratio: 6.966016e-02	ci left: 2.320511e-01	ci right 2.489003e-01	k: 2404	n:10000
ZBTB4   10000 perm   2 sec   (5698 perm/sec)   p_kst 2.404000e-01   p_cons 9.452000e-01   p_joint 8.825000e-01

Outputting figure to mutsig2_images.part000000000193/ZBTB4.2_3050_10000_0.2404_0.9452_0.8825.png
                gene_name: ZBTB4
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 33 percent done.
ZC3H12A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.073150e-02	ci left: 6.096996e-01	ci right 6.288309e-01	k: 6193	n:10000
Cons ci ratio: 4.868751e-02	ci left: 3.836086e-01	ci right 4.028536e-01	k: 3932	n:10000
KS ci ratio: 5.642880e-02	ci left: 3.162190e-01	ci right 3.346828e-01	k: 3254	n:10000
ZC3H12A   10000 perm   2 sec   (6249 perm/sec)   p_kst 3.254000e-01   p_cons 3.932000e-01   p_joint 6.193000e-01

Outputting figure to mutsig2_images.part000000000193/ZC3H12A.2_1820_10000_0.3254_0.3932_0.6193.png
                gene_name: ZC3H12A
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.63 

Current progress: 44 percent done.
ZC3H12B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 5.890920e-02	ci left: 2.977686e-01	ci right 3.159440e-01	k: 3068	n:10000
KS ci ratio: 1.842321e-02	ci left: 8.114128e-01	ci right 8.266008e-01	k: 8191	n:10000
ZC3H12B   10000 perm   2 sec   (5977 perm/sec)   p_kst 8.191000e-01   p_cons 3.068000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000193/ZC3H12B.2_2531_10000_0.8191_0.3068_1.png
                gene_name: ZC3H12B
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 56 percent done.
ZC3H14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.706816e-01	ci left: 4.580994e-02	ci right 5.445453e-02	k: 500	n:10000
Cons ci ratio: 3.123971e-01	ci left: 1.307848e-02	ci right 1.800961e-02	k: 154	n:10000
KS ci ratio: 3.541838e-01	ci left: 9.958933e-03	ci right 1.433217e-02	k: 120	n:10000
ZC3H14   10000 perm   2 sec   (6052 perm/sec)   p_kst 1.200000e-02   p_cons 1.540000e-02   p_joint 5.000000e-02

Joint ci ratio: 1.869915e-01	ci left: 1.948692e-02	ci right 2.355385e-02	k: 429	n:20000
Cons ci ratio: 2.201831e-01	ci left: 1.388097e-02	ci right 1.736192e-02	k: 311	n:20000
KS ci ratio: 2.478726e-01	ci left: 1.081866e-02	ci right 1.392552e-02	k: 246	n:20000
ZC3H14   20000 perm   4 sec   (5383 perm/sec)   p_kst 1.230000e-02   p_cons 1.555000e-02   p_joint 2.145000e-02

Joint ci ratio: 9.506734e-02	ci left: 5.107803e-02	ci right 5.620885e-02	k: 1608	n:30000
Cons ci ratio: 1.840202e-01	ci left: 1.352770e-02	ci right 1.630074e-02	k: 446	n:30000
KS ci ratio: 2.044948e-01	ci left: 1.086192e-02	ci right 1.336723e-02	k: 362	n:30000
ZC3H14   30000 perm   6 sec   (5132 perm/sec)   p_kst 1.206667e-02   p_cons 1.486667e-02   p_joint 5.360000e-02

Joint ci ratio: 8.636941e-02	ci left: 4.685586e-02	ci right 5.110992e-02	k: 1958	n:40000
Cons ci ratio: 1.615828e-01	ci left: 1.332738e-02	ci right 1.569388e-02	k: 579	n:40000
KS ci ratio: 1.749164e-01	ci left: 1.131462e-02	ci right 1.350702e-02	k: 495	n:40000
ZC3H14   40000 perm   8 sec   (4964 perm/sec)   p_kst 1.237500e-02   p_cons 1.447500e-02   p_joint 4.895000e-02

Joint ci ratio: 7.303214e-02	ci left: 5.248688e-02	ci right 5.648504e-02	k: 2723	n:50000
Cons ci ratio: 1.273396e-01	ci left: 1.741439e-02	ci right 1.980197e-02	k: 929	n:50000
KS ci ratio: 1.563227e-01	ci left: 1.144840e-02	ci right 1.340881e-02	k: 620	n:50000
ZC3H14   50000 perm   10 sec   (4829 perm/sec)   p_kst 1.240000e-02   p_cons 1.858000e-02   p_joint 5.446000e-02

Joint ci ratio: 7.435961e-02	ci left: 4.261823e-02	ci right 4.592603e-02	k: 2655	n:60000
Cons ci ratio: 1.164043e-01	ci left: 1.746917e-02	ci right 1.964442e-02	k: 1112	n:60000
KS ci ratio: 1.427221e-01	ci left: 1.152984e-02	ci right 1.331778e-02	k: 744	n:60000
ZC3H14   60000 perm   13 sec   (4713 perm/sec)   p_kst 1.240000e-02   p_cons 1.853333e-02   p_joint 4.425000e-02

Joint ci ratio: 7.836239e-02	ci left: 3.316016e-02	ci right 3.587861e-02	k: 2415	n:70000
Cons ci ratio: 1.078331e-01	ci left: 1.752853e-02	ci right 1.954023e-02	k: 1296	n:70000
KS ci ratio: 1.319176e-01	ci left: 1.163479e-02	ci right 1.329171e-02	k: 871	n:70000
ZC3H14   70000 perm   15 sec   (4614 perm/sec)   p_kst 1.244286e-02   p_cons 1.851429e-02   p_joint 3.450000e-02

Joint ci ratio: 5.632535e-02	ci left: 5.547728e-02	ci right 5.870493e-02	k: 4566	n:80000
Cons ci ratio: 1.011921e-01	ci left: 1.747997e-02	ci right 1.935519e-02	k: 1472	n:80000
KS ci ratio: 1.225028e-01	ci left: 1.186279e-02	ci right 1.342286e-02	k: 1010	n:80000
ZC3H14   80000 perm   18 sec   (4519 perm/sec)   p_kst 1.262500e-02   p_cons 1.840000e-02   p_joint 5.707500e-02

Joint ci ratio: 6.042941e-02	ci left: 4.331528e-02	ci right 4.602528e-02	k: 4019	n:90000
Cons ci ratio: 9.500051e-02	ci left: 1.768389e-02	ci right 1.945844e-02	k: 1670	n:90000
KS ci ratio: 1.149543e-01	ci left: 1.202180e-02	ci right 1.349874e-02	k: 1147	n:90000
ZC3H14   90000 perm   20 sec   (4429 perm/sec)   p_kst 1.274444e-02   p_cons 1.855556e-02   p_joint 4.465556e-02

Joint ci ratio: 5.727249e-02	ci left: 4.346690e-02	ci right 4.603959e-02	k: 4474	n:100000
Cons ci ratio: 9.081733e-02	ci left: 1.745870e-02	ci right 1.912940e-02	k: 1828	n:100000
KS ci ratio: 1.084350e-01	ci left: 1.220003e-02	ci right 1.360844e-02	k: 1289	n:100000
ZC3H14   100000 perm   23 sec   (4359 perm/sec)   p_kst 1.289000e-02   p_cons 1.828000e-02   p_joint 4.474000e-02

Joint ci ratio: 5.443091e-02	ci left: 4.380034e-02	ci right 4.626008e-02	k: 4952	n:110000
Cons ci ratio: 8.598133e-02	ci left: 1.774745e-02	ci right 1.935080e-02	k: 2039	n:110000
KS ci ratio: 1.027670e-01	ci left: 1.238322e-02	ci right 1.373354e-02	k: 1435	n:110000
ZC3H14   110000 perm   26 sec   (4287 perm/sec)   p_kst 1.304545e-02   p_cons 1.853636e-02   p_joint 4.501818e-02

Joint ci ratio: 5.203440e-02	ci left: 4.398206e-02	ci right 4.633998e-02	k: 5418	n:120000
Cons ci ratio: 8.236718e-02	ci left: 1.776141e-02	ci right 1.929532e-02	k: 2222	n:120000
KS ci ratio: 9.834566e-02	ci left: 1.242364e-02	ci right 1.371672e-02	k: 1567	n:120000
ZC3H14   120000 perm   28 sec   (4219 perm/sec)   p_kst 1.305833e-02   p_cons 1.851667e-02   p_joint 4.515000e-02

Outputting figure to mutsig2_images.part000000000193/ZC3H14.2_2668_120000_0.013058_0.018517_0.04515.png
                gene_name: ZC3H14
               theta_stop: 0.098 
                    nperm: 120000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.014 
                   p_cons: 0.019 
      ci_cons_bounds_left: 0.018 
     ci_cons_bounds_right: 0.019 
                  p_joint: 0.045 
     ci_joint_bounds_left: 0.044 
    ci_joint_bounds_right: 0.046 

Current progress: 67 percent done.
ZC3HAV1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.346348e-02	ci left: 5.686497e-01	ci right 5.881046e-01	k: 5784	n:10000
Cons ci ratio: 2.031471e-02	ci left: 7.801599e-01	ci right 7.962719e-01	k: 7883	n:10000
KS ci ratio: 5.738033e-02	ci left: 3.089757e-01	ci right 3.273303e-01	k: 3181	n:10000
ZC3HAV1   10000 perm   2 sec   (5990 perm/sec)   p_kst 3.181000e-01   p_cons 7.883000e-01   p_joint 5.784000e-01

Outputting figure to mutsig2_images.part000000000193/ZC3HAV1.2_2765_10000_0.3181_0.7883_0.5784.png
                gene_name: ZC3HAV1
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 78 percent done.
ZCCHC11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.463565e-03	ci left: 9.613148e-01	ci right 9.686110e-01	k: 9651	n:10000
Cons ci ratio: 4.814106e-02	ci left: 3.889845e-01	ci right 4.082746e-01	k: 3986	n:10000
KS ci ratio: 7.746257e-03	ci left: 9.585892e-01	ci right 9.661384e-01	k: 9625	n:10000
ZCCHC11   10000 perm   2 sec   (4957 perm/sec)   p_kst 9.625000e-01   p_cons 3.986000e-01   p_joint 9.651000e-01

Outputting figure to mutsig2_images.part000000000193/ZCCHC11.2_5054_10000_0.9625_0.3986_0.9651.png
                gene_name: ZCCHC11
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 89 percent done.
ZDBF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.814575e-02	ci left: 6.504187e-01	ci right 6.690882e-01	k: 6598	n:10000
Cons ci ratio: 3.314211e-02	ci left: 5.733634e-01	ci right 5.927881e-01	k: 5831	n:10000
KS ci ratio: 3.469341e-02	ci left: 5.509062e-01	ci right 5.704585e-01	k: 5607	n:10000
ZDBF2   10000 perm   2 sec   (4518 perm/sec)   p_kst 5.607000e-01   p_cons 5.831000e-01   p_joint 6.598000e-01

Outputting figure to mutsig2_images.part000000000193/ZDBF2.2_7077_10000_0.5607_0.5831_0.6598.png
                gene_name: ZDBF2
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000193
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 193 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1425>
Subject: Job 4398561: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1425>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000194> was used as the working directory.
Started at Wed Oct 24 16:18:20 2012
Results reported at Wed Oct 24 16:20:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000194.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000194.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 194  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000194.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    197.45 sec.
    Max Memory :      1552 MB
    Max Swap   :      3959 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
194
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 194
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 194: processing genes 17315 - 17404
Calculating significance of each gene.
Using projection method.
17315	ZDHHC14	1
17316	ZDHHC15	1
17317	ZDHHC16	1
17318	ZDHHC17	1
17319	ZDHHC18	1
17320	ZDHHC19	1
17321	ZDHHC2	1
17322	ZDHHC20	1
17323	ZDHHC21	1
17324	ZDHHC22	1
17325	ZDHHC23	1
17326	ZDHHC24	1
17327	ZDHHC3	1
17328	ZDHHC4	1
17329	ZDHHC5	1
17330	ZDHHC6	1
17331	ZDHHC7	1
17332	ZDHHC8	1
17333	ZDHHC9	1
17334	ZEB1	1
17335	ZEB2	1.469673e-01
17336	ZER1	9.749796e-02
17337	ZFAND1	1
17338	ZFAND2A	1
17339	ZFAND2B	1
17340	ZFAND3	1
17341	ZFAND5	5.970276e-04
17342	ZFAND6	1.016526e-01
17343	ZFAT	1
17344	ZFC3H1	6.607672e-01
17345	ZFHX3	5.467582e-01
17346	ZFHX4	4.466464e-01
17347	ZFP1	1
17348	ZFP106	1
17349	ZFP112	1
17350	ZFP14	1
17351	ZFP161	1.447247e-01
17352	ZFP2	1
17353	ZFP28	1
17354	ZFP3	1
17355	ZFP30	1.025533e-01
17356	ZFP36	5.386697e-02
17357	ZFP36L1	1.110135e-01
17358	ZFP36L2	1
17359	ZFP37	1
17360	ZFP41	1
17361	ZFP42	1
17362	ZFP57	9.724179e-02
17363	ZFP64	2.944288e-01
17364	ZFP82	1.594868e-01
17365	ZFP90	1
17366	ZFP91	2.596745e-01
17367	ZFPL1	1
17368	ZFPM1	1
17369	ZFPM2	1
17370	ZFR	1
17371	ZFR2	1
17372	ZFX	1
17373	ZFYVE1	1
17374	ZFYVE16	5.578609e-01
17375	ZFYVE19	1
17376	ZFYVE20	3.743501e-01
17377	ZFYVE21	1
17378	ZFYVE26	1
17379	ZFYVE27	1.385004e-01
17380	ZFYVE28	1
17381	ZFYVE9	1
17382	ZG16B	1
17383	ZGLP1	1
17384	ZGPAT	1
17385	ZHX1	3.688503e-01
17386	ZHX2	1
17387	ZHX3	3.294444e-01
17388	ZIC1	8.505445e-02
17389	ZIC2	1
17390	ZIC3	9.107542e-04
17391	ZIC4	1
17392	ZIC5	1
17393	ZIK1	1
17394	ZIM2	3.005581e-02
17395	ZIM3	1
17396	ZKSCAN1	1
17397	ZKSCAN2	2.839082e-01
17398	ZKSCAN3	1
17399	ZKSCAN4	1
17400	ZKSCAN5	1
17401	ZMAT1	9.332050e-02
17402	ZMAT2	1
17403	ZMAT3	1
17404	ZMAT4	1
Done

Running MutSig 2:
Scatter job 194: processing genes 17315 - 17404
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZEB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 3.839503e-02	ci left: 5.004505e-01	ci right 5.201435e-01	k: 5103	n:10000
KS ci ratio: 1.371664e-01	ci left: 7.029921e-02	ci right 8.074967e-02	k: 754	n:10000
ZEB2   10000 perm   2 sec   (4595 perm/sec)   p_kst 7.540000e-02   p_cons 5.103000e-01   p_joint 1

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 2.719213e-02	ci left: 5.025958e-01	ci right 5.165014e-01	k: 10191	n:20000
KS ci ratio: 9.661324e-02	ci left: 7.236421e-02	ci right 7.975961e-02	k: 1520	n:20000
ZEB2   20000 perm   8 sec   (2574 perm/sec)   p_kst 7.600000e-02   p_cons 5.095500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000194/ZEB2.2_3681_20000_0.076_0.50955_1.png
                gene_name: ZEB2
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.076 
        ci_ks_bounds_left: 0.072 
       ci_ks_bounds_right: 0.080 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.52 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 20 percent done.
ZFAND5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.156431e-02	ci left: 9.145095e-01	ci right 9.252444e-01	k: 9200	n:10000
Cons ci ratio: 2.049711e-02	ci left: 7.771196e-01	ci right 7.933139e-01	k: 7853	n:10000
KS ci ratio: 1.758489e-02	ci left: 8.250345e-01	ci right 8.397713e-01	k: 8325	n:10000
ZFAND5   10000 perm   1 sec   (6895 perm/sec)   p_kst 8.325000e-01   p_cons 7.853000e-01   p_joint 9.200000e-01

Outputting figure to mutsig2_images.part000000000194/ZFAND5.2_662_10000_0.8325_0.7853_0.92.png
                gene_name: ZFAND5
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.84 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.93 

Current progress: 40 percent done.
ZFC3H1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.165822e-02	ci left: 9.132737e-01	ci right 9.240809e-01	k: 9188	n:10000
Cons ci ratio: 1.153289e-02	ci left: 9.149216e-01	ci right 9.256321e-01	k: 9204	n:10000
KS ci ratio: 1.447174e-02	ci left: 8.735722e-01	ci right 8.864055e-01	k: 8801	n:10000
ZFC3H1   10000 perm   2 sec   (4159 perm/sec)   p_kst 8.801000e-01   p_cons 9.204000e-01   p_joint 9.188000e-01

Outputting figure to mutsig2_images.part000000000194/ZFC3H1.2_6110_10000_0.8801_0.9204_0.9188.png
                gene_name: ZFC3H1
               theta_stop: 0.014 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.87 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.92 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 60 percent done.
ZIC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.107243e-02	ci left: 1.491353e-01	ci right 1.634655e-01	k: 1562	n:10000
Cons ci ratio: 1.155520e-01	ci left: 9.720616e-02	ci right 1.092261e-01	k: 1031	n:10000
KS ci ratio: 4.896405e-02	ci left: 3.809211e-01	ci right 4.001427e-01	k: 3905	n:10000
ZIC3   10000 perm   2 sec   (6444 perm/sec)   p_kst 3.905000e-01   p_cons 1.031000e-01   p_joint 1.562000e-01

Joint ci ratio: 3.334776e-02	ci left: 4.017261e-01	ci right 4.154005e-01	k: 8171	n:20000
Cons ci ratio: 8.129255e-02	ci left: 9.990035e-02	ci right 1.084151e-01	k: 2082	n:20000
KS ci ratio: 3.382503e-02	ci left: 3.948954e-01	ci right 4.085332e-01	k: 8034	n:20000
ZIC3   20000 perm   4 sec   (5473 perm/sec)   p_kst 4.017000e-01   p_cons 1.041000e-01   p_joint 4.085500e-01

Outputting figure to mutsig2_images.part000000000194/ZIC3.2_1416_20000_0.4017_0.1041_0.40855.png
                gene_name: ZIC3
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.100 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 80 percent done.
ZIM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.115543e-02	ci left: 4.657702e-01	ci right 4.854441e-01	k: 4756	n:10000
Cons ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
KS ci ratio: 1.062005e-01	ci left: 1.134968e-01	ci right 1.263255e-01	k: 1198	n:10000
ZIM2   10000 perm   2 sec   (6532 perm/sec)   p_kst 1.198000e-01   p_cons 1   p_joint 4.756000e-01

Joint ci ratio: 3.134430e-02	ci left: 4.319069e-01	ci right 4.457109e-01	k: 8776	n:20000
Cons ci ratio: 2.771651e-04	ci left: 9.997214e-01	ci right 9.999987e-01	k: 19999	n:20000
KS ci ratio: 7.423726e-02	ci left: 1.177895e-01	ci right 1.269206e-01	k: 2446	n:20000
ZIM2   20000 perm   3 sec   (5743 perm/sec)   p_kst 1.223000e-01   p_cons 9.999500e-01   p_joint 4.388000e-01

Outputting figure to mutsig2_images.part000000000194/ZIM2.2_1600_20000_0.1223_0.99995_0.4388.png
                gene_name: ZIM2
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 1.00 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000194
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 194 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 4398567: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000195> was used as the working directory.
Started at Wed Oct 24 16:18:23 2012
Results reported at Wed Oct 24 16:20:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000195.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000195.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 195  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000195.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    178.78 sec.
    Max Memory :      1528 MB
    Max Swap   :      3974 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
195
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 195
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 195: processing genes 17405 - 17493
Calculating significance of each gene.
Using projection method.
17405	ZMAT5	1
17406	ZMIZ1	1
17407	ZMIZ2	1
17408	ZMPSTE24	1.455880e-01
17409	ZMYM1	1.248490e-01
17410	ZMYM2	2.438234e-01
17411	ZMYM3	1
17412	ZMYM4	2.806077e-01
17413	ZMYM5	1
17414	ZMYM6	1
17415	ZMYND10	1.310437e-01
17416	ZMYND11	1
17417	ZMYND12	1
17418	ZMYND15	1
17419	ZMYND17	1
17420	ZMYND19	7.243460e-02
17421	ZMYND8	1
17422	ZNF10	1
17423	ZNF100	1.364618e-01
17424	ZNF101	1
17425	ZNF107	1
17426	ZNF114	1.347303e-01
17427	ZNF117	1
17428	ZNF12	1
17429	ZNF121	1
17430	ZNF124	1
17431	ZNF131	1
17432	ZNF132	1
17433	ZNF133	1
17434	ZNF134	1
17435	ZNF135	1
17436	ZNF136	1
17437	ZNF138	1
17438	ZNF14	1.039829e-01
17439	ZNF140	1
17440	ZNF141	1
17441	ZNF142	1
17442	ZNF143	1.195067e-01
17443	ZNF146	1
17444	ZNF148	3.114866e-02
17445	ZNF154	1
17446	ZNF155	1
17447	ZNF157	1.437815e-02
17448	ZNF16	1
17449	ZNF160	2.219310e-01
17450	ZNF165	2.074466e-01
17451	ZNF167	1
17452	ZNF169	1
17453	ZNF17	1
17454	ZNF174	1
17455	ZNF175	1.125716e-01
17456	ZNF177	1
17457	ZNF18	1
17458	ZNF180	1
17459	ZNF181	1
17460	ZNF182	1.921637e-01
17461	ZNF184	1
17462	ZNF185	1.132993e-01
17463	ZNF187	1
17464	ZNF189	1.351389e-01
17465	ZNF19	1
17466	ZNF192	1
17467	ZNF193	6.850538e-02
17468	ZNF195	1
17469	ZNF197	1
17470	ZNF2	1
17471	ZNF20	1
17472	ZNF200	5.466807e-02
17473	ZNF202	1
17474	ZNF205	1
17475	ZNF207	1
17476	ZNF208	1
17477	ZNF211	1
17478	ZNF212	1
17479	ZNF213	1
17480	ZNF214	1
17481	ZNF215	1
17482	ZNF217	1
17483	ZNF219	8.713105e-03
17484	ZNF22	1
17485	ZNF221	1
17486	ZNF222	1.702322e-01
17487	ZNF223	1
17488	ZNF224	1
17489	ZNF225	1
17490	ZNF226	1.796128e-01
17491	ZNF227	1.556089e-01
17492	ZNF229	1
17493	ZNF23	1
Done

Running MutSig 2:
Scatter job 195: processing genes 17405 - 17493
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.849773e-02	ci left: 8.101938e-01	ci right 8.254206e-01	k: 8179	n:10000
KS ci ratio: 8.472899e-02	ci left: 1.687778e-01	ci right 1.838112e-01	k: 1762	n:10000
ZNF14   10000 perm   2 sec   (5926 perm/sec)   p_kst 1.762000e-01   p_cons 8.179000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000195/ZNF14.2_1945_10000_0.1762_0.8179_1.png
                gene_name: ZNF14
               theta_stop: 0.085 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 20 percent done.
ZNF148
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.079590e-03	ci left: 9.734446e-01	ci right 9.794734e-01	k: 9766	n:10000
Cons ci ratio: 3.130776e-02	ci left: 6.008614e-01	ci right 6.200742e-01	k: 6105	n:10000
KS ci ratio: 3.986605e-02	ci left: 4.816553e-01	ci right 5.013497e-01	k: 4915	n:10000
ZNF148   10000 perm   2 sec   (5893 perm/sec)   p_kst 4.915000e-01   p_cons 6.105000e-01   p_joint 9.766000e-01

Outputting figure to mutsig2_images.part000000000195/ZNF148.2_2409_10000_0.4915_0.6105_0.9766.png
                gene_name: ZNF148
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 40 percent done.
ZNF157
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.192327e-02	ci left: 5.915247e-01	ci right 6.108164e-01	k: 6012	n:10000
Cons ci ratio: 5.330361e-02	ci left: 3.415406e-01	ci right 3.603463e-01	k: 3509	n:10000
KS ci ratio: 2.130330e-02	ci left: 7.636486e-01	ci right 7.801928e-01	k: 7720	n:10000
ZNF157   10000 perm   2 sec   (6371 perm/sec)   p_kst 7.720000e-01   p_cons 3.509000e-01   p_joint 6.012000e-01

Outputting figure to mutsig2_images.part000000000195/ZNF157.2_1537_10000_0.772_0.3509_0.6012.png
                gene_name: ZNF157
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 60 percent done.
ZNF219
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.694391e-01	ci left: 4.648153e-02	ci right 5.518251e-02	k: 507	n:10000
Cons ci ratio: 2.937057e-01	ci left: 1.492852e-02	ci right 2.015795e-02	k: 174	n:10000
KS ci ratio: 2.401460e-02	ci left: 7.182540e-01	ci right 7.358135e-01	k: 7271	n:10000
ZNF219   10000 perm   2 sec   (6027 perm/sec)   p_kst 7.271000e-01   p_cons 1.740000e-02   p_joint 5.070000e-02

Joint ci ratio: 1.398453e-01	ci left: 3.515098e-02	ci right 4.048447e-02	k: 755	n:20000
Cons ci ratio: 2.032964e-01	ci left: 1.639270e-02	ci right 2.014922e-02	k: 364	n:20000
KS ci ratio: 1.724665e-02	ci left: 7.146266e-01	ci right 7.271091e-01	k: 14418	n:20000
ZNF219   20000 perm   4 sec   (5376 perm/sec)   p_kst 7.209000e-01   p_cons 1.820000e-02   p_joint 3.775000e-02

Joint ci ratio: 1.279587e-01	ci left: 2.838926e-02	ci right 3.230240e-02	k: 909	n:30000
Cons ci ratio: 1.662242e-01	ci left: 1.668552e-02	ci right 1.974213e-02	k: 545	n:30000
KS ci ratio: 1.406326e-02	ci left: 7.163226e-01	ci right 7.265012e-01	k: 21643	n:30000
ZNF219   30000 perm   6 sec   (5124 perm/sec)   p_kst 7.214333e-01   p_cons 1.816667e-02   p_joint 3.030000e-02

Joint ci ratio: 1.144326e-01	ci left: 2.686684e-02	ci right 3.015209e-02	k: 1139	n:40000
Cons ci ratio: 1.442580e-01	ci left: 1.681613e-02	ci right 1.945449e-02	k: 724	n:40000
KS ci ratio: 1.222944e-02	ci left: 7.153455e-01	ci right 7.241726e-01	k: 28791	n:40000
ZNF219   40000 perm   8 sec   (4942 perm/sec)   p_kst 7.197750e-01   p_cons 1.810000e-02   p_joint 2.847500e-02

Joint ci ratio: 8.926016e-02	ci left: 3.547980e-02	ci right 3.881421e-02	k: 1856	n:50000
Cons ci ratio: 1.199879e-01	ci left: 1.964460e-02	ci right 2.217145e-02	k: 1044	n:50000
KS ci ratio: 1.095613e-02	ci left: 7.151580e-01	ci right 7.230565e-01	k: 35956	n:50000
ZNF219   50000 perm   10 sec   (4820 perm/sec)   p_kst 7.191200e-01   p_cons 2.088000e-02   p_joint 3.712000e-02

Joint ci ratio: 6.496089e-02	ci left: 5.535497e-02	ci right 5.908800e-02	k: 3432	n:60000
Cons ci ratio: 1.092226e-01	ci left: 1.986759e-02	ci right 2.217907e-02	k: 1260	n:60000
KS ci ratio: 9.998328e-03	ci left: 7.156355e-01	ci right 7.228433e-01	k: 43155	n:60000
ZNF219   60000 perm   13 sec   (4627 perm/sec)   p_kst 7.192500e-01   p_cons 2.100000e-02   p_joint 5.720000e-02

Joint ci ratio: 5.524471e-02	ci left: 6.524329e-02	ci right 6.896412e-02	k: 4696	n:70000
Cons ci ratio: 1.009863e-01	ci left: 2.000629e-02	ci right 2.214795e-02	k: 1474	n:70000
KS ci ratio: 9.251915e-03	ci left: 7.161128e-01	ci right 7.227833e-01	k: 50362	n:70000
ZNF219   70000 perm   15 sec   (4536 perm/sec)   p_kst 7.194571e-01   p_cons 2.105714e-02   p_joint 6.708571e-02

Joint ci ratio: 5.323498e-02	ci left: 6.178273e-02	ci right 6.517401e-02	k: 5077	n:80000
Cons ci ratio: 9.388867e-02	ci left: 2.032285e-02	ci right 2.233707e-02	k: 1705	n:80000
KS ci ratio: 8.645155e-03	ci left: 7.167616e-01	ci right 7.229975e-01	k: 57591	n:80000
ZNF219   80000 perm   18 sec   (4457 perm/sec)   p_kst 7.198875e-01   p_cons 2.131250e-02   p_joint 6.346250e-02

Outputting figure to mutsig2_images.part000000000195/ZNF219.2_2185_80000_0.71989_0.021313_0.063463.png
                gene_name: ZNF219
               theta_stop: 0.094 
                    nperm: 80000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.021 
      ci_cons_bounds_left: 0.020 
     ci_cons_bounds_right: 0.022 
                  p_joint: 0.063 
     ci_joint_bounds_left: 0.062 
    ci_joint_bounds_right: 0.065 

Current progress: 80 percent done.
ZNF222
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.066559e-01	ci left: 1.126178e-01	ci right 1.254051e-01	k: 1189	n:10000
Cons ci ratio: 2.347668e-02	ci left: 7.272426e-01	ci right 7.446198e-01	k: 7360	n:10000
KS ci ratio: 3.683071e-01	ci left: 9.139894e-03	ci right 1.335208e-02	k: 111	n:10000
ZNF222   10000 perm   2 sec   (6620 perm/sec)   p_kst 1.110000e-02   p_cons 7.360000e-01   p_joint 1.189000e-01

Joint ci ratio: 7.717746e-02	ci left: 1.098234e-01	ci right 1.186891e-01	k: 2284	n:20000
Cons ci ratio: 1.658154e-02	ci left: 7.302852e-01	ci right 7.425460e-01	k: 14729	n:20000
KS ci ratio: 2.536541e-01	ci left: 1.030287e-02	ci right 1.334154e-02	k: 235	n:20000
ZNF222   20000 perm   3 sec   (5821 perm/sec)   p_kst 1.175000e-02   p_cons 7.364500e-01   p_joint 1.142000e-01

Joint ci ratio: 6.147184e-02	ci left: 1.156853e-01	ci right 1.230553e-01	k: 3580	n:30000
Cons ci ratio: 1.354523e-02	ci left: 7.312409e-01	ci right 7.412467e-01	k: 22088	n:30000
KS ci ratio: 1.992804e-01	ci left: 1.146358e-02	ci right 1.403207e-02	k: 381	n:30000
ZNF222   30000 perm   6 sec   (5376 perm/sec)   p_kst 1.270000e-02   p_cons 7.362667e-01   p_joint 1.193333e-01

Joint ci ratio: 4.642054e-02	ci left: 1.477765e-01	ci right 1.548242e-01	k: 6051	n:40000
Cons ci ratio: 1.177106e-02	ci left: 7.305702e-01	ci right 7.392457e-01	k: 29397	n:40000
KS ci ratio: 1.678608e-01	ci left: 1.232011e-02	ci right 1.460133e-02	k: 537	n:40000
ZNF222   40000 perm   8 sec   (5214 perm/sec)   p_kst 1.342500e-02   p_cons 7.349250e-01   p_joint 1.512750e-01

Joint ci ratio: 5.200451e-02	ci left: 9.938015e-02	ci right 1.047062e-01	k: 5101	n:50000
Cons ci ratio: 1.053229e-02	ci left: 7.308870e-01	ci right 7.386457e-01	k: 36739	n:50000
KS ci ratio: 1.506513e-01	ci left: 1.235273e-02	ci right 1.438435e-02	k: 667	n:50000
ZNF222   50000 perm   10 sec   (5081 perm/sec)   p_kst 1.334000e-02   p_cons 7.347800e-01   p_joint 1.020200e-01

Joint ci ratio: 3.081658e-02	ci left: 2.091164e-01	ci right 2.156781e-01	k: 12743	n:60000
Cons ci ratio: 9.605097e-03	ci left: 7.316164e-01	ci right 7.386942e-01	k: 44110	n:60000
KS ci ratio: 1.367153e-01	ci left: 1.259186e-02	ci right 1.445563e-02	k: 810	n:60000
ZNF222   60000 perm   12 sec   (4969 perm/sec)   p_kst 1.350000e-02   p_cons 7.351667e-01   p_joint 2.123833e-01

Joint ci ratio: 2.850020e-02	ci left: 2.097160e-01	ci right 2.157936e-01	k: 14892	n:70000
Cons ci ratio: 8.879114e-03	ci left: 7.324739e-01	ci right 7.390209e-01	k: 51503	n:70000
KS ci ratio: 1.280335e-01	ci left: 1.236761e-02	ci right 1.407310e-02	k: 924	n:70000
ZNF222   70000 perm   14 sec   (4866 perm/sec)   p_kst 1.320000e-02   p_cons 7.357571e-01   p_joint 2.127429e-01

Joint ci ratio: 2.659459e-02	ci left: 2.107268e-01	ci right 2.164190e-01	k: 17085	n:80000
Cons ci ratio: 8.316221e-03	ci left: 7.321905e-01	ci right 7.383174e-01	k: 58821	n:80000
KS ci ratio: 1.183621e-01	ci left: 1.272388e-02	ci right 1.433668e-02	k: 1081	n:80000
ZNF222   80000 perm   17 sec   (4768 perm/sec)   p_kst 1.351250e-02   p_cons 7.352625e-01   p_joint 2.135625e-01

Joint ci ratio: 2.627199e-02	ci left: 1.956993e-01	ci right 2.009202e-01	k: 17847	n:90000
Cons ci ratio: 7.851269e-03	ci left: 7.318360e-01	ci right 7.376155e-01	k: 66126	n:90000
KS ci ratio: 1.119314e-01	ci left: 1.269138e-02	ci right 1.420689e-02	k: 1209	n:90000
ZNF222   90000 perm   19 sec   (4673 perm/sec)   p_kst 1.343333e-02   p_cons 7.347333e-01   p_joint 1.983000e-01

Joint ci ratio: 2.884311e-02	ci left: 1.536566e-01	ci right 1.581633e-01	k: 15590	n:100000
Cons ci ratio: 7.436015e-03	ci left: 7.326341e-01	ci right 7.381122e-01	k: 73538	n:100000
KS ci ratio: 1.066485e-01	ci left: 1.261860e-02	ci right 1.404983e-02	k: 1332	n:100000
ZNF222   100000 perm   22 sec   (4586 perm/sec)   p_kst 1.332000e-02   p_cons 7.353800e-01   p_joint 1.559000e-01

Joint ci ratio: 2.359956e-02	ci left: 1.981555e-01	ci right 2.028967e-01	k: 22057	n:110000
Cons ci ratio: 7.085956e-03	ci left: 7.329831e-01	ci right 7.382045e-01	k: 80916	n:110000
KS ci ratio: 1.013114e-01	ci left: 1.274656e-02	ci right 1.411564e-02	k: 1476	n:110000
ZNF222   110000 perm   24 sec   (4516 perm/sec)   p_kst 1.341818e-02   p_cons 7.356000e-01   p_joint 2.005182e-01

Joint ci ratio: 2.648722e-02	ci left: 1.523018e-01	ci right 1.563983e-01	k: 18521	n:120000
Cons ci ratio: 6.800421e-03	ci left: 7.321672e-01	ci right 7.371715e-01	k: 88161	n:120000
KS ci ratio: 9.712896e-02	ci left: 1.274080e-02	ci right 1.404954e-02	k: 1606	n:120000
ZNF222   120000 perm   27 sec   (4431 perm/sec)   p_kst 1.338333e-02   p_cons 7.346750e-01   p_joint 1.543417e-01

Outputting figure to mutsig2_images.part000000000195/ZNF222.2_1511_120000_0.013383_0.73467_0.15434.png
                gene_name: ZNF222
               theta_stop: 0.097 
                    nperm: 120000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.013 
       ci_ks_bounds_right: 0.014 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.16 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000195
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 195 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1724>
Subject: Job 4398572: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1724>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000196> was used as the working directory.
Started at Wed Oct 24 16:18:23 2012
Results reported at Wed Oct 24 16:20:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000196.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000196.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 196  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000196.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     85.83 sec.
    Max Memory :      1021 MB
    Max Swap   :      3907 MB

    Max Processes  :         7
    Max Threads    :        69

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
196
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 196
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 196: processing genes 17494 - 17583
Calculating significance of each gene.
Using projection method.
17494	ZNF230	1
17495	ZNF232	8.924282e-02
17496	ZNF233	3.309677e-01
17497	ZNF234	1
17498	ZNF235	1
17499	ZNF236	2.370287e-01
17500	ZNF238	1.953395e-01
17501	ZNF239	1
17502	ZNF24	1
17503	ZNF248	1
17504	ZNF25	1
17505	ZNF250	1
17506	ZNF251	1
17507	ZNF253	1
17508	ZNF254	1
17509	ZNF256	1
17510	ZNF257	1
17511	ZNF259	1
17512	ZNF260	1
17513	ZNF263	1
17514	ZNF264	1
17515	ZNF266	2.024804e-01
17516	ZNF267	1
17517	ZNF268	1
17518	ZNF273	1
17519	ZNF274	1
17520	ZNF275	1
17521	ZNF276	2.617242e-01
17522	ZNF277	5.878266e-02
17523	ZNF28	1
17524	ZNF280A	1
17525	ZNF280B	1
17526	ZNF280C	1
17527	ZNF280D	1
17528	ZNF281	1
17529	ZNF282	1
17530	ZNF283	2.467103e-02
17531	ZNF284	1
17532	ZNF285	1
17533	ZNF286A	1
17534	ZNF287	1
17535	ZNF292	3.755926e-01
17536	ZNF295	1
17537	ZNF296	1
17538	ZNF3	1
17539	ZNF30	1
17540	ZNF300	1
17541	ZNF302	1
17542	ZNF304	1
17543	ZNF311	1
17544	ZNF317	1
17545	ZNF318	7.108576e-01
17546	ZNF319	1
17547	ZNF32	1
17548	ZNF320	1.485268e-01
17549	ZNF321	1
17550	ZNF322A	1
17551	ZNF322B	1
17552	ZNF323	1
17553	ZNF324	1
17554	ZNF324B	1
17555	ZNF326	1
17556	ZNF329	2.260669e-01
17557	ZNF330	1
17558	ZNF331	1
17559	ZNF333	1
17560	ZNF334	2.487122e-02
17561	ZNF335	1
17562	ZNF337	1
17563	ZNF33A	9.372275e-02
17564	ZNF33B	1
17565	ZNF34	4.543214e-02
17566	ZNF341	1
17567	ZNF343	1
17568	ZNF345	1
17569	ZNF346	1
17570	ZNF347	2.995613e-01
17571	ZNF35	1
17572	ZNF350	9.761627e-02
17573	ZNF354A	1
17574	ZNF354B	1
17575	ZNF354C	1
17576	ZNF358	1.586943e-02
17577	ZNF362	1
17578	ZNF365	1
17579	ZNF366	3.378004e-01
17580	ZNF367	1
17581	ZNF37A	1
17582	ZNF382	1
17583	ZNF383	1
Done

Running MutSig 2:
Scatter job 196: processing genes 17494 - 17583
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF283
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.715456e-02	ci left: 8.319533e-01	ci right 8.464485e-01	k: 8393	n:10000
Cons ci ratio: 2.869303e-02	ci left: 6.416654e-01	ci right 6.604465e-01	k: 6511	n:10000
KS ci ratio: 3.865703e-02	ci left: 4.970503e-01	ci right 5.167457e-01	k: 5069	n:10000
ZNF283   10000 perm   2 sec   (5433 perm/sec)   p_kst 5.069000e-01   p_cons 6.511000e-01   p_joint 8.393000e-01

Outputting figure to mutsig2_images.part000000000196/ZNF283.3_2056_10000_0.5069_0.6511_0.8393.png
                gene_name: ZNF283
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.85 

Current progress: 33 percent done.
ZNF236
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 2.488138e-02	ci left: 7.038210e-01	ci right 7.216550e-01	k: 7128	n:10000
KS ci ratio: 8.555495e-02	ci left: 1.660256e-01	ci right 1.809651e-01	k: 1734	n:10000
ZNF236   10000 perm   2 sec   (4927 perm/sec)   p_kst 1.734000e-01   p_cons 7.128000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000196/ZNF236.2_5662_10000_0.1734_0.7128_1.png
                gene_name: ZNF236
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.72 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
ZNF334
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.748669e-03	ci left: 9.678372e-01	ci right 9.744845e-01	k: 9713	n:10000
Cons ci ratio: 1.300507e-03	ci left: 9.981617e-01	ci right 9.995204e-01	k: 9990	n:10000
KS ci ratio: 2.613838e-02	ci left: 6.830481e-01	ci right 7.012398e-01	k: 6922	n:10000
ZNF334   10000 perm   2 sec   (6186 perm/sec)   p_kst 6.922000e-01   p_cons 9.990000e-01   p_joint 9.713000e-01

Outputting figure to mutsig2_images.part000000000196/ZNF334.2_2059_10000_0.6922_0.999_0.9713.png
                gene_name: ZNF334
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   p_cons: 1.00 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.97 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000196
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 196 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 4398574: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000197> was used as the working directory.
Started at Wed Oct 24 16:18:29 2012
Results reported at Wed Oct 24 16:21:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000197.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000197.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 197  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000197.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    207.66 sec.
    Max Memory :      1440 MB
    Max Swap   :      4116 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
197
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 197
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 197: processing genes 17584 - 17673
Calculating significance of each gene.
Using projection method.
17584	ZNF384	6.706865e-02
17585	ZNF385A	4.074891e-02
17586	ZNF385B	1
17587	ZNF385D	1
17588	ZNF391	1
17589	ZNF394	1
17590	ZNF395	1
17591	ZNF396	1
17592	ZNF397	1
17593	ZNF397OS	1
17594	ZNF398	2.212334e-01
17595	ZNF404	3.700437e-02
17596	ZNF407	5.809000e-01
17597	ZNF408	1
17598	ZNF41	3.475355e-01
17599	ZNF410	2.012130e-01
17600	ZNF415	1.680250e-01
17601	ZNF416	1
17602	ZNF417	1
17603	ZNF418	2.355368e-01
17604	ZNF419	1
17605	ZNF420	1
17606	ZNF423	1
17607	ZNF425	1
17608	ZNF426	1
17609	ZNF428	1
17610	ZNF429	1
17611	ZNF43	6.637572e-03
17612	ZNF430	1
17613	ZNF431	1
17614	ZNF432	1
17615	ZNF433	1.805387e-01
17616	ZNF434	1
17617	ZNF436	1
17618	ZNF438	1
17619	ZNF439	1
17620	ZNF44	1
17621	ZNF440	4.515228e-03
17622	ZNF441	1
17623	ZNF442	3.886109e-02
17624	ZNF443	1.355124e-01
17625	ZNF445	2.848465e-01
17626	ZNF446	1
17627	ZNF449	1
17628	ZNF45	1
17629	ZNF451	1
17630	ZNF454	1.125641e-01
17631	ZNF460	1
17632	ZNF461	1
17633	ZNF462	4.510380e-01
17634	ZNF467	1
17635	ZNF468	1
17636	ZNF470	1.246138e-02
17637	ZNF471	1
17638	ZNF473	1
17639	ZNF474	1
17640	ZNF479	1
17641	ZNF48	1
17642	ZNF480	1
17643	ZNF483	1
17644	ZNF484	2.624223e-01
17645	ZNF485	1
17646	ZNF486	1
17647	ZNF488	1
17648	ZNF490	1
17649	ZNF491	5.792411e-02
17650	ZNF492	1
17651	ZNF493	5.332024e-03
17652	ZNF496	2.984404e-01
17653	ZNF497	1
17654	ZNF498	1
17655	ZNF500	1
17656	ZNF501	1
17657	ZNF502	1
17658	ZNF503	1
17659	ZNF506	1
17660	ZNF507	1
17661	ZNF510	1
17662	ZNF511	1
17663	ZNF512	1
17664	ZNF512B	1
17665	ZNF513	1
17666	ZNF514	1
17667	ZNF516	1
17668	ZNF517	1
17669	ZNF518A	3.257295e-01
17670	ZNF518B	3.250863e-02
17671	ZNF519	1.222444e-01
17672	ZNF521	1.756313e-01
17673	ZNF524	1
Done

Running MutSig 2:
Scatter job 197: processing genes 17584 - 17673
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF440
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.029101e-02	ci left: 4.763591e-01	ci right 4.960489e-01	k: 4862	n:10000
Cons ci ratio: 2.348272e-02	ci left: 7.271416e-01	ci right 7.445209e-01	k: 7359	n:10000
KS ci ratio: 5.692071e-02	ci left: 3.124482e-01	ci right 3.308558e-01	k: 3216	n:10000
ZNF440   10000 perm   2 sec   (5616 perm/sec)   p_kst 3.216000e-01   p_cons 7.359000e-01   p_joint 4.862000e-01

Outputting figure to mutsig2_images.part000000000197/ZNF440.3_1804_10000_0.3216_0.7359_0.4862.png
                gene_name: ZNF440
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 17 percent done.
ZNF518B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.180519e-02	ci left: 3.545604e-01	ci right 3.735189e-01	k: 3640	n:10000
Cons ci ratio: 1.602799e-02	ci left: 8.497808e-01	ci right 8.636107e-01	k: 8568	n:10000
KS ci ratio: 7.503512e-02	ci left: 2.062917e-01	ci right 2.224751e-01	k: 2143	n:10000
ZNF518B   10000 perm   2 sec   (5073 perm/sec)   p_kst 2.143000e-01   p_cons 8.568000e-01   p_joint 3.640000e-01

Outputting figure to mutsig2_images.part000000000197/ZNF518B.3_3229_10000_0.2143_0.8568_0.364.png
                gene_name: ZNF518B
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 33 percent done.
ZNF43
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.699839e-02	ci left: 5.189593e-01	ci right 5.386240e-01	k: 5288	n:10000
Cons ci ratio: 3.531729e-02	ci left: 5.420892e-01	ci right 5.616806e-01	k: 5519	n:10000
KS ci ratio: 2.131928e-01	ci left: 2.920604e-02	ci right 3.626959e-02	k: 326	n:10000
ZNF43   10000 perm   2 sec   (5800 perm/sec)   p_kst 3.260000e-02   p_cons 5.519000e-01   p_joint 5.288000e-01

Joint ci ratio: 6.114873e-02	ci left: 1.652124e-01	ci right 1.756836e-01	k: 3408	n:20000
Cons ci ratio: 2.388266e-02	ci left: 5.670113e-01	ci right 5.807673e-01	k: 11478	n:20000
KS ci ratio: 1.529431e-01	ci left: 2.936331e-02	ci right 3.427405e-02	k: 635	n:20000
ZNF43   20000 perm   4 sec   (5100 perm/sec)   p_kst 3.175000e-02   p_cons 5.739000e-01   p_joint 1.704000e-01

Joint ci ratio: 5.467756e-02	ci left: 1.422527e-01	ci right 1.502826e-01	k: 4387	n:30000
Cons ci ratio: 1.945403e-02	ci left: 5.694492e-01	ci right 5.806696e-01	k: 17252	n:30000
KS ci ratio: 1.283227e-01	ci left: 2.822778e-02	ci right 3.213057e-02	k: 904	n:30000
ZNF43   30000 perm   6 sec   (4845 perm/sec)   p_kst 3.013333e-02   p_cons 5.750667e-01   p_joint 1.462333e-01

Joint ci ratio: 4.692408e-02	ci left: 1.450531e-01	ci right 1.520480e-01	k: 5941	n:40000
Cons ci ratio: 1.685015e-02	ci left: 5.701377e-01	ci right 5.798514e-01	k: 23000	n:40000
KS ci ratio: 1.125660e-01	ci left: 2.776630e-02	ci right 3.110248e-02	k: 1176	n:40000
ZNF43   40000 perm   9 sec   (4687 perm/sec)   p_kst 2.940000e-02   p_cons 5.750000e-01   p_joint 1.485250e-01

Joint ci ratio: 2.519444e-02	ci left: 3.220909e-01	ci right 3.303293e-01	k: 16310	n:50000
Cons ci ratio: 1.511021e-02	ci left: 5.693911e-01	ci right 5.780803e-01	k: 28687	n:50000
KS ci ratio: 1.005153e-01	ci left: 2.803426e-02	ci right 3.102069e-02	k: 1475	n:50000
ZNF43   50000 perm   11 sec   (4562 perm/sec)   p_kst 2.950000e-02   p_cons 5.737400e-01   p_joint 3.262000e-01

Joint ci ratio: 2.149615e-02	ci left: 3.527494e-01	ci right 3.604312e-01	k: 21395	n:60000
Cons ci ratio: 1.384238e-02	ci left: 5.680459e-01	ci right 5.759805e-01	k: 34321	n:60000
KS ci ratio: 9.224713e-02	ci left: 2.786729e-02	ci right 3.057851e-02	k: 1752	n:60000
ZNF43   60000 perm   13 sec   (4454 perm/sec)   p_kst 2.920000e-02   p_cons 5.720167e-01   p_joint 3.565833e-01

Outputting figure to mutsig2_images.part000000000197/ZNF43.2_2446_60000_0.0292_0.57202_0.35658.png
                gene_name: ZNF43
               theta_stop: 0.092 
                    nperm: 60000 
                     p_ks: 0.029 
        ci_ks_bounds_left: 0.028 
       ci_ks_bounds_right: 0.031 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.36 

Current progress: 50 percent done.
ZNF442
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.065542e-01	ci left: 1.128131e-01	ci right 1.256096e-01	k: 1191	n:10000
Cons ci ratio: 8.764072e-02	ci left: 1.593447e-01	ci right 1.740500e-01	k: 1666	n:10000
KS ci ratio: 7.256337e-02	ci left: 2.176360e-01	ci right 2.341240e-01	k: 2258	n:10000
ZNF442   10000 perm   2 sec   (6101 perm/sec)   p_kst 2.258000e-01   p_cons 1.666000e-01   p_joint 1.191000e-01

Joint ci ratio: 7.559884e-02	ci left: 1.140023e-01	ci right 1.230090e-01	k: 2369	n:20000
Cons ci ratio: 6.255865e-02	ci left: 1.589418e-01	ci right 1.692560e-01	k: 3281	n:20000
KS ci ratio: 5.004558e-02	ci left: 2.288403e-01	ci right 2.406369e-01	k: 4694	n:20000
ZNF442   20000 perm   4 sec   (5427 perm/sec)   p_kst 2.347000e-01   p_cons 1.640500e-01   p_joint 1.184500e-01

Outputting figure to mutsig2_images.part000000000197/ZNF442.2_1900_20000_0.2347_0.16405_0.11845.png
                gene_name: ZNF442
               theta_stop: 0.076 
                    nperm: 20000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

Current progress: 67 percent done.
ZNF470
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.298919e-03	ci left: 9.422194e-01	ci right 9.511181e-01	k: 9468	n:10000
Cons ci ratio: 1.313571e-02	ci left: 8.930299e-01	ci right 9.049365e-01	k: 8991	n:10000
KS ci ratio: 5.222166e-02	ci left: 3.508823e-01	ci right 3.697992e-01	k: 3603	n:10000
ZNF470   10000 perm   2 sec   (5748 perm/sec)   p_kst 3.603000e-01   p_cons 8.991000e-01   p_joint 9.468000e-01

Outputting figure to mutsig2_images.part000000000197/ZNF470.2_2170_10000_0.3603_0.8991_0.9468.png
                gene_name: ZNF470
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.95 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 83 percent done.
ZNF493
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.197123e-03	ci left: 9.433622e-01	ci right 9.521746e-01	k: 9479	n:10000
Cons ci ratio: 3.777008e-02	ci left: 5.086527e-01	ci right 5.283365e-01	k: 5185	n:10000
KS ci ratio: 1.014497e-01	ci left: 1.232714e-01	ci right 1.365450e-01	k: 1298	n:10000
ZNF493   10000 perm   2 sec   (5733 perm/sec)   p_kst 1.298000e-01   p_cons 5.185000e-01   p_joint 9.479000e-01

Joint ci ratio: 1.799235e-02	ci left: 6.971664e-01	ci right 7.098744e-01	k: 14071	n:20000
Cons ci ratio: 2.672008e-02	ci left: 5.113479e-01	ci right 5.252468e-01	k: 10366	n:20000
KS ci ratio: 7.229778e-02	ci left: 1.234976e-01	ci right 1.328108e-01	k: 2562	n:20000
ZNF493   20000 perm   4 sec   (5049 perm/sec)   p_kst 1.281000e-01   p_cons 5.183000e-01   p_joint 7.035500e-01

Outputting figure to mutsig2_images.part000000000197/ZNF493.2_2404_20000_0.1281_0.5183_0.70355.png
                gene_name: ZNF493
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.71 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000197
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 197 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1552>
Subject: Job 4398577: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1552>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000198> was used as the working directory.
Started at Wed Oct 24 16:18:32 2012
Results reported at Wed Oct 24 16:20:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000198.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000198.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 198  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000198.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    237.95 sec.
    Max Memory :      1394 MB
    Max Swap   :      3943 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
198
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 198
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 198: processing genes 17674 - 17763
Calculating significance of each gene.
Using projection method.
17674	ZNF526	1.589909e-01
17675	ZNF527	1
17676	ZNF528	1
17677	ZNF529	1
17678	ZNF530	1
17679	ZNF532	3.238662e-01
17680	ZNF534	1
17681	ZNF536	1
17682	ZNF540	1.555190e-01
17683	ZNF543	1
17684	ZNF544	1
17685	ZNF546	1
17686	ZNF547	1
17687	ZNF548	1
17688	ZNF549	1
17689	ZNF550	1
17690	ZNF551	5.464947e-02
17691	ZNF552	1
17692	ZNF554	1
17693	ZNF555	1
17694	ZNF556	1
17695	ZNF557	1
17696	ZNF558	1
17697	ZNF559	1.743877e-01
17698	ZNF560	1
17699	ZNF561	1
17700	ZNF562	1
17701	ZNF563	9.566757e-02
17702	ZNF564	2.206446e-01
17703	ZNF565	2.042490e-01
17704	ZNF566	3.570499e-02
17705	ZNF567	1
17706	ZNF568	7.249458e-02
17707	ZNF569	3.042922e-02
17708	ZNF57	1
17709	ZNF570	1.686377e-01
17710	ZNF571	1
17711	ZNF572	1
17712	ZNF573	3.647430e-03
17713	ZNF574	1
17714	ZNF575	1
17715	ZNF576	1
17716	ZNF577	1
17717	ZNF578	2.006613e-02
17718	ZNF581	1
17719	ZNF582	2.046130e-01
17720	ZNF583	1
17721	ZNF584	1
17722	ZNF585A	1
17723	ZNF585B	1
17724	ZNF586	1
17725	ZNF587	1
17726	ZNF589	1
17727	ZNF592	3.054805e-01
17728	ZNF593	1
17729	ZNF594	3.679121e-02
17730	ZNF595	1
17731	ZNF596	1
17732	ZNF597	1
17733	ZNF598	1
17734	ZNF599	1
17735	ZNF600	1
17736	ZNF605	1
17737	ZNF606	2.965925e-01
17738	ZNF607	3.492399e-02
17739	ZNF608	1
17740	ZNF609	3.316821e-01
17741	ZNF610	1
17742	ZNF611	2.626615e-01
17743	ZNF613	1
17744	ZNF614	1
17745	ZNF615	1
17746	ZNF616	1
17747	ZNF618	1
17748	ZNF619	1.818290e-01
17749	ZNF620	1
17750	ZNF621	1
17751	ZNF622	1
17752	ZNF623	1
17753	ZNF624	1
17754	ZNF625	1
17755	ZNF626	2.391969e-01
17756	ZNF627	1
17757	ZNF628	1
17758	ZNF629	1
17759	ZNF630	1
17760	ZNF638	3.365205e-01
17761	ZNF639	1
17762	ZNF641	1
17763	ZNF642	2.088954e-01
Done

Running MutSig 2:
Scatter job 198: processing genes 17674 - 17763
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF573
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.427484e-02	ci left: 1.404072e-01	ci right 1.543988e-01	k: 1473	n:10000
Cons ci ratio: 1.206707e-02	ci left: 9.078193e-01	ci right 9.189385e-01	k: 9135	n:10000
KS ci ratio: 1.699685e-01	ci left: 4.619368e-02	ci right 5.487054e-02	k: 504	n:10000
ZNF573   10000 perm   2 sec   (5886 perm/sec)   p_kst 5.040000e-02   p_cons 9.135000e-01   p_joint 1.473000e-01

Joint ci ratio: 6.221878e-02	ci left: 1.604228e-01	ci right 1.707746e-01	k: 3311	n:20000
Cons ci ratio: 8.482467e-03	ci left: 9.104371e-01	ci right 9.182419e-01	k: 18288	n:20000
KS ci ratio: 1.183488e-01	ci left: 4.891463e-02	ci right 5.511643e-02	k: 1039	n:20000
ZNF573   20000 perm   7 sec   (2988 perm/sec)   p_kst 5.195000e-02   p_cons 9.144000e-01   p_joint 1.655500e-01

Joint ci ratio: 5.606159e-02	ci left: 1.361907e-01	ci right 1.440791e-01	k: 4203	n:30000
Cons ci ratio: 6.950498e-03	ci left: 9.106011e-01	ci right 9.169852e-01	k: 27415	n:30000
KS ci ratio: 9.441802e-02	ci left: 5.176232e-02	ci right 5.692442e-02	k: 1629	n:30000
ZNF573   30000 perm   9 sec   (3389 perm/sec)   p_kst 5.430000e-02   p_cons 9.138333e-01   p_joint 1.401000e-01

Outputting figure to mutsig2_images.part000000000198/ZNF573.4_2139_30000_0.0543_0.91383_0.1401.png
                gene_name: ZNF573
               theta_stop: 0.094 
                    nperm: 30000 
                     p_ks: 0.054 
        ci_ks_bounds_left: 0.052 
       ci_ks_bounds_right: 0.057 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.14 

Current progress: 20 percent done.
ZNF607
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.382151e-02	ci left: 5.634356e-01	ci right 5.829217e-01	k: 5732	n:10000
Cons ci ratio: 6.353627e-02	ci left: 2.668589e-01	ci right 2.844719e-01	k: 2756	n:10000
KS ci ratio: 4.347016e-02	ci left: 4.386187e-01	ci right 4.582113e-01	k: 4484	n:10000
ZNF607   10000 perm   2 sec   (5875 perm/sec)   p_kst 4.484000e-01   p_cons 2.756000e-01   p_joint 5.732000e-01

Outputting figure to mutsig2_images.part000000000198/ZNF607.3_2107_10000_0.4484_0.2756_0.5732.png
                gene_name: ZNF607
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 40 percent done.
ZNF569
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.729154e-02	ci left: 6.642096e-01	ci right 6.826893e-01	k: 6735	n:10000
Cons ci ratio: 2.870566e-02	ci left: 6.414642e-01	ci right 6.602478e-01	k: 6509	n:10000
KS ci ratio: 4.914966e-02	ci left: 3.791296e-01	ci right 3.983352e-01	k: 3887	n:10000
ZNF569   10000 perm   2 sec   (6281 perm/sec)   p_kst 3.887000e-01   p_cons 6.509000e-01   p_joint 6.735000e-01

Outputting figure to mutsig2_images.part000000000198/ZNF569.2_2077_10000_0.3887_0.6509_0.6735.png
                gene_name: ZNF569
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    ci_joint_bounds_right: 0.68 

Current progress: 60 percent done.
ZNF578
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.955631e-02	ci left: 4.855531e-01	ci right 5.052495e-01	k: 4954	n:10000
Cons ci ratio: 4.999771e-02	ci left: 3.710696e-01	ci right 3.902000e-01	k: 3806	n:10000
KS ci ratio: 3.534585e-02	ci left: 5.416885e-01	ci right 5.612815e-01	k: 5515	n:10000
ZNF578   10000 perm   2 sec   (6520 perm/sec)   p_kst 5.515000e-01   p_cons 3.806000e-01   p_joint 4.954000e-01

Outputting figure to mutsig2_images.part000000000198/ZNF578.2_1785_10000_0.5515_0.3806_0.4954.png
                gene_name: ZNF578
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 80 percent done.
ZNF594
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.713205e-02	ci left: 3.991423e-01	ci right 4.185108e-01	k: 4088	n:10000
Cons ci ratio: 4.454027e-02	ci left: 4.266495e-01	ci right 4.461876e-01	k: 4364	n:10000
KS ci ratio: 7.864387e-02	ci left: 1.911149e-01	ci right 2.068608e-01	k: 1989	n:10000
ZNF594   10000 perm   2 sec   (6017 perm/sec)   p_kst 1.989000e-01   p_cons 4.364000e-01   p_joint 4.088000e-01

Outputting figure to mutsig2_images.part000000000198/ZNF594.2_2428_10000_0.1989_0.4364_0.4088.png
                gene_name: ZNF594
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000198
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 198 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 4398579: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000199> was used as the working directory.
Started at Wed Oct 24 16:18:35 2012
Results reported at Wed Oct 24 16:24:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000199.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000199.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 199  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000199.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    363.57 sec.
    Max Memory :      1344 MB
    Max Swap   :      3977 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
199
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 199
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 199: processing genes 17764 - 17852
Calculating significance of each gene.
Using projection method.
17764	ZNF643	1
17765	ZNF644	1
17766	ZNF645	3.072564e-03
17767	ZNF646	6.307004e-01
17768	ZNF648	1
17769	ZNF649	1
17770	ZNF652	6.102149e-02
17771	ZNF653	1
17772	ZNF654	1
17773	ZNF655	1
17774	ZNF658	1
17775	ZNF660	1.265948e-01
17776	ZNF662	1
17777	ZNF664	1
17778	ZNF665	9.586175e-02
17779	ZNF667	1
17780	ZNF668	1.571860e-01
17781	ZNF669	1
17782	ZNF670	1
17783	ZNF671	1
17784	ZNF672	1
17785	ZNF673	5.480558e-02
17786	ZNF674	1
17787	ZNF675	1
17788	ZNF676	1.862559e-01
17789	ZNF677	1
17790	ZNF678	1
17791	ZNF680	1.131917e-01
17792	ZNF681	1.793439e-01
17793	ZNF682	1
17794	ZNF683	1
17795	ZNF684	1
17796	ZNF687	1.130115e-01
17797	ZNF688	1
17798	ZNF689	1
17799	ZNF69	1
17800	ZNF691	1
17801	ZNF692	1.323907e-01
17802	ZNF695	1
17803	ZNF696	1
17804	ZNF697	1
17805	ZNF699	1
17806	ZNF7	1
17807	ZNF70	1
17808	ZNF700	2.502458e-01
17809	ZNF701	1
17810	ZNF704	1
17811	ZNF705A	1
17812	ZNF706	1
17813	ZNF707	1
17814	ZNF708	1
17815	ZNF709	1
17816	ZNF71	1
17817	ZNF710	1
17818	ZNF711	1.923117e-01
17819	ZNF713	1
17820	ZNF714	1
17821	ZNF718	1
17822	ZNF721	1
17823	ZNF74	5.539121e-02
17824	ZNF740	1
17825	ZNF746	1
17826	ZNF747	1
17827	ZNF749	1
17828	ZNF750	5.534427e-02
17829	ZNF75A	1
17830	ZNF75D	7.118273e-02
17831	ZNF76	1
17832	ZNF761	1
17833	ZNF763	1
17834	ZNF764	1
17835	ZNF765	1
17836	ZNF766	1
17837	ZNF768	1.603491e-01
17838	ZNF77	1
17839	ZNF770	1
17840	ZNF772	1
17841	ZNF773	8.596016e-02
17842	ZNF774	1
17843	ZNF775	1
17844	ZNF776	1.017594e-02
17845	ZNF777	6.622324e-02
17846	ZNF778	1
17847	ZNF780A	2.298708e-01
17848	ZNF780B	1
17849	ZNF781	1
17850	ZNF782	1
17851	ZNF784	1
17852	ZNF785	1
Done

Running MutSig 2:
Scatter job 199: processing genes 17764 - 17852
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF750
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.158024e-01	ci left: 9.681653e-02	ci right 1.088160e-01	k: 1027	n:10000
Cons ci ratio: 8.682941e-02	ci left: 1.618987e-01	ci right 1.766945e-01	k: 1692	n:10000
KS ci ratio: 9.715309e-02	ci left: 1.331568e-01	ci right 1.468536e-01	k: 1399	n:10000
ZNF750   10000 perm   2 sec   (5888 perm/sec)   p_kst 1.399000e-01   p_cons 1.692000e-01   p_joint 1.027000e-01

Joint ci ratio: 8.474023e-02	ci left: 9.253972e-02	ci right 1.007780e-01	k: 1932	n:20000
Cons ci ratio: 6.182768e-02	ci left: 1.621508e-01	ci right 1.725461e-01	k: 3346	n:20000
KS ci ratio: 6.956788e-02	ci left: 1.322134e-01	ci right 1.417924e-01	k: 2739	n:20000
ZNF750   20000 perm   5 sec   (3682 perm/sec)   p_kst 1.369500e-01   p_cons 1.673000e-01   p_joint 9.660000e-02

Outputting figure to mutsig2_images.part000000000199/ZNF750.3_2180_20000_0.13695_0.1673_0.0966.png
                gene_name: ZNF750
               theta_stop: 0.085 
                    nperm: 20000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.097 
     ci_joint_bounds_left: 0.093 
    ci_joint_bounds_right: 0.10 

Current progress: 17 percent done.
ZNF645
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.145810e-01	ci left: 1.943009e-03	ci right 4.162249e-03	k: 29	n:10000
Cons ci ratio: 1.615502e-01	ci left: 5.109258e-02	ci right 6.016847e-02	k: 555	n:10000
KS ci ratio: 8.163954e-01	ci left: 1.379226e-03	ci right 3.328943e-03	k: 22	n:10000
ZNF645   10000 perm   1 sec   (7110 perm/sec)   p_kst 2.200000e-03   p_cons 5.550000e-02   p_joint 2.900000e-03

Joint ci ratio: 8.988600e-01	ci left: 5.334815e-04	ci right 1.422016e-03	k: 18	n:20000
Cons ci ratio: 1.095653e-01	ci left: 5.684523e-02	ci right 6.348336e-02	k: 1202	n:20000
KS ci ratio: 5.052976e-01	ci left: 2.246412e-03	ci right 3.803657e-03	k: 59	n:20000
ZNF645   20000 perm   3 sec   (6304 perm/sec)   p_kst 2.950000e-03   p_cons 6.010000e-02   p_joint 9.000000e-04

Joint ci ratio: 2.715128e-01	ci left: 5.963539e-03	ci right 7.867170e-03	k: 206	n:30000
Cons ci ratio: 8.942081e-02	ci left: 5.750183e-02	ci right 6.291706e-02	k: 1805	n:30000
KS ci ratio: 4.015396e-01	ci left: 2.532772e-03	ci right 3.833062e-03	k: 94	n:30000
ZNF645   30000 perm   5 sec   (5985 perm/sec)   p_kst 3.133333e-03   p_cons 6.016667e-02   p_joint 6.866667e-03

Joint ci ratio: 3.132347e-01	ci left: 3.289902e-03	ci right 4.533824e-03	k: 155	n:40000
Cons ci ratio: 7.761260e-02	ci left: 5.761854e-02	ci right 6.229559e-02	k: 2397	n:40000
KS ci ratio: 3.618692e-01	ci left: 2.396900e-03	ci right 3.477268e-03	k: 116	n:40000
ZNF645   40000 perm   7 sec   (5780 perm/sec)   p_kst 2.900000e-03   p_cons 5.992500e-02   p_joint 3.875000e-03

Joint ci ratio: 2.794479e-01	ci left: 3.372652e-03	ci right 4.486161e-03	k: 195	n:50000
Cons ci ratio: 6.933903e-02	ci left: 5.799299e-02	ci right 6.217827e-02	k: 3003	n:50000
KS ci ratio: 3.284884e-01	ci left: 2.374263e-03	ci right 3.324917e-03	k: 141	n:50000
ZNF645   50000 perm   9 sec   (5617 perm/sec)   p_kst 2.820000e-03   p_cons 6.006000e-02   p_joint 3.900000e-03

Joint ci ratio: 2.062681e-01	ci left: 5.366103e-03	ci right 6.615741e-03	k: 358	n:60000
Cons ci ratio: 6.306349e-02	ci left: 5.858889e-02	ci right 6.242043e-02	k: 3629	n:60000
KS ci ratio: 3.066182e-01	ci left: 2.300674e-03	ci right 3.148566e-03	k: 162	n:60000
ZNF645   60000 perm   11 sec   (5477 perm/sec)   p_kst 2.700000e-03   p_cons 6.048333e-02   p_joint 5.966667e-03

Joint ci ratio: 1.954378e-01	ci left: 5.155734e-03	ci right 6.285831e-03	k: 399	n:70000
Cons ci ratio: 5.824656e-02	ci left: 5.899859e-02	ci right 6.255222e-02	k: 4253	n:70000
KS ci ratio: 2.774842e-01	ci left: 2.448732e-03	ci right 3.250503e-03	k: 198	n:70000
ZNF645   70000 perm   13 sec   (5350 perm/sec)   p_kst 2.828571e-03   p_cons 6.075714e-02   p_joint 5.700000e-03

Joint ci ratio: 2.910397e-01	ci left: 1.933593e-03	ci right 2.603322e-03	k: 180	n:80000
Cons ci ratio: 5.432259e-02	ci left: 5.944997e-02	ci right 6.278194e-02	k: 4888	n:80000
KS ci ratio: 2.586683e-01	ci left: 2.492474e-03	ci right 3.244298e-03	k: 228	n:80000
ZNF645   80000 perm   15 sec   (5231 perm/sec)   p_kst 2.850000e-03   p_cons 6.110000e-02   p_joint 2.250000e-03

Joint ci ratio: 2.708356e-01	ci left: 2.007980e-03	ci right 2.646997e-03	k: 208	n:90000
Cons ci ratio: 5.098485e-02	ci left: 6.005978e-02	ci right 6.321299e-02	k: 5546	n:90000
KS ci ratio: 2.446500e-01	ci left: 2.496624e-03	ci right 3.202691e-03	k: 255	n:90000
ZNF645   90000 perm   18 sec   (5105 perm/sec)   p_kst 2.833333e-03   p_cons 6.162222e-02   p_joint 2.311111e-03

Joint ci ratio: 2.576177e-01	ci left: 2.012618e-03	ci right 2.616829e-03	k: 230	n:100000
Cons ci ratio: 4.839501e-02	ci left: 6.007803e-02	ci right 6.306747e-02	k: 6156	n:100000
KS ci ratio: 2.306542e-01	ci left: 2.547930e-03	ci right 3.221417e-03	k: 287	n:100000
ZNF645   100000 perm   20 sec   (4991 perm/sec)   p_kst 2.870000e-03   p_cons 6.156000e-02   p_joint 2.300000e-03

Joint ci ratio: 2.279240e-01	ci left: 2.376256e-03	ci right 2.995882e-03	k: 294	n:110000
Cons ci ratio: 4.600439e-02	ci left: 6.049197e-02	ci right 6.334936e-02	k: 6810	n:110000
KS ci ratio: 2.188147e-01	ci left: 2.590848e-03	ci right 3.235803e-03	k: 319	n:110000
ZNF645   110000 perm   23 sec   (4887 perm/sec)   p_kst 2.900000e-03   p_cons 6.190909e-02   p_joint 2.672727e-03

Joint ci ratio: 1.697360e-01	ci left: 4.049335e-03	ci right 4.808254e-03	k: 530	n:120000
Cons ci ratio: 4.409707e-02	ci left: 6.041931e-02	ci right 6.315192e-02	k: 7413	n:120000
KS ci ratio: 2.098283e-01	ci left: 2.595758e-03	ci right 3.211988e-03	k: 347	n:120000
ZNF645   120000 perm   25 sec   (4791 perm/sec)   p_kst 2.891667e-03   p_cons 6.177500e-02   p_joint 4.416667e-03

Joint ci ratio: 1.291338e-01	ci left: 6.583748e-03	ci right 7.499987e-03	k: 914	n:130000
Cons ci ratio: 4.232734e-02	ci left: 6.058078e-02	ci right 6.320804e-02	k: 8045	n:130000
KS ci ratio: 2.013289e-01	ci left: 2.614980e-03	ci right 3.207538e-03	k: 377	n:130000
ZNF645   130000 perm   28 sec   (4696 perm/sec)   p_kst 2.900000e-03   p_cons 6.188462e-02   p_joint 7.030769e-03

Joint ci ratio: 1.133430e-01	ci left: 7.991035e-03	ci right 8.958059e-03	k: 1185	n:140000
Cons ci ratio: 4.096159e-02	ci left: 6.014095e-02	ci right 6.266297e-02	k: 8595	n:140000
KS ci ratio: 1.912171e-01	ci left: 2.706682e-03	ci right 3.285635e-03	k: 418	n:140000
ZNF645   140000 perm   30 sec   (4606 perm/sec)   p_kst 2.985714e-03   p_cons 6.139286e-02   p_joint 8.464286e-03

Joint ci ratio: 8.632658e-02	ci left: 1.297427e-02	ci right 1.415131e-02	k: 2033	n:150000
Cons ci ratio: 3.949050e-02	ci left: 6.042146e-02	ci right 6.286218e-02	k: 9245	n:150000
KS ci ratio: 1.838987e-01	ci left: 2.742268e-03	ci right 3.303882e-03	k: 452	n:150000
ZNF645   150000 perm   33 sec   (4511 perm/sec)   p_kst 3.013333e-03   p_cons 6.163333e-02   p_joint 1.355333e-02

Joint ci ratio: 8.367534e-02	ci left: 1.296472e-02	ci right 1.410300e-02	k: 2164	n:160000
Cons ci ratio: 3.829116e-02	ci left: 6.029668e-02	ci right 6.265674e-02	k: 9835	n:160000
KS ci ratio: 1.779116e-01	ci left: 2.755856e-03	ci right 3.299900e-03	k: 483	n:160000
ZNF645   160000 perm   36 sec   (4421 perm/sec)   p_kst 3.018750e-03   p_cons 6.146875e-02   p_joint 1.352500e-02

Joint ci ratio: 8.079180e-02	ci left: 1.310667e-02	ci right 1.421589e-02	k: 2321	n:170000
Cons ci ratio: 3.720815e-02	ci left: 6.014676e-02	ci right 6.243294e-02	k: 10418	n:170000
KS ci ratio: 1.718055e-01	ci left: 2.790624e-03	ci right 3.320665e-03	k: 518	n:170000
ZNF645   170000 perm   39 sec   (4339 perm/sec)   p_kst 3.047059e-03   p_cons 6.128235e-02   p_joint 1.365294e-02

Joint ci ratio: 1.119867e-01	ci left: 6.382322e-03	ci right 7.144805e-03	k: 1216	n:180000
Cons ci ratio: 3.609345e-02	ci left: 6.038893e-02	ci right 6.261411e-02	k: 11069	n:180000
KS ci ratio: 1.662879e-01	ci left: 2.821812e-03	ci right 3.338842e-03	k: 553	n:180000
ZNF645   180000 perm   42 sec   (4260 perm/sec)   p_kst 3.072222e-03   p_cons 6.149444e-02   p_joint 6.755556e-03

Joint ci ratio: 7.652877e-02	ci left: 1.309949e-02	ci right 1.414700e-02	k: 2587	n:190000
Cons ci ratio: 3.508601e-02	ci left: 6.056475e-02	ci right 6.273286e-02	k: 11712	n:190000
KS ci ratio: 1.612698e-01	ci left: 2.849961e-03	ci right 3.354862e-03	k: 588	n:190000
ZNF645   190000 perm   45 sec   (4188 perm/sec)   p_kst 3.094737e-03   p_cons 6.164211e-02   p_joint 1.361579e-02

Joint ci ratio: 7.473314e-02	ci left: 1.306260e-02	ci right 1.408158e-02	k: 2713	n:200000
Cons ci ratio: 3.422792e-02	ci left: 6.049064e-02	ci right 6.260209e-02	k: 12308	n:200000
KS ci ratio: 1.566802e-01	ci left: 2.875504e-03	ci right 3.369071e-03	k: 623	n:200000
ZNF645   200000 perm   49 sec   (4117 perm/sec)   p_kst 3.115000e-03   p_cons 6.154000e-02   p_joint 1.356500e-02

Joint ci ratio: 7.499594e-02	ci left: 1.236096e-02	ci right 1.332874e-02	k: 2696	n:210000
Cons ci ratio: 3.341191e-02	ci left: 6.048560e-02	ci right 6.254557e-02	k: 12917	n:210000
KS ci ratio: 1.517698e-01	ci left: 2.926286e-03	ci right 3.411398e-03	k: 664	n:210000
ZNF645   210000 perm   52 sec   (4048 perm/sec)   p_kst 3.161905e-03   p_cons 6.150952e-02   p_joint 1.283810e-02

Joint ci ratio: 9.256228e-02	ci left: 7.711902e-03	ci right 8.464781e-03	k: 1778	n:220000
Cons ci ratio: 3.269672e-02	ci left: 6.032369e-02	ci right 6.233334e-02	k: 13491	n:220000
KS ci ratio: 1.484587e-01	ci left: 2.924515e-03	ci right 3.397816e-03	k: 694	n:220000
ZNF645   220000 perm   55 sec   (3984 perm/sec)   p_kst 3.154545e-03   p_cons 6.132273e-02   p_joint 8.081818e-03

Joint ci ratio: 6.958852e-02	ci left: 1.313489e-02	ci right 1.408612e-02	k: 3129	n:230000
Cons ci ratio: 3.196749e-02	ci left: 6.038343e-02	ci right 6.234938e-02	k: 14113	n:230000
KS ci ratio: 1.441632e-01	ci left: 2.973292e-03	ci right 3.439367e-03	k: 736	n:230000
ZNF645   230000 perm   59 sec   (3921 perm/sec)   p_kst 3.200000e-03   p_cons 6.136087e-02   p_joint 1.360435e-02

Joint ci ratio: 7.007502e-02	ci left: 1.241959e-02	ci right 1.332556e-02	k: 3088	n:240000
Cons ci ratio: 3.126125e-02	ci left: 6.052551e-02	ci right 6.245177e-02	k: 14756	n:240000
KS ci ratio: 1.416875e-01	ci left: 2.953862e-03	ci right 3.408268e-03	k: 762	n:240000
ZNF645   240000 perm   62 sec   (3860 perm/sec)   p_kst 3.175000e-03   p_cons 6.148333e-02   p_joint 1.286667e-02

Joint ci ratio: 8.077778e-02	ci left: 8.954874e-03	ci right 9.712567e-03	k: 2332	n:250000
Cons ci ratio: 3.063376e-02	ci left: 6.052957e-02	ci right 6.241661e-02	k: 15367	n:250000
KS ci ratio: 1.386317e-01	ci left: 2.966940e-03	ci right 3.412701e-03	k: 796	n:250000
ZNF645   250000 perm   66 sec   (3801 perm/sec)   p_kst 3.184000e-03   p_cons 6.146800e-02   p_joint 9.328000e-03

Joint ci ratio: 6.736076e-02	ci left: 1.242438e-02	ci right 1.329422e-02	k: 3342	n:260000
Cons ci ratio: 3.004360e-02	ci left: 6.052986e-02	ci right 6.237993e-02	k: 15977	n:260000
KS ci ratio: 1.364259e-01	ci left: 2.949384e-03	ci right 3.384884e-03	k: 822	n:260000
ZNF645   260000 perm   69 sec   (3745 perm/sec)   p_kst 3.161538e-03   p_cons 6.145000e-02   p_joint 1.285385e-02

Joint ci ratio: 7.776960e-02	ci left: 8.959526e-03	ci right 9.688102e-03	k: 2516	n:270000
Cons ci ratio: 2.948534e-02	ci left: 6.053414e-02	ci right 6.234937e-02	k: 16588	n:270000
KS ci ratio: 1.342428e-01	ci left: 2.936761e-03	ci right 3.362904e-03	k: 849	n:270000
ZNF645   270000 perm   73 sec   (3692 perm/sec)   p_kst 3.144444e-03   p_cons 6.143704e-02   p_joint 9.318519e-03

Joint ci ratio: 7.626835e-02	ci left: 8.989812e-03	ci right 9.706113e-03	k: 2616	n:280000
Cons ci ratio: 2.894364e-02	ci left: 6.059161e-02	ci right 6.237462e-02	k: 17214	n:280000
KS ci ratio: 1.317850e-01	ci left: 2.942360e-03	ci right 3.360886e-03	k: 881	n:280000
ZNF645   280000 perm   77 sec   (3637 perm/sec)   p_kst 3.146429e-03   p_cons 6.147857e-02   p_joint 9.342857e-03

Joint ci ratio: 7.467069e-02	ci left: 9.062132e-03	ci right 9.768413e-03	k: 2729	n:290000
Cons ci ratio: 2.844603e-02	ci left: 6.058374e-02	ci right 6.233538e-02	k: 17822	n:290000
KS ci ratio: 1.300295e-01	ci left: 2.920945e-03	ci right 3.330463e-03	k: 905	n:290000
ZNF645   290000 perm   81 sec   (3584 perm/sec)   p_kst 3.120690e-03   p_cons 6.145517e-02   p_joint 9.410345e-03

Joint ci ratio: 7.751171e-02	ci left: 8.125542e-03	ci right 8.784007e-03	k: 2535	n:300000
Cons ci ratio: 2.797243e-02	ci left: 6.057996e-02	ci right 6.230185e-02	k: 18431	n:300000
KS ci ratio: 1.283423e-01	ci left: 2.900993e-03	ci right 3.302034e-03	k: 929	n:300000
ZNF645   300000 perm   85 sec   (3535 perm/sec)   p_kst 3.096667e-03   p_cons 6.143667e-02   p_joint 8.450000e-03

Joint ci ratio: 7.463844e-02	ci left: 8.490048e-03	ci right 9.151442e-03	k: 2733	n:310000
Cons ci ratio: 2.754331e-02	ci left: 6.048691e-02	ci right 6.217937e-02	k: 19012	n:310000
KS ci ratio: 1.267190e-01	ci left: 2.882360e-03	ci right 3.275407e-03	k: 953	n:310000
ZNF645   310000 perm   89 sec   (3481 perm/sec)   p_kst 3.074194e-03   p_cons 6.132903e-02   p_joint 8.816129e-03

Joint ci ratio: 7.347864e-02	ci left: 8.491574e-03	ci right 9.142368e-03	k: 2820	n:320000
Cons ci ratio: 2.711345e-02	ci left: 6.048371e-02	ci right 6.214925e-02	k: 19620	n:320000
KS ci ratio: 1.248999e-01	ci left: 2.877032e-03	ci right 3.263304e-03	k: 981	n:320000
ZNF645   320000 perm   93 sec   (3436 perm/sec)   p_kst 3.065625e-03   p_cons 6.131250e-02   p_joint 8.812500e-03

Joint ci ratio: 8.486292e-02	ci left: 6.151517e-03	ci right 6.699629e-03	k: 2119	n:330000
Cons ci ratio: 2.670943e-02	ci left: 6.045379e-02	ci right 6.209332e-02	k: 20219	n:330000
KS ci ratio: 1.228524e-01	ci left: 2.886751e-03	ci right 3.267512e-03	k: 1014	n:330000
ZNF645   330000 perm   97 sec   (3391 perm/sec)   p_kst 3.072727e-03   p_cons 6.126970e-02   p_joint 6.421212e-03

Joint ci ratio: 7.087217e-02	ci left: 8.601477e-03	ci right 9.236347e-03	k: 3031	n:340000
Cons ci ratio: 2.634655e-02	ci left: 6.032350e-02	ci right 6.193693e-02	k: 20783	n:340000
KS ci ratio: 1.208444e-01	ci left: 2.898800e-03	ci right 3.274454e-03	k: 1048	n:340000
ZNF645   340000 perm   102 sec   (3349 perm/sec)   p_kst 3.082353e-03   p_cons 6.112647e-02   p_joint 8.914706e-03

Joint ci ratio: 5.864257e-02	ci left: 1.223590e-02	ci right 1.297792e-02	k: 4411	n:350000
Cons ci ratio: 2.596570e-02	ci left: 6.034279e-02	ci right 6.193306e-02	k: 21397	n:350000
KS ci ratio: 1.192082e-01	ci left: 2.896346e-03	ci right 3.266242e-03	k: 1077	n:350000
ZNF645   350000 perm   106 sec   (3306 perm/sec)   p_kst 3.077143e-03   p_cons 6.113429e-02   p_joint 1.260286e-02

Joint ci ratio: 5.198826e-02	ci left: 1.514286e-02	ci right 1.595385e-02	k: 5596	n:360000
Cons ci ratio: 2.560833e-02	ci left: 6.032803e-02	ci right 6.189571e-02	k: 21999	n:360000
KS ci ratio: 1.178505e-01	ci left: 2.883277e-03	ci right 3.247017e-03	k: 1102	n:360000
ZNF645   360000 perm   110 sec   (3260 perm/sec)   p_kst 3.061111e-03   p_cons 6.110833e-02   p_joint 1.554444e-02

Joint ci ratio: 5.498883e-02	ci left: 1.317594e-02	ci right 1.392360e-02	k: 5012	n:370000
Cons ci ratio: 2.523739e-02	ci left: 6.044049e-02	ci right 6.198801e-02	k: 22648	n:370000
KS ci ratio: 1.155154e-01	ci left: 2.923426e-03	ci right 3.284426e-03	k: 1147	n:370000
ZNF645   370000 perm   115 sec   (3215 perm/sec)   p_kst 3.100000e-03   p_cons 6.121081e-02   p_joint 1.354595e-02

Joint ci ratio: 5.060577e-02	ci left: 1.515120e-02	ci right 1.594042e-02	k: 5906	n:380000
Cons ci ratio: 2.491402e-02	ci left: 6.040068e-02	ci right 6.192708e-02	k: 23241	n:380000
KS ci ratio: 1.142298e-01	ci left: 2.912948e-03	ci right 3.268381e-03	k: 1173	n:380000
ZNF645   380000 perm   120 sec   (3160 perm/sec)   p_kst 3.086842e-03   p_cons 6.116053e-02   p_joint 1.554211e-02

Joint ci ratio: 4.994627e-02	ci left: 1.516021e-02	ci right 1.593932e-02	k: 6063	n:390000
Cons ci ratio: 2.461433e-02	ci left: 6.030949e-02	ci right 6.181499e-02	k: 23813	n:390000
KS ci ratio: 1.128449e-01	ci left: 2.910504e-03	ci right 3.261046e-03	k: 1202	n:390000
ZNF645   390000 perm   125 sec   (3123 perm/sec)   p_kst 3.082051e-03   p_cons 6.105897e-02   p_joint 1.554615e-02

Joint ci ratio: 4.931592e-02	ci left: 1.516637e-02	ci right 1.593567e-02	k: 6219	n:400000
Cons ci ratio: 2.431351e-02	ci left: 6.027765e-02	ci right 6.176371e-02	k: 24407	n:400000
KS ci ratio: 1.114184e-01	ci left: 2.913068e-03	ci right 3.259193e-03	k: 1233	n:400000
ZNF645   400000 perm   130 sec   (3083 perm/sec)   p_kst 3.082500e-03   p_cons 6.101750e-02   p_joint 1.554750e-02

Joint ci ratio: 4.827235e-02	ci left: 1.544701e-02	ci right 1.621351e-02	k: 6489	n:410000
Cons ci ratio: 2.402244e-02	ci left: 6.025233e-02	ci right 6.171974e-02	k: 25003	n:410000
KS ci ratio: 1.097406e-01	ci left: 2.932138e-03	ci right 3.274944e-03	k: 1271	n:410000
ZNF645   410000 perm   135 sec   (3040 perm/sec)   p_kst 3.100000e-03   p_cons 6.098293e-02   p_joint 1.582683e-02

Joint ci ratio: 4.767343e-02	ci left: 1.546502e-02	ci right 1.622263e-02	k: 6653	n:420000
Cons ci ratio: 2.374058e-02	ci left: 6.023305e-02	ci right 6.168254e-02	k: 25601	n:420000
KS ci ratio: 1.088049e-01	ci left: 2.913273e-03	ci right 3.250783e-03	k: 1293	n:420000
ZNF645   420000 perm   140 sec   (3005 perm/sec)   p_kst 3.078571e-03   p_cons 6.095476e-02   p_joint 1.584048e-02

Joint ci ratio: 4.711031e-02	ci left: 1.547305e-02	ci right 1.622186e-02	k: 6813	n:430000
Cons ci ratio: 2.347319e-02	ci left: 6.019163e-02	ci right 6.162359e-02	k: 26189	n:430000
KS ci ratio: 1.079750e-01	ci left: 2.890772e-03	ci right 3.222957e-03	k: 1313	n:430000
ZNF645   430000 perm   145 sec   (2970 perm/sec)   p_kst 3.053488e-03   p_cons 6.090465e-02   p_joint 1.584419e-02

Joint ci ratio: 4.702788e-02	ci left: 1.517974e-02	ci right 1.591303e-02	k: 6839	n:440000
Cons ci ratio: 2.319758e-02	ci left: 6.023582e-02	ci right 6.165178e-02	k: 26814	n:440000
KS ci ratio: 1.066836e-01	ci left: 2.895848e-03	ci right 3.224387e-03	k: 1345	n:440000
ZNF645   440000 perm   150 sec   (2937 perm/sec)   p_kst 3.056818e-03   p_cons 6.094091e-02   p_joint 1.554318e-02

Joint ci ratio: 4.467989e-02	ci left: 1.644188e-02	ci right 1.719547e-02	k: 7567	n:450000
Cons ci ratio: 2.293768e-02	ci left: 6.024720e-02	ci right 6.164735e-02	k: 27425	n:450000
KS ci ratio: 1.055913e-01	ci left: 2.892066e-03	ci right 3.216608e-03	k: 1373	n:450000
ZNF645   450000 perm   155 sec   (2905 perm/sec)   p_kst 3.051111e-03   p_cons 6.094444e-02   p_joint 1.681556e-02

Joint ci ratio: 4.604295e-02	ci left: 1.515573e-02	ci right 1.587213e-02	k: 7135	n:460000
Cons ci ratio: 2.268547e-02	ci left: 6.026249e-02	ci right 6.164740e-02	k: 28038	n:460000
KS ci ratio: 1.046442e-01	ci left: 2.882113e-03	ci right 3.202458e-03	k: 1398	n:460000
ZNF645   460000 perm   160 sec   (2874 perm/sec)   p_kst 3.039130e-03   p_cons 6.095217e-02   p_joint 1.551087e-02

Joint ci ratio: 4.328471e-02	ci left: 1.677969e-02	ci right 1.752415e-02	k: 8060	n:470000
Cons ci ratio: 2.244223e-02	ci left: 6.027298e-02	ci right 6.164308e-02	k: 28649	n:470000
KS ci ratio: 1.033227e-01	ci left: 2.895396e-03	ci right 3.212907e-03	k: 1434	n:470000
ZNF645   470000 perm   165 sec   (2843 perm/sec)   p_kst 3.051064e-03   p_cons 6.095532e-02   p_joint 1.714894e-02

Joint ci ratio: 4.035020e-02	ci left: 1.889410e-02	ci right 1.967422e-02	k: 9255	n:480000
Cons ci ratio: 2.221919e-02	ci left: 6.021885e-02	ci right 6.157395e-02	k: 29229	n:480000
KS ci ratio: 1.021545e-01	ci left: 2.902059e-03	ci right 3.216487e-03	k: 1467	n:480000
ZNF645   480000 perm   173 sec   (2782 perm/sec)   p_kst 3.056250e-03   p_cons 6.089375e-02   p_joint 1.928125e-02

Joint ci ratio: 3.976468e-02	ci left: 1.906010e-02	ci right 1.983540e-02	k: 9528	n:490000
Cons ci ratio: 2.199284e-02	ci left: 6.021777e-02	ci right 6.155886e-02	k: 29834	n:490000
KS ci ratio: 1.012622e-01	ci left: 2.894544e-03	ci right 3.205255e-03	k: 1493	n:490000
ZNF645   490000 perm   180 sec   (2725 perm/sec)   p_kst 3.046939e-03   p_cons 6.088571e-02   p_joint 1.944490e-02

Joint ci ratio: 3.969197e-02	ci left: 1.875408e-02	ci right 1.951551e-02	k: 9566	n:500000
Cons ci ratio: 2.176491e-02	ci left: 6.026056e-02	ci right 6.158853e-02	k: 30461	n:500000
KS ci ratio: 1.003597e-01	ci left: 2.889291e-03	ci right 3.196512e-03	k: 1520	n:500000
ZNF645   500000 perm   185 sec   (2696 perm/sec)   p_kst 3.040000e-03   p_cons 6.092200e-02   p_joint 1.913200e-02

Joint ci ratio: 3.927084e-02	ci left: 1.878629e-02	ci right 1.954075e-02	k: 9772	n:510000
Cons ci ratio: 2.155758e-02	ci left: 6.022957e-02	ci right 6.154405e-02	k: 31051	n:510000
KS ci ratio: 9.973982e-02	ci left: 2.868960e-03	ci right 3.172024e-03	k: 1539	n:510000
ZNF645   510000 perm   191 sec   (2668 perm/sec)   p_kst 3.017647e-03   p_cons 6.088431e-02   p_joint 1.916078e-02

Outputting figure to mutsig2_images.part000000000199/ZNF645.2_1282_510000_0.0030176_0.060884_0.019161.png
                gene_name: ZNF645
               theta_stop: 0.100 
                    nperm: 510000 
                     p_ks: 0.0030 
        ci_ks_bounds_left: 0.0029 
       ci_ks_bounds_right: 0.0032 
                   p_cons: 0.061 
      ci_cons_bounds_left: 0.060 
     ci_cons_bounds_right: 0.062 
                  p_joint: 0.019 
     ci_joint_bounds_left: 0.019 
    ci_joint_bounds_right: 0.020 

Current progress: 33 percent done.
ZNF646
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.499402e-02	ci left: 1.385451e-01	ci right 1.524621e-01	k: 1454	n:10000
Cons ci ratio: 5.176048e-02	ci left: 3.549581e-01	ci right 3.739210e-01	k: 3644	n:10000
KS ci ratio: 2.217497e-01	ci left: 2.693317e-02	ci right 3.374407e-02	k: 302	n:10000
ZNF646   10000 perm   2 sec   (4773 perm/sec)   p_kst 3.020000e-02   p_cons 3.644000e-01   p_joint 1.454000e-01

Joint ci ratio: 6.669000e-02	ci left: 1.423655e-01	ci right 1.522373e-01	k: 2945	n:20000
Cons ci ratio: 3.779490e-02	ci left: 3.430882e-01	ci right 3.563555e-01	k: 6994	n:20000
KS ci ratio: 1.569380e-01	ci left: 2.787170e-02	ci right 3.266616e-02	k: 604	n:20000
ZNF646   20000 perm   5 sec   (4318 perm/sec)   p_kst 3.020000e-02   p_cons 3.497000e-01   p_joint 1.472500e-01

Joint ci ratio: 4.249491e-02	ci left: 2.162492e-01	ci right 2.256716e-01	k: 6628	n:30000
Cons ci ratio: 3.074552e-02	ci left: 3.459957e-01	ci right 3.568331e-01	k: 10542	n:30000
KS ci ratio: 1.268135e-01	ci left: 2.890608e-02	ci right 3.285213e-02	k: 925	n:30000
ZNF646   30000 perm   9 sec   (3369 perm/sec)   p_kst 3.083333e-02   p_cons 3.514000e-01   p_joint 2.209333e-01

Joint ci ratio: 3.018539e-02	ci left: 2.920765e-01	ci right 3.010531e-01	k: 11862	n:40000
Cons ci ratio: 2.662980e-02	ci left: 3.466701e-01	ci right 3.560515e-01	k: 14054	n:40000
KS ci ratio: 1.094436e-01	ci left: 2.937180e-02	ci right 3.279672e-02	k: 1242	n:40000
ZNF646   40000 perm   12 sec   (3308 perm/sec)   p_kst 3.105000e-02   p_cons 3.513500e-01   p_joint 2.965500e-01

Joint ci ratio: 2.729106e-02	ci left: 2.880964e-01	ci right 2.960877e-01	k: 14604	n:50000
Cons ci ratio: 2.384116e-02	ci left: 3.467355e-01	ci right 3.551218e-01	k: 17546	n:50000
KS ci ratio: 9.657435e-02	ci left: 3.035735e-02	ci right 3.345731e-02	k: 1594	n:50000
ZNF646   50000 perm   15 sec   (3274 perm/sec)   p_kst 3.188000e-02   p_cons 3.509200e-01   p_joint 2.920800e-01

Outputting figure to mutsig2_images.part000000000199/ZNF646.2_5507_50000_0.03188_0.35092_0.29208.png
                gene_name: ZNF646
               theta_stop: 0.097 
                    nperm: 50000 
                     p_ks: 0.032 
        ci_ks_bounds_left: 0.030 
       ci_ks_bounds_right: 0.033 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.30 

Current progress: 50 percent done.
ZNF687
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.621882e-02	ci left: 5.295704e-01	ci right 5.492067e-01	k: 5394	n:10000
Cons ci ratio: 7.268807e-02	ci left: 2.170439e-01	ci right 2.335164e-01	k: 2252	n:10000
KS ci ratio: 1.820536e-02	ci left: 8.149692e-01	ci right 8.300424e-01	k: 8226	n:10000
ZNF687   10000 perm   2 sec   (5556 perm/sec)   p_kst 8.226000e-01   p_cons 2.252000e-01   p_joint 5.394000e-01

Outputting figure to mutsig2_images.part000000000199/ZNF687.2_3746_10000_0.8226_0.2252_0.5394.png
                gene_name: ZNF687
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 67 percent done.
ZNF776
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.192588e-01	ci left: 9.165653e-02	ci right 1.033791e-01	k: 974	n:10000
Cons ci ratio: 1.246431e-01	ci left: 8.436377e-02	ci right 9.567638e-02	k: 899	n:10000
KS ci ratio: 4.638942e-02	ci left: 4.068133e-01	ci right 4.262354e-01	k: 4165	n:10000
ZNF776   10000 perm   2 sec   (6525 perm/sec)   p_kst 4.165000e-01   p_cons 8.990000e-02   p_joint 9.740000e-02

Joint ci ratio: 1.009147e-01	ci left: 6.659926e-02	ci right 7.372632e-02	k: 1402	n:20000
Cons ci ratio: 8.778979e-02	ci left: 8.665663e-02	ci right 9.466284e-02	k: 1812	n:20000
KS ci ratio: 3.306991e-02	ci left: 4.057653e-01	ci right 4.194601e-01	k: 8252	n:20000
ZNF776   20000 perm   3 sec   (5769 perm/sec)   p_kst 4.126000e-01   p_cons 9.060000e-02   p_joint 7.010000e-02

Joint ci ratio: 6.430954e-02	ci left: 1.066449e-01	ci right 1.137641e-01	k: 3305	n:30000
Cons ci ratio: 6.569112e-02	ci left: 1.026039e-01	ci right 1.096060e-01	k: 3182	n:30000
KS ci ratio: 2.695224e-02	ci left: 4.079193e-01	ci right 4.190974e-01	k: 12405	n:30000
ZNF776   30000 perm   6 sec   (5429 perm/sec)   p_kst 4.135000e-01   p_cons 1.060667e-01   p_joint 1.101667e-01

Outputting figure to mutsig2_images.part000000000199/ZNF776.2_1569_30000_0.4135_0.10607_0.11017.png
                gene_name: ZNF776
               theta_stop: 0.066 
                    nperm: 30000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.11 

Current progress: 83 percent done.
ZNF777
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.023176e-02	ci left: 3.688810e-01	ci right 3.879899e-01	k: 3784	n:10000
Cons ci ratio: 2.732877e-02	ci left: 6.636054e-01	ci right 6.820938e-01	k: 6729	n:10000
KS ci ratio: 6.981304e-02	ci left: 2.312609e-01	ci right 2.480910e-01	k: 2396	n:10000
ZNF777   10000 perm   2 sec   (6116 perm/sec)   p_kst 2.396000e-01   p_cons 6.729000e-01   p_joint 3.784000e-01

Outputting figure to mutsig2_images.part000000000199/ZNF777.2_2516_10000_0.2396_0.6729_0.3784.png
                gene_name: ZNF777
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000199
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 199 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 4398582: <scatter_215935> Done

Job <scatter_215935> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000200> was used as the working directory.
Started at Wed Oct 24 16:18:35 2012
Results reported at Wed Oct 24 16:27:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000200.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000200.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 200  -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000200.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    588.62 sec.
    Max Memory :      1543 MB
    Max Swap   :      3990 MB

    Max Processes  :         7
    Max Threads    :        58

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
-whichjob
200
-i
CESC
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/db/ucsc/hg19/R.mat
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
-jobcount
200

              perform_mutsig2_analysis: 1
    use_sample_specific_mutation_rates: 1
       analyze_silent_nonsilent_ratios: 1
                sig_calculation_method: 'projection'
                          print_report: 0
                               patlist: [1x117 char]
                               covfile: [1x133 char]
                               mutfile: [1x108 char]
                               catfile: [1x134 char]
                              genelist: [1x73 char]
                                 build: 'hg19'
                            contextdir: []
               geneset_collection_file: [1x72 char]
                          build_cosmic: 'hg19'
                           cosmic_file: [1x70 char]
                          build_refseq: [1x41 char]
                             build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
                   build_genome_region: '/xchip/cga1/annotation/db/ucsc/hg19'
                                 quick: 0
              output_per_exon_coverage: 1
             output_per_exon_mutations: 0
            output_final_mutation_list: 1
              output_per_gene_coverage: 1
       output_per_gene_mutation_counts: 1
          output_sample_sig_gene_table: 1
    mutation_preprocessing_report_file: [1x138 char]
        mutation_filtering_report_file: './CESC.mutation_filtering_report.txt'
                  using_scatter_gather: 1
               scatter_gather_jobcount: 200
               scatter_gather_whichjob: 200
                            is_scatter: 1
                             is_gather: 0

LOADING MUTATION DATA FOR SET "CESC"
Loading coverage... 

The following 920 genes have very low coverage and are being omitted:
    'A2LD1'            [         0]
    'ACTR3C'           [         0]
    'ADRB3'            [    0.2258]
    'AG2'              [         0]
    'AGAP5'            [         0]
    'AGAP6'            [         0]
    'AGBL3'            [         0]
    'AGBL4'            [    0.2349]
    'ALG1L2'           [         0]
    'AMELY'            [         0]
    'AMH'              [    0.1726]
    'AMY1A'            [    0.1078]
    'AMY1B'            [    0.1078]
    'AMY1C'            [    0.1078]
    'ANKRD18A'         [         0]
    'ANKRD20A2'        [    0.0708]
    'ANKRD20A3'        [    0.1850]
    'ANKRD30B'         [         0]
    'ANKRD31'          [         0]
    'ANKRD33B'         [         0]
    'ANKRD34C'         [         0]
    'ANKRD36'          [    0.0638]
    'ANKRD36B'         [    0.2220]
    'ANKRD43'          [    0.1750]
    'ANKRD9'           [    0.0934]
    'ANXA8'            [    0.0189]
    'ANXA8L1'          [    0.0189]
    'ANXA8L2'          [    0.1585]
    'APLN'             [    0.1336]
    'ARHGAP23'         [         0]
    'ARHGAP40'         [         0]
    'ARHGAP42'         [         0]
    'ARHGEF33'         [         0]
    'ARL17A'           [    0.0023]
    'ARL17B'           [    0.0047]
    'ARL5C'            [         0]
    'ARX'              [    0.2317]
    'ASAH2B'           [    0.2128]
    'ASCL2'            [         0]
    'ATAD3C'           [    0.1139]
    'ATP5D'            [    0.1878]
    'ATP5L2'           [         0]
    'ATXN1L'           [         0]
    'ATXN7L1'          [    0.1697]
    'ATXN7L3B'         [         0]
    'B3GALT6'          [    0.1342]
    'BBC3'             [    0.1755]
    'BCORL2'           [         0]
    'BEAN'             [         0]
    'BET3L'            [         0]
    'BHLHA15'          [    0.0380]
    'BHLHA9'           [         0]
    'BHLHE22'          [    0.2157]
    'BOLA2'            [         0]
    'BOLA2B'           [         0]
    'BOP1'             [    0.0968]
    'BPY2'             [         0]
    'BPY2B'            [         0]
    'BPY2C'            [         0]
    'BSPH1'            [         0]
    'BTBD18'           [         0]
    'BTBD19'           [         0]
    'C10orf105'        [         0]
    'C10orf122'        [         0]
    'C10orf131'        [         0]
    'C10orf55'         [    0.2413]
    'C11orf20'         [    0.1766]
    'C11orf21'         [         0]
    'C11orf34'         [         0]
    'C11orf86'         [         0]
    'C11orf90'         [         0]
    'C11orf91'         [         0]
    'C11orf93'         [         0]
    'C11orf95'         [         0]
    'C12orf70'         [         0]
    'C12orf73'         [         0]
    'C12orf75'         [         0]
    'C13orf38'         [         0]
    'C14orf176'        [         0]
    'C14orf180'        [    0.2431]
    'C14orf184'        [    0.2396]
    'C14orf38'         [         0]
    'C14orf80'         [    0.1857]
    'C15orf56'         [    0.2208]
    'C15orf61'         [         0]
    'C15orf62'         [         0]
    'C16orf52'         [         0]
    'C16orf74'         [    0.1369]
    'C17orf100'        [    0.2243]
    'C17orf105'        [         0]
    'C17orf106'        [         0]
    'C17orf107'        [         0]
    'C17orf50'         [    0.2299]
    'C17orf51'         [         0]
    'C17orf55'         [    0.2029]
    'C17orf72'         [         0]
    'C17orf89'         [    0.1376]
    'C17orf96'         [         0]
    'C17orf97'         [3.7092e-04]
    'C17orf99'         [         0]
    'C18orf56'         [    0.1032]
    'C19orf20'         [    0.0514]
    'C19orf24'         [         0]
    'C19orf25'         [    0.1520]
    'C19orf38'         [         0]
    'C19orf60'         [    0.2005]
    'C19orf69'         [         0]
    'C19orf71'         [         0]
    'C19orf76'         [    0.1647]
    'C19orf77'         [         0]
    'C1orf185'         [         0]
    'C1orf204'         [6.0496e-04]
    'C1orf212'         [         0]
    'C1orf223'         [         0]
    'C1orf228'         [         0]
    'C1orf229'         [1.6393e-04]
    'C1orf230'         [         0]
    'C1orf68'          [         0]
    'C1orf70'          [         0]
    'C20orf123'        [         0]
    'C20orf144'        [    0.2476]
    'C20orf173'        [         0]
    'C20orf201'        [    0.1360]
    'C20orf202'        [         0]
    'C20orf203'        [         0]
    'C22orf26'         [         0]
    'C22orf30'         [    0.1016]
    'C22orf41'         [         0]
    'C22orf46'         [         0]
    'C2CD4A'           [    0.2282]
    'C2CD4B'           [    0.0247]
    'C2CD4C'           [         0]
    'C2CD4D'           [         0]
    'C2orf27A'         [    0.0532]
    'C2orf27B'         [    0.0796]
    'C2orf72'          [         0]
    'C2orf74'          [         0]
    'C2orf81'          [         0]
    'C2orf82'          [7.6104e-04]
    'C3orf16'          [         0]
    'C3orf77'          [         0]
    'C3orf78'          [         0]
    'C4A'              [    0.1129]
    'C4B'              [    0.1129]
    'C4orf47'          [         0]
    'C4orf48'          [         0]
    'C4orf52'          [         0]
    'C5orf36'          [    0.2485]
    'C5orf47'          [         0]
    'C5orf52'          [         0]
    'C5orf60'          [         0]
    'C5orf62'          [    0.0291]
    'C6orf103'         [         0]
    'C6orf132'         [         0]
    'C6orf141'         [         0]
    'C6orf163'         [         0]
    'C6orf52'          [         0]
    'C6orf94'          [         0]
    'C7orf71'          [         0]
    'C7orf72'          [         0]
    'C8orf30A'         [    0.0426]
    'C8orf48'          [         0]
    'C8orf55'          [    0.0713]
    'C8orf83'          [         0]
    'C9orf140'         [    0.2022]
    'C9orf144B'        [         0]
    'C9orf167'         [    0.0971]
    'C9orf169'         [         0]
    'C9orf57'          [         0]
    'CALHM3'           [         0]
    'CAPN14'           [         0]
    'CAPN8'            [         0]
    'CBWD3'            [    0.1673]
    'CBWD5'            [    0.2272]
    'CBY3'             [         0]
    'CCDC152'          [         0]
    'CCDC154'          [         0]
    'CCDC42B'          [         0]
    'CCDC79'           [         0]
    'CCDC85B'          [    0.0795]
    'CCDC85C'          [         0]
    'CCL3L1'           [    0.1448]
    'CCL3L3'           [    0.1448]
    'CCL4L1'           [    0.2344]
    'CCL4L2'           [    0.2344]
    'CD24'             [         0]
    'CDC42EP5'         [    0.0091]
    'CDHR4'            [    0.1175]
    'CDKN1C'           [    0.0446]
    'CDR2L'            [    0.1710]
    'CDY1'             [         0]
    'CDY1B'            [         0]
    'CDY2A'            [         0]
    'CDY2B'            [         0]
    'CEBPA'            [    0.2318]
    'CEBPB'            [    0.2050]
    'CECR6'            [    0.2410]
    'CFC1'             [    0.1365]
    'CFC1B'            [    0.1365]
    'CFD'              [    0.2019]
    'CHADL'            [         0]
    'CHIC1'            [    0.2184]
    'CISD3'            [         0]
    'CITED4'           [    0.0045]
    'CLDN24'           [         0]
    'CLEC2A'           [         0]
    'COL6A5'           [    0.2159]
    'COMTD1'           [    0.2384]
    'CPSF4L'           [         0]
    'CSAG2'            [         0]
    'CSAG3'            [         0]
    'CT45A1'           [    0.1009]
    'CT45A2'           [    0.0030]
    'CT45A3'           [         0]
    'CT45A4'           [    0.0282]
    'CT45A6'           [         0]
    'CT47A1'           [    0.0059]
    'CT47A10'          [4.0427e-05]
    'CT47A11'          [4.0427e-05]
    'CT47A2'           [4.0427e-05]
    'CT47A3'           [4.0427e-05]
    'CT47A4'           [4.0427e-05]
    'CT47A5'           [4.0427e-05]
    'CT47A6'           [    0.0217]
    'CT47A7'           [         0]
    'CT47A8'           [4.0427e-05]
    'CT47A9'           [4.0427e-05]
    'CT47B1'           [         0]
    'CTAG1A'           [         0]
    'CTAG1B'           [         0]
    'CTAGE4'           [         0]
    'CTAGE9'           [         0]
    'CTF1'             [    0.2167]
    'CTRB1'            [    0.2201]
    'CTRB2'            [    0.1994]
    'CTU1'             [    0.0271]
    'CTXN2'            [         0]
    'CXorf30'          [         0]
    'CXorf49'          [         0]
    'CXorf49B'         [         0]
    'CXorf51'          [         0]
    'CXorf64'          [         0]
    'CYS1'             [    0.1624]
    'CYorf15A'         [         0]
    'CYorf15B'         [         0]
    'DACT2'            [         0]
    'DACT3'            [    0.1402]
    'DAZ1'             [         0]
    'DAZ2'             [         0]
    'DAZ3'             [         0]
    'DAZ4'             [         0]
    'DCAF8L2'          [         0]
    'DDT'              [    0.2144]
    'DDX3Y'            [         0]
    'DEFA1'            [    0.2142]
    'DEFA1B'           [    0.2142]
    'DEFB103A'         [         0]
    'DEFB103B'         [         0]
    'DEFB105A'         [    0.1051]
    'DEFB105B'         [    0.1051]
    'DEFB107A'         [    0.0761]
    'DEFB107B'         [    0.0761]
    'DEFB130'          [         0]
    'DEFB133'          [         0]
    'DKFZP781G0119'    [         0]
    'DLEU7'            [    0.1347]
    'DMRTA2'           [    0.2308]
    'DMRTC1'           [    0.1256]
    'DMRTC1B'          [    0.1256]
    'DNAH12'           [    0.1437]
    'DNAH14'           [    0.0494]
    'DNAH6'            [    0.0992]
    'DOC2B'            [         0]
    'DPCR1'            [    0.1725]
    'DPH3B'            [         0]
    'DTHD1'            [         0]
    'DUX4'             [         0]
    'EBF4'             [         0]
    'EFCAB9'           [         0]
    'EFR3B'            [         0]
    'EIF1AY'           [         0]
    'EIF3C'            [    0.0787]
    'EIF3CL'           [    0.0787]
    'ELFN1'            [         0]
    'EML6'             [         0]
    'ENDOG'            [    0.2089]
    'EVPLL'            [         0]
    'EXOSC6'           [    0.0357]
    'EYS'              [    0.1845]
    'F8A1'             [         0]
    'F8A2'             [    0.0678]
    'F8A3'             [         0]
    'FAM136B'          [         0]
    'FAM149B1'         [         0]
    'FAM156A'          [         0]
    'FAM156B'          [         0]
    'FAM157A'          [         0]
    'FAM157B'          [         0]
    'FAM159B'          [         0]
    'FAM160A1'         [         0]
    'FAM163B'          [    0.0428]
    'FAM170B'          [         0]
    'FAM171A2'         [         0]
    'FAM178B'          [    0.1717]
    'FAM180B'          [         0]
    'FAM181B'          [    0.1506]
    'FAM184B'          [         0]
    'FAM185A'          [         0]
    'FAM186A'          [         0]
    'FAM189A1'         [         0]
    'FAM194B'          [         0]
    'FAM196B'          [         0]
    'FAM198A'          [         0]
    'FAM200A'          [    0.1087]
    'FAM200B'          [         0]
    'FAM20C'           [    0.2177]
    'FAM23A'           [    0.0452]
    'FAM25A'           [         0]
    'FAM25B'           [         0]
    'FAM25C'           [         0]
    'FAM25G'           [         0]
    'FAM38A'           [         0]
    'FAM38B'           [    0.1996]
    'FAM47E'           [         0]
    'FAM55B'           [         0]
    'FAM59B'           [         0]
    'FAM69A'           [    0.2295]
    'FAM71E2'          [         0]
    'FAM72D'           [         0]
    'FAM75A1'          [    0.1787]
    'FAM75A2'          [    0.1787]
    'FAM75A5'          [    0.0500]
    'FAM75A6'          [         0]
    'FAM75A7'          [    0.0500]
    'FAM75C1'          [         0]
    'FAM86B2'          [         0]
    'FAM90A10'         [         0]
    'FAM90A13'         [         0]
    'FAM90A14'         [         0]
    'FAM90A18'         [         0]
    'FAM90A19'         [         0]
    'FAM90A20'         [         0]
    'FAM90A5'          [         0]
    'FAM90A7'          [         0]
    'FAM90A8'          [         0]
    'FAM90A9'          [         0]
    'FBRSL1'           [         0]
    'FBXL8'            [    0.2439]
    'FHAD1'            [         0]
    'FIGNL2'           [    0.1450]
    'FLJ25363'         [         0]
    'FLJ36031'         [    0.0555]
    'FLJ43859'         [         0]
    'FLJ44082'         [         0]
    'FLJ44606'         [         0]
    'FOXD1'            [    0.2398]
    'FOXD4L2'          [         0]
    'FOXD4L4'          [         0]
    'FOXD4L5'          [         0]
    'FOXD4L6'          [    0.0507]
    'FOXI2'            [    0.1778]
    'FOXI3'            [         0]
    'FRAT1'            [    0.1024]
    'FRAT2'            [    0.0583]
    'FREM3'            [         0]
    'FRG2'             [    0.0917]
    'FRG2C'            [         0]
    'FSCN2'            [    0.1815]
    'FSD1L'            [         0]
    'FSIP2'            [    0.2211]
    'FXYD2'            [    0.2202]
    'GAGE12B'          [    0.0127]
    'GAGE12C'          [    0.0369]
    'GAGE12D'          [    0.0360]
    'GAGE12E'          [    0.0360]
    'GAGE12F'          [    0.0424]
    'GAGE12G'          [    0.0076]
    'GAGE12H'          [    0.0539]
    'GAGE12I'          [    0.1211]
    'GAGE12J'          [    0.2325]
    'GAGE13'           [         0]
    'GAGE2A'           [    0.1706]
    'GAGE2D'           [    0.2475]
    'GAGE2E'           [    0.2077]
    'GAGE4'            [    0.1211]
    'GAGE5'            [    0.1211]
    'GAGE6'            [         0]
    'GAGE7'            [    0.1211]
    'GAGE8'            [    0.2078]
    'GAS1'             [    0.2255]
    'GATSL1'           [         0]
    'GATSL2'           [         0]
    'GCNT7'            [         0]
    'GDF1'             [    0.0074]
    'GFRA4'            [    0.1265]
    'GIYD1'            [    0.1773]
    'GIYD2'            [    0.1773]
    'GJD3'             [    0.0872]
    'GLTSCR1'          [    0.2059]
    'GLYATL3'          [         0]
    'GOLGA6C'          [         0]
    'GOLGA6D'          [         0]
    'GOLGA6L1'         [    0.0191]
    'GOLGA6L10'        [         0]
    'GOLGA6L6'         [         0]
    'GOLGA6L9'         [         0]
    'GOLGA8A'          [    0.1568]
    'GOLGA8B'          [    0.0893]
    'GP1BB'            [    0.0071]
    'GPR144'           [         0]
    'GPR150'           [    0.1228]
    'GPR44'            [    0.1721]
    'GPR88'            [    0.1994]
    'GPR89C'           [         0]
    'GRAP'             [    0.2162]
    'GRAPL'            [         0]
    'GREB1L'           [         0]
    'GRID2IP'          [         0]
    'GRRP1'            [    0.0304]
    'GSC2'             [    0.1069]
    'GSTT2'            [    0.1877]
    'GSTT2B'           [    0.1400]
    'GTF2H2'           [    0.2264]
    'H2AFB1'           [    0.2358]
    'H2AFB2'           [         0]
    'H2AFB3'           [    0.2358]
    'H2BFM'            [         0]
    'HBZ'              [    0.2250]
    'HCP5'             [         0]
    'HCRT'             [    0.1448]
    'HEATR7A'          [    0.2338]
    'HES2'             [    0.1911]
    'HES5'             [    0.1974]
    'HES7'             [    0.1535]
    'HGC6.3'           [         0]
    'HHLA1'            [         0]
    'HIST2H2AA3'       [         0]
    'HIST2H2AA4'       [         0]
    'HIST2H3A'         [         0]
    'HIST2H3C'         [         0]
    'HIST2H4A'         [         0]
    'HIST2H4B'         [         0]
    'HMGXB3'           [         0]
    'HRK'              [         0]
    'HRNBP3'           [         0]
    'HSBP1L1'          [         0]
    'HSD11B1L'         [    0.2279]
    'HSFX1'            [         0]
    'HSFX2'            [         0]
    'HSFY1'            [         0]
    'HSFY2'            [         0]
    'HSPB6'            [    0.0130]
    'ID4'              [    0.2006]
    'IFFO2'            [         0]
    'IGFN1'            [    0.2333]
    'IKBKG'            [    0.2113]
    'IL11'             [    0.2299]
    'INSM1'            [    0.2291]
    'IQCF5'            [         0]
    'IQCF6'            [         0]
    'IRGM'             [         0]
    'IRS2'             [    0.2137]
    'KBTBD11'          [    0.0073]
    'KBTBD13'          [    0.1569]
    'KCP'              [         0]
    'KDM4DL'           [         0]
    'KDM5D'            [         0]
    'KHDC1L'           [         0]
    'KIAA0040'         [         0]
    'KIAA1107'         [         0]
    'KIAA1239'         [         0]
    'KIAA1671'         [         0]
    'KIAA1731'         [         0]
    'KILLIN'           [         0]
    'KIR3DP1'          [         0]
    'KISS1R'           [    0.0984]
    'KLF16'            [    0.2234]
    'KLF2'             [    0.1726]
    'KLHL29'           [         0]
    'KLHL33'           [         0]
    'KPNA7'            [         0]
    'KRTAP2-1'         [         0]
    'KRTAP2-2'         [         0]
    'KRTAP2-4'         [    0.0129]
    'KRTAP20-3'        [         0]
    'KRTAP21-3'        [         0]
    'KRTAP22-2'        [         0]
    'KRTAP25-1'        [         0]
    'KRTAP4-11'        [         0]
    'KRTAP4-7'         [         0]
    'KRTAP4-8'         [         0]
    'KRTAP4-9'         [         0]
    'KRTAP5-4'         [         0]
    'KRTAP7-1'         [         0]
    'LCE6A'            [         0]
    'LEUTX'            [         0]
    'LGALS7'           [    0.1013]
    'LIMS3'            [         0]
    'LIPM'             [         0]
    'LIPT2'            [         0]
    'LOC100128071'     [         0]
    'LOC100128542'     [         0]
    'LOC100130274'     [         0]
    'LOC100130932'     [         0]
    'LOC100130933'     [         0]
    'LOC100131801'     [         0]
    'LOC100132247'     [         0]
    'LOC100132963'     [         0]
    'LOC100133893'     [         0]
    'LOC100287428'     [         0]
    'LOC100287718'     [         0]
    'LOC100288797'     [         0]
    'LOC200030'        [    0.0465]
    'LOC221710'        [         0]
    'LOC283999'        [         0]
    'LOC339047'        [         0]
    'LOC342346'        [         0]
    'LOC360030'        [         0]
    'LOC375190'        [         0]
    'LOC388588'        [         0]
    'LOC388946'        [         0]
    'LOC389333'        [         0]
    'LOC389493'        [         0]
    'LOC390595'        [         0]
    'LOC391322'        [         0]
    'LOC400696'        [         0]
    'LOC401097'        [         0]
    'LOC401387'        [         0]
    'LOC402644'        [         0]
    'LOC402778'        [         0]
    'LOC440563'        [         0]
    'LOC441056'        [         0]
    'LOC441294'        [    0.1218]
    'LOC441869'        [         0]
    'LOC642597'        [         0]
    'LOC643008'        [         0]
    'LOC643596'        [         0]
    'LOC643677'        [         0]
    'LOC644538'        [         0]
    'LOC645961'        [         0]
    'LOC646627'        [         0]
    'LOC646851'        [         0]
    'LOC647309'        [         0]
    'LOC653543'        [         0]
    'LOC653544'        [    0.0206]
    'LOC653545'        [    0.0206]
    'LOC653548'        [    0.0206]
    'LOC728392'        [         0]
    'LOC728410'        [    0.0231]
    'LOC729020'        [         0]
    'LOC729991'        [         0]
    'LOC730755'        [         0]
    'LOR'              [    0.1634]
    'LOXHD1'           [         0]
    'LRRC10B'          [         0]
    'LRRC26'           [    0.0269]
    'LRRC37A'          [    0.1814]
    'LRRC69'           [         0]
    'LUZP6'            [         0]
    'LYL1'             [    0.1541]
    'MAFA'             [    0.1778]
    'MAGEA2'           [         0]
    'MAGEA2B'          [         0]
    'MAGEA9'           [    0.0815]
    'MAGEA9B'          [    0.0815]
    'MAGED4'           [4.1483e-04]
    'MAGED4B'          [5.3937e-04]
    'MAP6D1'           [    0.2235]
    'MARVELD1'         [         0]
    'MBD3L2'           [7.2175e-04]
    'MBD3L3'           [         0]
    'MBD3L4'           [         0]
    'MBD3L5'           [         0]
    'MBOAT4'           [         0]
    'MESP1'            [    0.1420]
    'METRN'            [    0.1891]
    'METTL11B'         [         0]
    'MGC70857'         [    0.2090]
    'MGC87042'         [         0]
    'MICA'             [         0]
    'MMP23B'           [    0.0682]
    'MORN2'            [         0]
    'MRC1'             [    0.2244]
    'MRC1L1'           [    0.2244]
    'MRGPRG'           [         0]
    'MSL3L2'           [         0]
    'MUC12'            [         0]
    'MYADML2'          [         0]
    'NACAD'            [         0]
    'NAIP'             [    0.1530]
    'NANOS1'           [    0.1883]
    'NAT14'            [    0.0278]
    'NBPF10'           [         0]
    'NBPF11'           [    0.0465]
    'NBPF4'            [         0]
    'NBPF6'            [         0]
    'NBPF9'            [         0]
    'NEURL1B'          [         0]
    'NHSL1'            [         0]
    'NKPD1'            [    0.1918]
    'NKX1-2'           [         0]
    'NKX2-4'           [    0.1843]
    'NKX2-6'           [         0]
    'NKX3-2'           [    0.2214]
    'NLGN4Y'           [    0.0207]
    'NOTO'             [         0]
    'NPIPL3'           [    0.1097]
    'NRTN'             [    0.2163]
    'NXF2'             [    0.2013]
    'NXF2B'            [    0.2013]
    'OLIG1'            [    0.0903]
    'ONECUT3'          [    0.0046]
    'OR2T29'           [    0.2390]
    'OR4C45'           [         0]
    'OR4F16'           [         0]
    'OR4F29'           [         0]
    'OR4F3'            [         0]
    'OR56A5'           [         0]
    'OR6P1'            [         0]
    'OST4'             [         0]
    'OTUD1'            [         0]
    'PABPC1L2A'        [    0.0930]
    'PABPC1L2B'        [    0.0011]
    'PABPC4L'          [         0]
    'PALM3'            [         0]
    'PARG'             [         0]
    'PATE3'            [         0]
    'PATE4'            [         0]
    'PATL2'            [         0]
    'PCDH11Y'          [         0]
    'PCSK1N'           [    0.0557]
    'PDF'              [    0.2416]
    'PET117'           [         0]
    'PGA4'             [         0]
    'PHGR1'            [         0]
    'PHOSPHO1'         [    0.1971]
    'PHOX2A'           [    0.2480]
    'PKD1L3'           [         0]
    'PL-5283'          [         0]
    'PLGLB1'           [    0.2403]
    'PLGLB2'           [    0.2403]
    'PNMA6A'           [         0]
    'PNRC2'            [    0.0317]
    'POLR2J2'          [    0.2345]
    'POLR2J3'          [    0.1502]
    'POM121L2'         [         0]
    'POTEB'            [    0.0639]
    'POTEC'            [         0]
    'POTED'            [    0.1949]
    'POTEM'            [         0]
    'POU5F1B'          [         0]
    'PPIAL4A'          [    0.0726]
    'PPIAL4B'          [    0.0726]
    'PPIAL4C'          [         0]
    'PPIAL4D'          [         0]
    'PPIAL4E'          [         0]
    'PPIAL4F'          [         0]
    'PPP1R3G'          [         0]
    'PRAMEF11'         [         0]
    'PRAMEF13'         [    0.2438]
    'PRAMEF15'         [         0]
    'PRAMEF16'         [    0.2076]
    'PRAMEF20'         [    0.0751]
    'PRAMEF21'         [    0.0751]
    'PRAMEF22'         [    0.2128]
    'PRAMEF3'          [    0.0505]
    'PRAMEF5'          [    0.0291]
    'PRAMEF6'          [    0.1808]
    'PRAMEF7'          [    0.1927]
    'PRAMEF8'          [    0.1284]
    'PRAMEF9'          [         0]
    'PRDM6'            [         0]
    'PRR18'            [    0.0744]
    'PRR20A'           [         0]
    'PRR20B'           [         0]
    'PRR20C'           [         0]
    'PRR20D'           [         0]
    'PRR20E'           [         0]
    'PRR23A'           [         0]
    'PRR23C'           [         0]
    'PRR24'            [         0]
    'PRRT4'            [         0]
    'PRSS2'            [         0]
    'PRSS41'           [         0]
    'PRTN3'            [    0.2445]
    'PRY'              [         0]
    'PRY2'             [         0]
    'PSMG4'            [         0]
    'PTGER1'           [    0.1074]
    'PTPN20A'          [    0.0863]
    'PTPN20B'          [    0.0863]
    'PTPRQ'            [         0]
    'R3HCC1'           [         0]
    'RAD21L1'          [         0]
    'RASA4'            [    0.0912]
    'RASL10A'          [    0.2431]
    'RASSF10'          [    0.2238]
    'RBM20'            [         0]
    'RBMXL3'           [         0]
    'RBMY1A1'          [         0]
    'RBMY1B'           [         0]
    'RBMY1D'           [         0]
    'RBMY1E'           [         0]
    'RBMY1F'           [         0]
    'RBMY1J'           [         0]
    'RESP18'           [         0]
    'REXO1L1'          [    0.0772]
    'RFPL4A'           [         0]
    'RFX8'             [         0]
    'RGPD1'            [    0.1289]
    'RGPD2'            [    0.1293]
    'RGPD3'            [         0]
    'RGPD4'            [         0]
    'RGPD5'            [1.2927e-04]
    'RGPD6'            [1.9250e-04]
    'RGPD8'            [         0]
    'RGSL1'            [         0]
    'RIMBP3'           [    0.2399]
    'RIMBP3B'          [         0]
    'RIMBP3C'          [         0]
    'RNF187'           [         0]
    'RNF222'           [         0]
    'RPS17'            [         0]
    'RPS4Y1'           [         0]
    'RPS4Y2'           [         0]
    'RTL1'             [    0.1208]
    'SAP25'            [         0]
    'SCGB3A1'          [    0.1021]
    'SCT'              [         0]
    'SCXA'             [         0]
    'SCXB'             [         0]
    'SDHAF1'           [    0.0094]
    'SERF1A'           [         0]
    'SERF1B'           [         0]
    'SETD1B'           [         0]
    'SFRS13A'          [    0.0569]
    'SFT2D3'           [         0]
    'SH3D20'           [    0.0810]
    'SHISA6'           [         0]
    'SHISA7'           [         0]
    'SHISA9'           [         0]
    'SLC15A5'          [         0]
    'SLC16A8'          [    0.2416]
    'SLC22A18AS'       [         0]
    'SLC22A24'         [         0]
    'SLC35E2'          [    0.1926]
    'SLC48A1'          [    0.1561]
    'SLFN12L'          [         0]
    'SLFN14'           [         0]
    'SMN1'             [    0.0547]
    'SMN2'             [    0.0537]
    'SOD3'             [    0.1838]
    'SOX18'            [    0.2479]
    'SP9'              [         0]
    'SPACA5'           [    0.1348]
    'SPACA5B'          [    0.1348]
    'SPANXA1'          [         0]
    'SPANXA2'          [         0]
    'SPANXB1'          [         0]
    'SPANXB2'          [         0]
    'SPANXF1'          [         0]
    'SPATA24'          [         0]
    'SPATA3'           [         0]
    'SPDYE2'           [    0.0027]
    'SPDYE2L'          [    0.0027]
    'SPDYE4'           [         0]
    'SPDYE6'           [         0]
    'SPINT3'           [         0]
    'SPRN'             [    0.0301]
    'SRRM3'            [    0.2149]
    'SRRM5'            [    0.0271]
    'SRY'              [         0]
    'SSC5D'            [         0]
    'SSX2'             [         0]
    'SSX2B'            [         0]
    'SSX4'             [    0.1692]
    'SSX4B'            [    0.1692]
    'STAG3L1'          [    0.0456]
    'STAG3L3'          [    0.2464]
    'STARD9'           [         0]
    'SULT1A3'          [    0.0078]
    'SULT1A4'          [    0.0078]
    'SYCE1L'           [         0]
    'TARM1'            [         0]
    'TBC1D10B'         [    0.2457]
    'TBC1D3'           [    0.1164]
    'TBC1D3C'          [    0.0616]
    'TBC1D3F'          [    0.1164]
    'TBC1D3G'          [    0.1786]
    'TBC1D3H'          [         0]
    'TBL1Y'            [         0]
    'TCEB3CL'          [    0.2090]
    'TCF15'            [    0.0746]
    'TCP10L2'          [         0]
    'TCTEX1D4'         [    0.2286]
    'TDRD12'           [         0]
    'TEX28'            [         0]
    'TGIF2LY'          [         0]
    'TIGD1'            [         0]
    'TLCD2'            [         0]
    'TMEM114'          [         0]
    'TMEM121'          [    0.2156]
    'TMEM129'          [    0.1260]
    'TMEM132C'         [         0]
    'TMEM151B'         [         0]
    'TMEM158'          [         0]
    'TMEM160'          [    0.1794]
    'TMEM194B'         [         0]
    'TMEM212'          [         0]
    'TMEM229A'         [         0]
    'TMEM232'          [         0]
    'TMEM233'          [         0]
    'TMEM88B'          [         0]
    'TMPRSS11BNL'      [         0]
    'TMPRSS5'          [    0.2025]
    'TMSB4Y'           [         0]
    'TOMM6'            [         0]
    'TP53TG3'          [         0]
    'TP53TG3B'         [         0]
    'TRIM43B'          [         0]
    'TRIM49L'          [    0.0019]
    'TRIM64'           [         0]
    'TRIM64B'          [         0]
    'TRIM66'           [         0]
    'TRIM77'           [         0]
    'TRNP1'            [         0]
    'TSPY1'            [         0]
    'TSPY2'            [         0]
    'TSPY3'            [         0]
    'TSPY4'            [         0]
    'TSTD1'            [         0]
    'TTC28'            [         0]
    'TUSC1'            [    0.0288]
    'TXNRD3'           [         0]
    'TYW1B'            [         0]
    'UBE2QL1'          [         0]
    'UBTFL1'           [         0]
    'UNC80'            [    0.0865]
    'UNCX'             [    0.2050]
    'UNKL'             [    0.2373]
    'UPF0639'          [         0]
    'UPK3BL'           [         0]
    'URB1'             [         0]
    'USP17'            [    0.0012]
    'USP27X'           [         0]
    'USP9Y'            [         0]
    'UTF1'             [    0.0303]
    'UTS2R'            [    0.2487]
    'UTY'              [         0]
    'VCY'              [         0]
    'VCY1B'            [         0]
    'VPS37D'           [    0.2147]
    'VSIG10L'          [         0]
    'VSTM2B'           [         0]
    'VWA5B1'           [         0]
    'VWA5B2'           [5.1318e-04]
    'VWDE'             [         0]
    'WASH1'            [    0.1299]
    'WDFY4'            [         0]
    'WDR87'            [         0]
    'XAGE1A'           [         0]
    'XAGE1B'           [         0]
    'XAGE1C'           [         0]
    'XAGE1D'           [         0]
    'XAGE1E'           [         0]
    'XAGE2'            [         0]
    'XAGE2B'           [         0]
    'XKR5'             [    0.2343]
    'XKRY'             [         0]
    'XKRY2'            [         0]
    'ZAR1L'            [         0]
    'ZBED3'            [         0]
    'ZBED5'            [         0]
    'ZBED6'            [         0]
    'ZBTB42'           [         0]
    'ZBTB8B'           [         0]
    'ZCCHC18'          [         0]
    'ZFP62'            [         0]
    'ZFP92'            [         0]
    'ZFY'              [         0]
    'ZG16'             [         0]
    'ZNF26'            [         0]
    'ZNF286B'          [         0]
    'ZNF389'           [         0]
    'ZNF414'           [    0.2179]
    'ZNF444'           [    0.1281]
    'ZNF469'           [         0]
    'ZNF541'           [         0]
    'ZNF579'           [    0.1673]
    'ZNF580'           [    0.2278]
    'ZNF679'           [         0]
    'ZNF703'           [    0.1661]
    'ZNF705D'          [    0.1820]
    'ZNF705G'          [         0]
    'ZNF716'           [         0]
    'ZNF717'           [         0]
    'ZNF720'           [         0]
    'ZNF727'           [         0]
    'ZNF732'           [         0]
    'ZNF735'           [         0]
    'ZNF736'           [         0]
    'ZNF737'           [         0]
    'ZNF771'           [    0.0312]
    'ZNF805'           [         0]
    'ZNF814'           [         0]
    'ZNF826'           [         0]
    'ZNF837'           [         0]
    'ZNF84'            [         0]
    'ZNF841'           [         0]
    'ZNF843'           [         0]
    'ZNF844'           [         0]
    'ZNF845'           [         0]
    'ZNF853'           [         0]
    'ZNF860'           [         0]
    'ZNF879'           [         0]
    'ZNF90'            [         0]
    'ZSCAN12'          [         0]
    'ZSCAN23'          [         0]
    'ZSWIM6'           [         0]
    'ZYG11A'           [         0]

The above 920 genes have very low coverage and are being omitted.
Loading gene list... 

The following 920 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'ACTR3C'
    'ADRB3'
    'AG2'
    'AGAP5'
    'AGAP6'
    'AGBL3'
    'AGBL4'
    'ALG1L2'
    'AMELY'
    'AMH'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD30B'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD36'
    'ANKRD36B'
    'ANKRD43'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATAD3C'
    'ATP5D'
    'ATP5L2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BHLHE22'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf55'
    'C11orf20'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf180'
    'C14orf184'
    'C14orf38'
    'C14orf80'
    'C15orf56'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf100'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf50'
    'C17orf51'
    'C17orf55'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C18orf56'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    'C19orf60'
    'C19orf69'
    'C19orf71'
    'C19orf76'
    'C19orf77'
    'C1orf185'
    'C1orf204'
    'C1orf212'
    'C1orf223'
    'C1orf228'
    'C1orf229'
    'C1orf230'
    'C1orf68'
    'C1orf70'
    'C20orf123'
    'C20orf144'
    'C20orf173'
    'C20orf201'
    'C20orf202'
    'C20orf203'
    'C22orf26'
    'C22orf30'
    'C22orf41'
    'C22orf46'
    'C2CD4A'
    'C2CD4B'
    'C2CD4C'
    'C2CD4D'
    'C2orf27A'
    'C2orf27B'
    'C2orf72'
    'C2orf74'
    'C2orf81'
    'C2orf82'
    'C3orf16'
    'C3orf77'
    'C3orf78'
    'C4A'
    'C4B'
    'C4orf47'
    'C4orf48'
    'C4orf52'
    'C5orf36'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C5orf62'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf140'
    'C9orf144B'
    'C9orf167'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CEBPB'
    'CECR6'
    'CFC1'
    'CFC1B'
    'CFD'
    'CHADL'
    'CHIC1'
    'CISD3'
    'CITED4'
    'CLDN24'
    'CLEC2A'
    'COL6A5'
    'COMTD1'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CT47B1'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTAGE9'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'CYorf15A'
    'CYorf15B'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DCAF8L2'
    'DDT'
    'DDX3Y'
    'DEFA1'
    'DEFA1B'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DLEU7'
    'DMRTA2'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DPH3B'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF1AY'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'ENDOG'
    'EVPLL'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM136B'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM181B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM55B'
    'FAM59B'
    'FAM69A'
    'FAM71E2'
    'FAM72D'
    'FAM75A1'
    'FAM75A2'
    'FAM75A5'
    'FAM75A6'
    'FAM75A7'
    'FAM75C1'
    'FAM86B2'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FBXL8'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L5'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSCN2'
    'FSD1L'
    'FSIP2'
    'FXYD2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE13'
    'GAGE2A'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GAS1'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6C'
    'GOLGA6D'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR150'
    'GPR44'
    'GPR88'
    'GPR89C'
    'GRAP'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC2'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB1'
    'H2AFB2'
    'H2AFB3'
    'H2BFM'
    'HBZ'
    'HCP5'
    'HCRT'
    'HEATR7A'
    'HES2'
    'HES5'
    'HES7'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSD11B1L'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'INSM1'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'IRS2'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KDM4DL'
    'KDM5D'
    'KHDC1L'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KILLIN'
    'KIR3DP1'
    'KISS1R'
    'KLF16'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP4-11'
    'KRTAP4-7'
    'KRTAP4-8'
    'KRTAP4-9'
    'KRTAP5-4'
    'KRTAP7-1'
    'LCE6A'
    'LEUTX'
    'LGALS7'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130932'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402644'
    'LOC402778'
    'LOC440563'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC645961'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    'LOC729020'
    'LOC729991'
    'LOC730755'
    'LOR'
    'LOXHD1'
    'LRRC10B'
    'LRRC26'
    'LRRC37A'
    'LRRC69'
    'LUZP6'
    'LYL1'
    'MAFA'
    'MAGEA2'
    'MAGEA2B'
    'MAGEA9'
    'MAGEA9B'
    'MAGED4'
    'MAGED4B'
    'MAP6D1'
    'MARVELD1'
    'MBD3L2'
    'MBD3L3'
    'MBD3L4'
    'MBD3L5'
    'MBOAT4'
    'MESP1'
    'METRN'
    'METTL11B'
    'MGC70857'
    'MGC87042'
    'MICA'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MSL3L2'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF10'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NBPF9'
    'NEURL1B'
    'NHSL1'
    'NKPD1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX3-2'
    'NLGN4Y'
    'NOTO'
    'NPIPL3'
    'NRTN'
    'NXF2'
    'NXF2B'
    'OLIG1'
    'ONECUT3'
    'OR2T29'
    'OR4C45'
    'OR4F16'
    'OR4F29'
    'OR4F3'
    'OR56A5'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCDH11Y'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOSPHO1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTEC'
    'POTED'
    'POTEM'
    'POU5F1B'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4E'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF11'
    'PRAMEF13'
    'PRAMEF15'
    'PRAMEF16'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR18'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR23A'
    'PRR23C'
    'PRR24'
    'PRRT4'
    'PRSS2'
    'PRSS41'
    'PRTN3'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RASL10A'
    'RASSF10'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD3'
    'RGPD4'
    'RGPD5'
    'RGPD6'
    'RGPD8'
    'RGSL1'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RPS4Y1'
    'RPS4Y2'
    'RTL1'
    'SAP25'
    'SCGB3A1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC16A8'
    'SLC22A18AS'
    'SLC22A24'
    'SLC35E2'
    'SLC48A1'
    'SLFN12L'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SOD3'
    'SOX18'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPDYE4'
    'SPDYE6'
    'SPINT3'
    'SPRN'
    'SRRM3'
    'SRRM5'
    'SRY'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D10B'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TBL1Y'
    'TCEB3CL'
    'TCF15'
    'TCP10L2'
    'TCTEX1D4'
    'TDRD12'
    'TEX28'
    'TGIF2LY'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TMPRSS5'
    'TMSB4Y'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY1'
    'TSPY2'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'TYW1B'
    'UBE2QL1'
    'UBTFL1'
    'UNC80'
    'UNCX'
    'UNKL'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'USP9Y'
    'UTF1'
    'UTS2R'
    'UTY'
    'VCY'
    'VCY1B'
    'VPS37D'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKR5'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZCCHC18'
    'ZFP62'
    'ZFP92'
    'ZFY'
    'ZG16'
    'ZNF26'
    'ZNF286B'
    'ZNF389'
    'ZNF414'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF679'
    'ZNF703'
    'ZNF705D'
    'ZNF705G'
    'ZNF716'
    'ZNF717'
    'ZNF720'
    'ZNF727'
    'ZNF732'
    'ZNF735'
    'ZNF736'
    'ZNF737'
    'ZNF771'
    'ZNF805'
    'ZNF814'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF841'
    'ZNF843'
    'ZNF844'
    'ZNF845'
    'ZNF853'
    'ZNF860'
    'ZNF879'
    'ZNF90'
    'ZSCAN12'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 9 double-null mutations.
Removed assignments of their 9 partner-null mutations; these will be omitted from analysis.

                         0     1    2     3    4    5  6      TOTAL  
      Frame_Shift_Del    0     0    0     0    0   21  0         21  
      Frame_Shift_Ins    0     0    0     0    0   18  0         18  
         In_Frame_Del    0     0    0     0    0    9  0          9  
         In_Frame_Ins    0     0    0     0    0    1  0          1  
             Missense    0     4    2     6    1    2  0         15  
    Missense_Mutation    0  3281  170  1019  286    0  0       4756  
    Nonsense_Mutation    9     0    0     0    0  443  8        460  
     Nonstop_Mutation    0     0    0     0    0   11  0         11  
               Silent    0  1267   69   453  106    0  0       1895  
          Splice_Site    0     0    0     0    0   84  1         85  

                TOTAL    9  4552  241  1478  393  589  9       7271  

0 unassigned     
1 Tp*C->(T/G)    
2 Tp*C->A        
3 (A/C/G)p*C->mut
4 A->mut         
5 indel+null     
6 double_null    
Mutations not in gene set:
         BHLHE22: [1]
        C15orf56: [1]
        C1orf212: [1]
           CEBPA: [1]
          CT45A1: [1]
          DNAH12: [1]
           ESPNP: [1]
             EYS: [1]
           GP1BA: [1]
          GPBAR1: [1]
             H19: [1]
           IGLL3: [1]
          KISS1R: [1]
    LOC100133957: [1]
            LYL1: [1]
      NCRNA00188: [1]
         NSUN5P2: [1]
           NXF2B: [1]
          RIMBP3: [1]
           SRRM3: [1]
            UNCX: [1]
          ZNF703: [1]
           DNAH6: [2]
            HSN2: [2]
           IGFN1: [2]
       LOC200030: [2]
          ZNF271: [3]
         Unknown: [8]
       ----TOTAL: [41]
Categories not in categ set:
          NaN: [9]
    ----TOTAL: [9]
Mutations not in categ set:
        AGBL5: [1]
       ARID1A: [1]
        BAZ2A: [1]
        DNMBP: [1]
         MLL2: [1]
         MLL3: [1]
        RBBP8: [1]
        ROCK1: [1]
         SPEN: [1]
    ----TOTAL: [9]

Mutations in this patient+gene+categ set: 7221/7271
	0 mutations not in patient set
	41 mutations not in gene set
	9 mutations not in categ set
		(Note: at least 9 of these are excluded because they are partners to double-nulls.)
Ignoring 0 flank indels

Building coverage table...
Building mutation tables

All data loaded
Finding number of unique sites, unique patients: 1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 
Projection mode warning: n subtotals in output table still reflect total mutation counts, not # mutated patients

Estimated nonsilent background mutation rates

        Tp*C->(T/G)   2.35e-05   23.5/Mb  (relative = 4.60)  expected NS/S ratio = 3.0
            Tp*C->A   1.24e-06    1.2/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   5.59e-07    0.6/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.58e-07    0.6/Mb  (relative = 0.11)
        double_null   8.62e-09    0.0/Mb  (relative = 0.00)
              Total   5.11e-06    5.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

CESC-BI-A0VR-TP
        Tp*C->(T/G)   1.32e-05   13.2/Mb  (relative = 3.70)  expected NS/S ratio = 3.0
            Tp*C->A   1.52e-06    1.5/Mb  (relative = 0.43)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.92e-06    2.9/Mb  (relative = 0.82)  expected NS/S ratio = 3.2
             A->mut   5.49e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   2.35e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-BI-A0VS-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.61)  expected NS/S ratio = 3.0
            Tp*C->A   2.53e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.39e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.81e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.36e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.09e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A0TN-TP
        Tp*C->(T/G)   1.83e-06    1.8/Mb  (relative = 2.20)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.11e-06    1.1/Mb  (relative = 1.33)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.25)  expected NS/S ratio = 3.9
         indel+null   6.94e-08    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.33e-07    0.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BE-TP
        Tp*C->(T/G)   6.73e-06    6.7/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   7.77e-07    0.8/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.38e-06    2.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   6.30e-07    0.6/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.68e-06    2.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BF-TP
        Tp*C->(T/G)   1.06e-05   10.6/Mb  (relative = 3.54)  expected NS/S ratio = 3.0
            Tp*C->A   7.76e-07    0.8/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.12e-06    2.1/Mb  (relative = 0.71)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   4.82e-07    0.5/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.00e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BI-TP
        Tp*C->(T/G)   2.02e-05   20.2/Mb  (relative = 5.37)  expected NS/S ratio = 3.0
            Tp*C->A   5.18e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.57e-06    1.6/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.79e-07    0.3/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   2.76e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.76e-06    3.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BJ-TP
        Tp*C->(T/G)   3.02e-05   30.2/Mb  (relative = 5.14)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   2.82e-07    0.3/Mb  (relative = 0.05)  expected NS/S ratio = 3.9
         indel+null   6.57e-07    0.7/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.88e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BK-TP
        Tp*C->(T/G)   2.74e-05   27.4/Mb  (relative = 4.63)  expected NS/S ratio = 3.0
            Tp*C->A   1.03e-06    1.0/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.04e-06    3.0/Mb  (relative = 0.51)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   7.92e-07    0.8/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.92e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BL-TP
        Tp*C->(T/G)   3.53e-05   35.3/Mb  (relative = 4.51)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.21e-06    4.2/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   9.30e-07    0.9/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.82e-06    7.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BM-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 4.61)  expected NS/S ratio = 3.0
            Tp*C->A   7.79e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.22e-06    2.2/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   4.91e-07    0.5/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   5.88e-07    0.6/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.56e-06    4.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1BN-TP
        Tp*C->(T/G)   6.36e-06    6.4/Mb  (relative = 2.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.65e-07    0.3/Mb  (relative = 0.12)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.98e-06    2.0/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   5.72e-07    0.6/Mb  (relative = 0.26)  expected NS/S ratio = 3.9
         indel+null   3.17e-07    0.3/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.22e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M5-TP
        Tp*C->(T/G)   5.74e-06    5.7/Mb  (relative = 2.47)  expected NS/S ratio = 3.1
            Tp*C->A   7.83e-07    0.8/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.61e-06    2.6/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   2.11e-07    0.2/Mb  (relative = 0.09)  expected NS/S ratio = 3.8
         indel+null   3.82e-07    0.4/Mb  (relative = 0.16)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.33e-06    2.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M6-TP
        Tp*C->(T/G)   1.90e-05   19.0/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.78e-06    2.8/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   5.61e-07    0.6/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   5.54e-07    0.6/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.53e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M7-TP
        Tp*C->(T/G)   1.51e-05   15.1/Mb  (relative = 4.23)  expected NS/S ratio = 3.0
            Tp*C->A   1.04e-06    1.0/Mb  (relative = 0.29)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.76e-06    1.8/Mb  (relative = 0.49)  expected NS/S ratio = 3.2
             A->mut   7.01e-07    0.7/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   4.15e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.57e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M8-TP
        Tp*C->(T/G)   5.24e-06    5.2/Mb  (relative = 2.42)  expected NS/S ratio = 3.1
            Tp*C->A   5.24e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.00e-06    3.0/Mb  (relative = 1.39)  expected NS/S ratio = 3.2
             A->mut   1.41e-07    0.1/Mb  (relative = 0.07)  expected NS/S ratio = 3.8
         indel+null   2.09e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.16e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1M9-TP
        Tp*C->(T/G)   3.10e-06    3.1/Mb  (relative = 2.25)  expected NS/S ratio = 3.0
            Tp*C->A   2.59e-07    0.3/Mb  (relative = 0.19)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.29e-06    1.3/Mb  (relative = 0.94)  expected NS/S ratio = 3.2
             A->mut   4.19e-07    0.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   2.41e-07    0.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.38e-06    1.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ME-TP
        Tp*C->(T/G)   5.26e-06    5.3/Mb  (relative = 2.12)  expected NS/S ratio = 3.0
            Tp*C->A   5.26e-07    0.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.62e-06    2.6/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   9.92e-07    1.0/Mb  (relative = 0.40)  expected NS/S ratio = 3.8
         indel+null   2.45e-07    0.2/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.48e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MF-TP
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.62)  expected NS/S ratio = 3.1
            Tp*C->A   2.63e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.36e-06    2.4/Mb  (relative = 0.77)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 3.8
         indel+null   4.21e-07    0.4/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.05e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MH-TP
        Tp*C->(T/G)   9.68e-05   96.8/Mb  (relative = 5.31)  expected NS/S ratio = 3.0
            Tp*C->A   3.96e-06    4.0/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.53e-06    5.5/Mb  (relative = 0.30)  expected NS/S ratio = 3.2
             A->mut   1.78e-06    1.8/Mb  (relative = 0.10)  expected NS/S ratio = 3.9
         indel+null   1.89e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.82e-05   18.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MI-TP
        Tp*C->(T/G)   4.46e-06    4.5/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.95e-06    2.0/Mb  (relative = 1.10)  expected NS/S ratio = 3.2
             A->mut   4.96e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   1.39e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.78e-06    1.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MJ-TP
        Tp*C->(T/G)   1.00e-05   10.0/Mb  (relative = 3.36)  expected NS/S ratio = 3.0
            Tp*C->A   1.32e-06    1.3/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.71e-06    2.7/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   4.97e-07    0.5/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.10e-07    0.2/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.97e-06    3.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MK-TP
        Tp*C->(T/G)   5.31e-05   53.1/Mb  (relative = 5.38)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-06    2.6/Mb  (relative = 0.27)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.79e-06    3.8/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   8.68e-07    0.9/Mb  (relative = 0.09)
        double_null   6.94e-08    0.1/Mb  (relative = 0.01)
              Total   9.86e-06    9.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1ML-TP
        Tp*C->(T/G)   7.70e-06    7.7/Mb  (relative = 3.25)  expected NS/S ratio = 3.1
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.71e-06    1.7/Mb  (relative = 0.72)  expected NS/S ratio = 3.2
             A->mut   7.87e-07    0.8/Mb  (relative = 0.33)  expected NS/S ratio = 3.8
         indel+null   2.83e-07    0.3/Mb  (relative = 0.12)
        double_null   3.53e-08    0.0/Mb  (relative = 0.01)
              Total   2.37e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MN-TP
        Tp*C->(T/G)   1.77e-05   17.7/Mb  (relative = 3.91)  expected NS/S ratio = 3.0
            Tp*C->A   2.11e-06    2.1/Mb  (relative = 0.47)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.90e-06    2.9/Mb  (relative = 0.64)  expected NS/S ratio = 3.2
             A->mut   7.11e-07    0.7/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   4.55e-07    0.5/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.52e-06    4.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MP-TP
        Tp*C->(T/G)   6.83e-06    6.8/Mb  (relative = 3.69)  expected NS/S ratio = 3.0
            Tp*C->A   5.25e-07    0.5/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.58e-06    1.6/Mb  (relative = 0.86)  expected NS/S ratio = 3.2
             A->mut   2.84e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.08)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.85e-06    1.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-C5-A1MQ-TP
        Tp*C->(T/G)   3.93e-06    3.9/Mb  (relative = 2.97)  expected NS/S ratio = 3.0
            Tp*C->A   2.62e-07    0.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.21e-06    1.2/Mb  (relative = 0.91)  expected NS/S ratio = 3.2
             A->mut   2.12e-07    0.2/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   1.74e-07    0.2/Mb  (relative = 0.13)
        double_null   3.48e-08    0.0/Mb  (relative = 0.03)
              Total   1.32e-06    1.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZL-TP
        Tp*C->(T/G)   5.29e-06    5.3/Mb  (relative = 2.60)  expected NS/S ratio = 3.0
            Tp*C->A   7.56e-07    0.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.47e-06    2.5/Mb  (relative = 1.21)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.20)  expected NS/S ratio = 3.9
         indel+null   1.00e-07    0.1/Mb  (relative = 0.05)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.04e-06    2.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DR-A0ZM-TP
        Tp*C->(T/G)   2.57e-04  256.7/Mb  (relative = 5.97)  expected NS/S ratio = 3.0
            Tp*C->A   7.07e-06    7.1/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.78e-06    7.8/Mb  (relative = 0.18)  expected NS/S ratio = 3.2
             A->mut   9.59e-07    1.0/Mb  (relative = 0.02)  expected NS/S ratio = 3.9
         indel+null   4.52e-06    4.5/Mb  (relative = 0.11)
        double_null   1.34e-07    0.1/Mb  (relative = 0.00)
              Total   4.30e-05   43.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VK-TP
        Tp*C->(T/G)   1.57e-05   15.7/Mb  (relative = 4.73)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.77e-06    1.8/Mb  (relative = 0.53)  expected NS/S ratio = 3.2
             A->mut   4.11e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   2.01e-07    0.2/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.31e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VL-TP
        Tp*C->(T/G)   8.98e-06    9.0/Mb  (relative = 3.56)  expected NS/S ratio = 3.0
            Tp*C->A         00    0.0/Mb  (relative = 0.00)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.99e-06    2.0/Mb  (relative = 0.79)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.11)  expected NS/S ratio = 3.9
         indel+null   4.43e-07    0.4/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.52e-06    2.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VM-TP
        Tp*C->(T/G)   4.51e-05   45.1/Mb  (relative = 4.88)  expected NS/S ratio = 3.0
            Tp*C->A   3.80e-06    3.8/Mb  (relative = 0.41)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.19e-06    3.2/Mb  (relative = 0.35)  expected NS/S ratio = 3.2
             A->mut   8.23e-07    0.8/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   1.11e-06    1.1/Mb  (relative = 0.12)
        double_null   3.36e-08    0.0/Mb  (relative = 0.00)
              Total   9.23e-06    9.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-DS-A0VN-TP
        Tp*C->(T/G)   1.74e-05   17.4/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   7.59e-07    0.8/Mb  (relative = 0.18)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.83e-06    2.8/Mb  (relative = 0.69)  expected NS/S ratio = 3.1
             A->mut   6.86e-07    0.7/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   3.01e-07    0.3/Mb  (relative = 0.07)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   4.12e-06    4.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EA-A1QT-TP
        Tp*C->(T/G)   3.69e-06    3.7/Mb  (relative = 1.70)  expected NS/S ratio = 3.0
            Tp*C->A   5.27e-07    0.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.43e-06    2.4/Mb  (relative = 1.12)  expected NS/S ratio = 3.2
             A->mut   1.14e-06    1.1/Mb  (relative = 0.52)  expected NS/S ratio = 3.9
         indel+null   1.40e-07    0.1/Mb  (relative = 0.06)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   2.17e-06    2.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-EX-A1H5-TP
        Tp*C->(T/G)   2.85e-06    2.9/Mb  (relative = 1.65)  expected NS/S ratio = 3.0
            Tp*C->A   2.60e-07    0.3/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.32e-06    2.3/Mb  (relative = 1.34)  expected NS/S ratio = 3.2
             A->mut   2.80e-07    0.3/Mb  (relative = 0.16)  expected NS/S ratio = 3.9
         indel+null   3.11e-07    0.3/Mb  (relative = 0.18)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.73e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23K-TP
        Tp*C->(T/G)   1.49e-05   14.9/Mb  (relative = 4.24)  expected NS/S ratio = 3.0
            Tp*C->A   1.54e-06    1.5/Mb  (relative = 0.44)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.09e-06    2.1/Mb  (relative = 0.59)  expected NS/S ratio = 3.2
             A->mut   2.78e-07    0.3/Mb  (relative = 0.08)  expected NS/S ratio = 3.9
         indel+null   4.10e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.52e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

CESC-FU-A23L-TP
        Tp*C->(T/G)   2.10e-05   21.0/Mb  (relative = 3.86)  expected NS/S ratio = 3.0
            Tp*C->A   2.85e-06    2.9/Mb  (relative = 0.52)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.47)  expected NS/S ratio = 3.2
             A->mut   1.54e-06    1.5/Mb  (relative = 0.28)  expected NS/S ratio = 3.9
         indel+null   5.52e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.45e-06    5.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/17942 2000/17942 3000/17942 4000/17942 5000/17942 6000/17942 7000/17942 8000/17942 9000/17942 10000/17942 11000/17942 12000/17942 13000/17942 14000/17942 15000/17942 16000/17942 17000/17942 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 200: processing genes 17853 - 17942
Calculating significance of each gene.
Using projection method.
17853	ZNF786	1
17854	ZNF787	1
17855	ZNF789	1
17856	ZNF79	1
17857	ZNF790	1
17858	ZNF791	1.674144e-01
17859	ZNF792	2.903699e-01
17860	ZNF793	1
17861	ZNF799	1.155388e-01
17862	ZNF8	1
17863	ZNF80	1
17864	ZNF800	1
17865	ZNF804A	1
17866	ZNF804B	1
17867	ZNF808	2.578969e-01
17868	ZNF81	1
17869	ZNF813	1
17870	ZNF816A	1
17871	ZNF821	1
17872	ZNF823	1
17873	ZNF827	1
17874	ZNF828	1.854676e-01
17875	ZNF829	1
17876	ZNF83	1
17877	ZNF830	6.279670e-02
17878	ZNF831	1
17879	ZNF835	1
17880	ZNF836	3.207871e-01
17881	ZNF839	1
17882	ZNF846	7.721562e-03
17883	ZNF85	1
17884	ZNF862	1
17885	ZNF878	1
17886	ZNF880	1
17887	ZNF883	1
17888	ZNF91	1
17889	ZNF92	3.343966e-02
17890	ZNF93	1
17891	ZNF98	5.589916e-02
17892	ZNF99	1
17893	ZNFX1	1.858455e-01
17894	ZNHIT1	1
17895	ZNHIT2	1
17896	ZNHIT3	1
17897	ZNHIT6	1.240081e-01
17898	ZNRD1	1
17899	ZNRF1	1
17900	ZNRF2	1
17901	ZNRF3	1
17902	ZNRF4	1
17903	ZP1	1
17904	ZP2	1
17905	ZP3	1
17906	ZP4	1.647756e-01
17907	ZPBP	1
17908	ZPBP2	1.194343e-01
17909	ZPLD1	1.268196e-01
17910	ZRANB1	1
17911	ZRANB2	1
17912	ZRANB3	1
17913	ZRSR2	1
17914	ZSCAN1	2.291513e-02
17915	ZSCAN10	1
17916	ZSCAN16	1
17917	ZSCAN18	1.308310e-02
17918	ZSCAN2	1
17919	ZSCAN20	1.164046e-01
17920	ZSCAN21	1.581145e-01
17921	ZSCAN22	1.295417e-01
17922	ZSCAN29	1
17923	ZSCAN4	1.837527e-01
17924	ZSCAN5A	1.226870e-01
17925	ZSCAN5B	1
17926	ZSWIM1	1
17927	ZSWIM2	3.899580e-02
17928	ZSWIM3	1
17929	ZSWIM4	1.077839e-01
17930	ZSWIM5	1
17931	ZSWIM7	1
17932	ZUFSP	1
17933	ZW10	2.879012e-01
17934	ZWILCH	1
17935	ZWINT	1
17936	ZXDA	1
17937	ZXDB	1
17938	ZXDC	1.980903e-01
17939	ZYG11B	1
17940	ZYX	1
17941	ZZEF1	3.019414e-01
17942	ZZZ3	1
Done

Running MutSig 2:
Scatter job 200: processing genes 17853 - 17942
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF91
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.111420e-02	ci left: 4.662695e-01	ci right 4.859444e-01	k: 4761	n:10000
Cons ci ratio: 7.728861e-02	ci left: 1.966317e-01	ci right 2.125408e-01	k: 2045	n:10000
KS ci ratio: 5.141594e-02	ci left: 3.580403e-01	ci right 3.770370e-01	k: 3675	n:10000
ZNF91   10000 perm   2 sec   (5058 perm/sec)   p_kst 3.675000e-01   p_cons 2.045000e-01   p_joint 4.761000e-01

Outputting figure to mutsig2_images.part000000000200/ZNF91.3_3592_10000_0.3675_0.2045_0.4761.png
                gene_name: ZNF91
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 10 percent done.
ZZEF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.928093e-02	ci left: 2.340268e-01	ci right 2.509234e-01	k: 2424	n:10000
Cons ci ratio: 2.381504e-02	ci left: 7.215864e-01	ci right 7.390793e-01	k: 7304	n:10000
KS ci ratio: 9.162892e-02	ci left: 1.475656e-01	ci right 1.618362e-01	k: 1546	n:10000
ZZEF1   10000 perm   2 sec   (4120 perm/sec)   p_kst 1.546000e-01   p_cons 7.304000e-01   p_joint 2.424000e-01

Outputting figure to mutsig2_images.part000000000200/ZZEF1.3_9106_10000_0.1546_0.7304_0.2424.png
                gene_name: ZZEF1
               theta_stop: 0.092 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.25 

Current progress: 20 percent done.
ZNF846
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.920006e-01	ci left: 7.963073e-03	ci right 1.193024e-02	k: 98	n:10000
Cons ci ratio: 7.829804e-01	ci left: 1.538312e-03	ci right 3.568919e-03	k: 24	n:10000
KS ci ratio: 6.043923e-02	ci left: 2.870634e-01	ci right 3.050555e-01	k: 2960	n:10000
ZNF846   10000 perm   2 sec   (6359 perm/sec)   p_kst 2.960000e-01   p_cons 2.400000e-03   p_joint 9.800000e-03

Joint ci ratio: 2.993624e-01	ci left: 7.228280e-03	ci right 9.817657e-03	k: 169	n:20000
Cons ci ratio: 5.711043e-01	ci left: 1.684366e-03	ci right 3.066699e-03	k: 46	n:20000
KS ci ratio: 4.267061e-02	ci left: 2.903741e-01	ci right 3.030851e-01	k: 5934	n:20000
ZNF846   20000 perm   4 sec   (5651 perm/sec)   p_kst 2.967000e-01   p_cons 2.300000e-03   p_joint 8.450000e-03

Joint ci ratio: 2.597662e-01	ci left: 6.554965e-03	ci right 8.542192e-03	k: 225	n:30000
Cons ci ratio: 4.973175e-01	ci left: 1.555685e-03	ci right 2.611146e-03	k: 61	n:30000
KS ci ratio: 3.499270e-02	ci left: 2.897434e-01	ci right 3.000964e-01	k: 8847	n:30000
ZNF846   30000 perm   6 sec   (5375 perm/sec)   p_kst 2.949000e-01   p_cons 2.033333e-03   p_joint 7.500000e-03

Joint ci ratio: 1.813164e-01	ci left: 1.050210e-02	ci right 1.261970e-02	k: 461	n:40000
Cons ci ratio: 4.298239e-01	ci left: 1.630748e-03	ci right 2.543961e-03	k: 82	n:40000
KS ci ratio: 3.017816e-02	ci left: 2.921760e-01	ci right 3.011535e-01	k: 11866	n:40000
ZNF846   40000 perm   8 sec   (5071 perm/sec)   p_kst 2.966500e-01   p_cons 2.050000e-03   p_joint 1.152500e-02

Joint ci ratio: 1.350125e-01	ci left: 1.545955e-02	ci right 1.771708e-02	k: 828	n:50000
Cons ci ratio: 3.821471e-01	ci left: 1.699817e-03	ci right 2.519713e-03	k: 104	n:50000
KS ci ratio: 2.692603e-02	ci left: 2.936740e-01	ci right 3.017095e-01	k: 14884	n:50000
ZNF846   50000 perm   10 sec   (4950 perm/sec)   p_kst 2.976800e-01   p_cons 2.080000e-03   p_joint 1.656000e-02

Joint ci ratio: 7.093403e-02	ci left: 4.671272e-02	ci right 5.016446e-02	k: 2905	n:60000
Cons ci ratio: 3.474725e-01	ci left: 1.749648e-03	ci right 2.499817e-03	k: 126	n:60000
KS ci ratio: 2.463104e-02	ci left: 2.931627e-01	ci right 3.004903e-01	k: 17809	n:60000
ZNF846   60000 perm   12 sec   (4843 perm/sec)   p_kst 2.968167e-01   p_cons 2.100000e-03   p_joint 4.841667e-02

Joint ci ratio: 9.091427e-02	ci left: 2.469397e-02	ci right 2.705984e-02	k: 1810	n:70000
Cons ci ratio: 3.197213e-01	ci left: 1.800802e-03	ci right 2.498640e-03	k: 149	n:70000
KS ci ratio: 2.287460e-02	ci left: 2.921499e-01	ci right 2.989242e-01	k: 20687	n:70000
ZNF846   70000 perm   15 sec   (4713 perm/sec)   p_kst 2.955286e-01   p_cons 2.128571e-03   p_joint 2.585714e-02

Joint ci ratio: 8.307952e-02	ci left: 2.594900e-02	ci right 2.821047e-02	k: 2165	n:80000
Cons ci ratio: 3.021150e-01	ci left: 1.783157e-03	ci right 2.428804e-03	k: 167	n:80000
KS ci ratio: 2.139237e-02	ci left: 2.924641e-01	ci right 2.988007e-01	k: 23650	n:80000
ZNF846   80000 perm   17 sec   (4603 perm/sec)   p_kst 2.956250e-01   p_cons 2.087500e-03   p_joint 2.706250e-02

Joint ci ratio: 5.627477e-02	ci left: 4.971416e-02	ci right 5.260375e-02	k: 4603	n:90000
Cons ci ratio: 2.804112e-01	ci left: 1.863151e-03	ci right 2.480750e-03	k: 194	n:90000
KS ci ratio: 2.019013e-02	ci left: 2.922100e-01	ci right 2.981810e-01	k: 26567	n:90000
ZNF846   90000 perm   20 sec   (4523 perm/sec)   p_kst 2.951889e-01   p_cons 2.155556e-03   p_joint 5.114444e-02

Joint ci ratio: 5.915136e-02	ci left: 4.082421e-02	ci right 4.332244e-02	k: 4206	n:100000
Cons ci ratio: 2.689398e-01	ci left: 1.835129e-03	ci right 2.414357e-03	k: 211	n:100000
KS ci ratio: 1.917201e-02	ci left: 2.919750e-01	ci right 2.976369e-01	k: 29480	n:100000
ZNF846   100000 perm   23 sec   (4444 perm/sec)   p_kst 2.948000e-01   p_cons 2.110000e-03   p_joint 4.206000e-02

Joint ci ratio: 5.073222e-02	ci left: 5.017425e-02	ci right 5.279491e-02	k: 5662	n:110000
Cons ci ratio: 2.554382e-01	ci left: 1.863659e-03	ci right 2.417660e-03	k: 234	n:110000
KS ci ratio: 1.827544e-02	ci left: 2.922062e-01	ci right 2.976047e-01	k: 32439	n:110000
ZNF846   110000 perm   25 sec   (4367 perm/sec)   p_kst 2.949000e-01   p_cons 2.127273e-03   p_joint 5.147273e-02

Joint ci ratio: 6.601858e-02	ci left: 2.759858e-02	ci right 2.949096e-02	k: 3424	n:120000
Cons ci ratio: 2.452179e-01	ci left: 1.864569e-03	ci right 2.393287e-03	k: 254	n:120000
KS ci ratio: 1.748517e-02	ci left: 2.926117e-01	ci right 2.977815e-01	k: 35423	n:120000
ZNF846   120000 perm   28 sec   (4288 perm/sec)   p_kst 2.951917e-01   p_cons 2.116667e-03   p_joint 2.853333e-02

Joint ci ratio: 6.346751e-02	ci left: 2.760216e-02	ci right 2.941895e-02	k: 3705	n:130000
Cons ci ratio: 2.374352e-01	ci left: 1.844002e-03	ci right 2.347852e-03	k: 271	n:130000
KS ci ratio: 1.679176e-02	ci left: 2.928977e-01	ci right 2.978653e-01	k: 38399	n:130000
ZNF846   130000 perm   31 sec   (4216 perm/sec)   p_kst 2.953769e-01   p_cons 2.084615e-03   p_joint 2.850000e-02

Joint ci ratio: 5.818727e-02	ci left: 3.048558e-02	ci right 3.231961e-02	k: 4395	n:140000
Cons ci ratio: 2.279898e-01	ci left: 1.867001e-03	ci right 2.353989e-03	k: 294	n:140000
KS ci ratio: 1.619480e-02	ci left: 2.926332e-01	ci right 2.974181e-01	k: 41303	n:140000
ZNF846   140000 perm   34 sec   (4150 perm/sec)   p_kst 2.950214e-01   p_cons 2.100000e-03   p_joint 3.139286e-02

Joint ci ratio: 6.001722e-02	ci left: 2.682274e-02	ci right 2.848891e-02	k: 4147	n:150000
Cons ci ratio: 2.206342e-01	ci left: 1.868377e-03	ci right 2.337868e-03	k: 314	n:150000
KS ci ratio: 1.564699e-02	ci left: 2.926795e-01	ci right 2.973018e-01	k: 44248	n:150000
ZNF846   150000 perm   37 sec   (4085 perm/sec)   p_kst 2.949867e-01   p_cons 2.093333e-03   p_joint 2.764667e-02

Joint ci ratio: 5.186749e-02	ci left: 3.357401e-02	ci right 3.536791e-02	k: 5514	n:160000
Cons ci ratio: 2.126788e-01	ci left: 1.893469e-03	ci right 2.349873e-03	k: 338	n:160000
KS ci ratio: 1.513056e-02	ci left: 2.932899e-01	ci right 2.977675e-01	k: 47284	n:160000
ZNF846   160000 perm   40 sec   (4021 perm/sec)   p_kst 2.955250e-01   p_cons 2.112500e-03   p_joint 3.446250e-02

Joint ci ratio: 5.026863e-02	ci left: 3.366648e-02	ci right 3.540826e-02	k: 5870	n:170000
Cons ci ratio: 2.072498e-01	ci left: 1.882403e-03	ci right 2.323088e-03	k: 356	n:170000
KS ci ratio: 1.467617e-02	ci left: 2.934314e-01	ci right 2.977755e-01	k: 50252	n:170000
ZNF846   170000 perm   43 sec   (3962 perm/sec)   p_kst 2.956000e-01   p_cons 2.094118e-03   p_joint 3.452941e-02

Joint ci ratio: 4.887413e-02	ci left: 3.366159e-02	ci right 3.535345e-02	k: 6210	n:180000
Cons ci ratio: 2.016782e-01	ci left: 1.883248e-03	ci right 2.310819e-03	k: 376	n:180000
KS ci ratio: 1.427163e-02	ci left: 2.932319e-01	ci right 2.974524e-01	k: 53161	n:180000
ZNF846   180000 perm   46 sec   (3903 perm/sec)   p_kst 2.953389e-01   p_cons 2.088889e-03   p_joint 3.450000e-02

Joint ci ratio: 4.757832e-02	ci left: 3.367342e-02	ci right 3.531977e-02	k: 6553	n:190000
Cons ci ratio: 1.982926e-01	ci left: 1.849122e-03	ci right 2.261045e-03	k: 389	n:190000
KS ci ratio: 1.389546e-02	ci left: 2.931548e-01	ci right 2.972620e-01	k: 56089	n:190000
ZNF846   190000 perm   49 sec   (3845 perm/sec)   p_kst 2.952053e-01   p_cons 2.047368e-03   p_joint 3.448947e-02

Joint ci ratio: 4.654139e-02	ci left: 3.345719e-02	ci right 3.505635e-02	k: 6850	n:200000
Cons ci ratio: 1.936327e-01	ci left: 1.847005e-03	ci right 2.247648e-03	k: 408	n:200000
KS ci ratio: 1.354901e-02	ci left: 2.930417e-01	ci right 2.970442e-01	k: 59008	n:200000
ZNF846   200000 perm   53 sec   (3789 perm/sec)   p_kst 2.950400e-01   p_cons 2.040000e-03   p_joint 3.425000e-02

Joint ci ratio: 4.658068e-02	ci left: 3.186337e-02	ci right 3.338766e-02	k: 6850	n:210000
Cons ci ratio: 1.897314e-01	ci left: 1.836119e-03	ci right 2.225451e-03	k: 425	n:210000
KS ci ratio: 1.321770e-02	ci left: 2.932401e-01	ci right 2.971465e-01	k: 61990	n:210000
ZNF846   210000 perm   56 sec   (3734 perm/sec)   p_kst 2.951905e-01   p_cons 2.023810e-03   p_joint 3.261905e-02

Joint ci ratio: 4.554659e-02	ci left: 3.183035e-02	ci right 3.331837e-02	k: 7165	n:220000
Cons ci ratio: 1.864791e-01	ci left: 1.817628e-03	ci right 2.195685e-03	k: 440	n:220000
KS ci ratio: 1.291422e-02	ci left: 2.932717e-01	ci right 2.970882e-01	k: 64939	n:220000
ZNF846   220000 perm   60 sec   (3675 perm/sec)   p_kst 2.951773e-01   p_cons 2.000000e-03   p_joint 3.256818e-02

Joint ci ratio: 4.744721e-02	ci left: 2.813747e-02	ci right 2.950923e-02	k: 6628	n:230000
Cons ci ratio: 1.831872e-01	ci left: 1.804947e-03	ci right 2.173002e-03	k: 456	n:230000
KS ci ratio: 1.263113e-02	ci left: 2.932886e-01	ci right 2.970210e-01	k: 67885	n:230000
ZNF846   230000 perm   64 sec   (3621 perm/sec)   p_kst 2.951522e-01   p_cons 1.982609e-03   p_joint 2.881739e-02

Joint ci ratio: 4.723163e-02	ci left: 2.724063e-02	ci right 2.856247e-02	k: 6695	n:240000
Cons ci ratio: 1.793056e-01	ci left: 1.809294e-03	ci right 2.169570e-03	k: 476	n:240000
KS ci ratio: 1.237132e-02	ci left: 2.931218e-01	ci right 2.967748e-01	k: 70787	n:240000
ZNF846   240000 perm   67 sec   (3561 perm/sec)   p_kst 2.949458e-01   p_cons 1.983333e-03   p_joint 2.789583e-02

Joint ci ratio: 4.624668e-02	ci left: 2.728956e-02	ci right 2.858542e-02	k: 6983	n:250000
Cons ci ratio: 1.770947e-01	ci left: 1.782779e-03	ci right 2.132929e-03	k: 488	n:250000
KS ci ratio: 1.213321e-02	ci left: 2.927535e-01	ci right 2.963312e-01	k: 73635	n:250000
ZNF846   250000 perm   71 sec   (3506 perm/sec)   p_kst 2.945400e-01   p_cons 1.952000e-03   p_joint 2.793200e-02

Joint ci ratio: 4.533692e-02	ci left: 2.731597e-02	ci right 2.858689e-02	k: 7266	n:260000
Cons ci ratio: 1.746147e-01	ci left: 1.765685e-03	ci right 2.107109e-03	k: 502	n:260000
KS ci ratio: 1.189808e-02	ci left: 2.927713e-01	ci right 2.962794e-01	k: 76576	n:260000
ZNF846   260000 perm   75 sec   (3456 perm/sec)   p_kst 2.945231e-01   p_cons 1.930769e-03   p_joint 2.794615e-02

Joint ci ratio: 4.453954e-02	ci left: 2.726738e-02	ci right 2.851316e-02	k: 7529	n:270000
Cons ci ratio: 1.712432e-01	ci left: 1.771158e-03	ci right 2.106345e-03	k: 522	n:270000
KS ci ratio: 1.167778e-02	ci left: 2.927293e-01	ci right 2.961714e-01	k: 79501	n:270000
ZNF846   270000 perm   79 sec   (3411 perm/sec)   p_kst 2.944481e-01   p_cons 1.933333e-03   p_joint 2.788519e-02

Joint ci ratio: 4.788819e-02	ci left: 2.281145e-02	ci right 2.393416e-02	k: 6543	n:280000
Cons ci ratio: 1.683708e-01	ci left: 1.769456e-03	ci right 2.098133e-03	k: 540	n:280000
KS ci ratio: 1.147105e-02	ci left: 2.926266e-01	ci right 2.960062e-01	k: 82408	n:280000
ZNF846   280000 perm   83 sec   (3366 perm/sec)   p_kst 2.943143e-01   p_cons 1.928571e-03   p_joint 2.336786e-02

Joint ci ratio: 4.705783e-02	ci left: 2.281876e-02	ci right 2.392183e-02	k: 6776	n:290000
Cons ci ratio: 1.649009e-01	ci left: 1.784444e-03	ci right 2.108397e-03	k: 563	n:290000
KS ci ratio: 1.126931e-02	ci left: 2.927381e-01	ci right 2.960591e-01	k: 85375	n:290000
ZNF846   290000 perm   87 sec   (3318 perm/sec)   p_kst 2.943966e-01   p_cons 1.941379e-03   p_joint 2.336552e-02

Joint ci ratio: 4.623883e-02	ci left: 2.285540e-02	ci right 2.394050e-02	k: 7018	n:300000
Cons ci ratio: 1.628931e-01	ci left: 1.769714e-03	ci right 2.086698e-03	k: 577	n:300000
KS ci ratio: 1.107501e-02	ci left: 2.929491e-01	ci right 2.962149e-01	k: 88374	n:300000
ZNF846   300000 perm   92 sec   (3277 perm/sec)   p_kst 2.945800e-01   p_cons 1.923333e-03   p_joint 2.339333e-02

Joint ci ratio: 4.776126e-02	ci left: 2.075954e-02	ci right 2.177847e-02	k: 6592	n:310000
Cons ci ratio: 1.605498e-01	ci left: 1.765245e-03	ci right 2.076442e-03	k: 594	n:310000
KS ci ratio: 1.088890e-02	ci left: 2.932049e-01	ci right 2.964183e-01	k: 91391	n:310000
ZNF846   310000 perm   96 sec   (3233 perm/sec)   p_kst 2.948097e-01   p_cons 1.916129e-03   p_joint 2.126452e-02

Joint ci ratio: 4.472756e-02	ci left: 2.291608e-02	ci right 2.396758e-02	k: 7500	n:320000
Cons ci ratio: 1.580462e-01	ci left: 1.767090e-03	ci right 2.073293e-03	k: 613	n:320000
KS ci ratio: 1.072048e-02	ci left: 2.931113e-01	ci right 2.962736e-01	k: 94301	n:320000
ZNF846   320000 perm   100 sec   (3193 perm/sec)   p_kst 2.946906e-01   p_cons 1.915625e-03   p_joint 2.343750e-02

Joint ci ratio: 4.406918e-02	ci left: 2.289889e-02	ci right 2.393374e-02	k: 7726	n:330000
Cons ci ratio: 1.555332e-01	ci left: 1.771770e-03	ci right 2.073447e-03	k: 633	n:330000
KS ci ratio: 1.055957e-02	ci left: 2.930268e-01	ci right 2.961404e-01	k: 97212	n:330000
ZNF846   330000 perm   105 sec   (3155 perm/sec)   p_kst 2.945818e-01   p_cons 1.918182e-03   p_joint 2.341212e-02

Joint ci ratio: 4.336095e-02	ci left: 2.296430e-02	ci right 2.398502e-02	k: 7980	n:340000
Cons ci ratio: 1.529023e-01	ci left: 1.781869e-03	ci right 2.079664e-03	k: 655	n:340000
KS ci ratio: 1.040974e-02	ci left: 2.927861e-01	ci right 2.958527e-01	k: 100068	n:340000
ZNF846   340000 perm   109 sec   (3118 perm/sec)   p_kst 2.943176e-01   p_cons 1.926471e-03   p_joint 2.347059e-02

Joint ci ratio: 4.266723e-02	ci left: 2.304590e-02	ci right 2.405344e-02	k: 8241	n:350000
Cons ci ratio: 1.504006e-01	ci left: 1.791431e-03	ci right 2.085484e-03	k: 677	n:350000
KS ci ratio: 1.025566e-02	ci left: 2.929816e-01	ci right 2.960046e-01	k: 103072	n:350000
ZNF846   350000 perm   114 sec   (3083 perm/sec)   p_kst 2.944914e-01   p_cons 1.934286e-03   p_joint 2.354571e-02

Joint ci ratio: 4.206661e-02	ci left: 2.305709e-02	ci right 2.405060e-02	k: 8478	n:360000
Cons ci ratio: 1.481238e-01	ci left: 1.797824e-03	ci right 2.088064e-03	k: 698	n:360000
KS ci ratio: 1.011141e-02	ci left: 2.930363e-01	ci right 2.960171e-01	k: 106029	n:360000
ZNF846   360000 perm   118 sec   (3048 perm/sec)   p_kst 2.945250e-01   p_cons 1.938889e-03   p_joint 2.355000e-02

Joint ci ratio: 4.148823e-02	ci left: 2.307045e-02	ci right 2.405054e-02	k: 8716	n:370000
Cons ci ratio: 1.461509e-01	ci left: 1.798695e-03	ci right 2.084871e-03	k: 717	n:370000
KS ci ratio: 9.974691e-03	ci left: 2.930207e-01	ci right 2.959608e-01	k: 108961	n:370000
ZNF846   370000 perm   123 sec   (3012 perm/sec)   p_kst 2.944892e-01   p_cons 1.937838e-03   p_joint 2.355676e-02

Joint ci ratio: 3.674998e-02	ci left: 2.853655e-02	ci right 2.960749e-02	k: 11046	n:380000
Cons ci ratio: 1.432841e-01	ci left: 1.824916e-03	ci right 2.109080e-03	k: 746	n:380000
KS ci ratio: 9.837331e-03	ci left: 2.932612e-01	ci right 2.961630e-01	k: 111990	n:380000
ZNF846   380000 perm   128 sec   (2977 perm/sec)   p_kst 2.947105e-01   p_cons 1.963158e-03   p_joint 2.906842e-02

Joint ci ratio: 3.627364e-02	ci left: 2.854673e-02	ci right 2.960387e-02	k: 11338	n:390000
Cons ci ratio: 1.415886e-01	ci left: 1.822632e-03	ci right 2.102799e-03	k: 764	n:390000
KS ci ratio: 9.710281e-03	ci left: 2.932848e-01	ci right 2.961491e-01	k: 114939	n:390000
ZNF846   390000 perm   133 sec   (2939 perm/sec)   p_kst 2.947154e-01   p_cons 1.958974e-03   p_joint 2.907179e-02

Joint ci ratio: 3.650482e-02	ci left: 2.750827e-02	ci right 2.853358e-02	k: 11207	n:400000
Cons ci ratio: 1.396842e-01	ci left: 1.827719e-03	ci right 2.104575e-03	k: 785	n:400000
KS ci ratio: 9.584168e-03	ci left: 2.934746e-01	ci right 2.963033e-01	k: 117955	n:400000
ZNF846   400000 perm   138 sec   (2906 perm/sec)   p_kst 2.948875e-01   p_cons 1.962500e-03   p_joint 2.801750e-02

Joint ci ratio: 3.602657e-02	ci left: 2.756000e-02	ci right 2.857351e-02	k: 11506	n:410000
Cons ci ratio: 1.381981e-01	ci left: 1.823162e-03	ci right 2.096148e-03	k: 802	n:410000
KS ci ratio: 9.466449e-03	ci left: 2.934971e-01	ci right 2.962911e-01	k: 120906	n:410000
ZNF846   410000 perm   143 sec   (2871 perm/sec)   p_kst 2.948927e-01   p_cons 1.956098e-03   p_joint 2.806341e-02

Joint ci ratio: 3.554651e-02	ci left: 2.764004e-02	ci right 2.864267e-02	k: 11818	n:420000
Cons ci ratio: 1.367585e-01	ci left: 1.818837e-03	ci right 2.088108e-03	k: 819	n:420000
KS ci ratio: 9.353929e-03	ci left: 2.934760e-01	ci right 2.962364e-01	k: 123839	n:420000
ZNF846   420000 perm   148 sec   (2838 perm/sec)   p_kst 2.948548e-01   p_cons 1.950000e-03   p_joint 2.813810e-02

Joint ci ratio: 3.842788e-02	ci left: 2.317367e-02	ci right 2.408392e-02	k: 10159	n:430000
Cons ci ratio: 1.357699e-01	ci left: 1.803494e-03	ci right 2.068406e-03	k: 831	n:430000
KS ci ratio: 9.244190e-03	ci left: 2.935071e-01	ci right 2.962352e-01	k: 126794	n:430000
ZNF846   430000 perm   153 sec   (2805 perm/sec)   p_kst 2.948698e-01   p_cons 1.932558e-03   p_joint 2.362558e-02

Joint ci ratio: 3.805299e-02	ci left: 2.310169e-02	ci right 2.400006e-02	k: 10361	n:440000
Cons ci ratio: 1.341667e-01	ci left: 1.806425e-03	ci right 2.068385e-03	k: 851	n:440000
KS ci ratio: 9.138225e-03	ci left: 2.935370e-01	ci right 2.962339e-01	k: 129749	n:440000
ZNF846   440000 perm   159 sec   (2775 perm/sec)   p_kst 2.948841e-01   p_cons 1.934091e-03   p_joint 2.354773e-02

Joint ci ratio: 3.757428e-02	ci left: 2.317165e-02	ci right 2.406116e-02	k: 10626	n:450000
Cons ci ratio: 1.330786e-01	ci left: 1.796353e-03	ci right 2.054572e-03	k: 865	n:450000
KS ci ratio: 9.037948e-03	ci left: 2.934680e-01	ci right 2.961346e-01	k: 132660	n:450000
ZNF846   450000 perm   164 sec   (2746 perm/sec)   p_kst 2.948000e-01   p_cons 1.922222e-03   p_joint 2.361333e-02

Joint ci ratio: 3.401405e-02	ci left: 2.758551e-02	ci right 2.854218e-02	k: 12908	n:460000
Cons ci ratio: 1.314936e-01	ci left: 1.801443e-03	ci right 2.057069e-03	k: 886	n:460000
KS ci ratio: 8.938797e-03	ci left: 2.935000e-01	ci right 2.961374e-01	k: 135616	n:460000
ZNF846   460000 perm   169 sec   (2717 perm/sec)   p_kst 2.948174e-01   p_cons 1.926087e-03   p_joint 2.806087e-02

Joint ci ratio: 3.364321e-02	ci left: 2.760196e-02	ci right 2.854856e-02	k: 13194	n:470000
Cons ci ratio: 1.302517e-01	ci left: 1.798100e-03	ci right 2.050656e-03	k: 903	n:470000
KS ci ratio: 8.841843e-03	ci left: 2.935774e-01	ci right 2.961868e-01	k: 138594	n:470000
ZNF846   470000 perm   175 sec   (2688 perm/sec)   p_kst 2.948809e-01   p_cons 1.921277e-03   p_joint 2.807234e-02

Joint ci ratio: 3.329441e-02	ci left: 2.760123e-02	ci right 2.853781e-02	k: 13472	n:480000
Cons ci ratio: 1.291849e-01	ci left: 1.790875e-03	ci right 2.040198e-03	k: 918	n:480000
KS ci ratio: 8.746313e-03	ci left: 2.937309e-01	ci right 2.963133e-01	k: 141610	n:480000
ZNF846   480000 perm   180 sec   (2661 perm/sec)   p_kst 2.950208e-01   p_cons 1.912500e-03   p_joint 2.806667e-02

Joint ci ratio: 3.296116e-02	ci left: 2.759249e-02	ci right 2.851922e-02	k: 13746	n:490000
Cons ci ratio: 1.284197e-01	ci left: 1.776052e-03	ci right 2.021734e-03	k: 929	n:490000
KS ci ratio: 8.657931e-03	ci left: 2.936805e-01	ci right 2.962362e-01	k: 144529	n:490000
ZNF846   490000 perm   186 sec   (2633 perm/sec)   p_kst 2.949571e-01   p_cons 1.895918e-03   p_joint 2.805306e-02

Joint ci ratio: 3.261141e-02	ci left: 2.762780e-02	ci right 2.854568e-02	k: 14042	n:500000
Cons ci ratio: 1.266605e-01	ci left: 1.790872e-03	ci right 2.034957e-03	k: 955	n:500000
KS ci ratio: 8.567478e-03	ci left: 2.938600e-01	ci right 2.963904e-01	k: 147562	n:500000
ZNF846   500000 perm   192 sec   (2607 perm/sec)   p_kst 2.951240e-01   p_cons 1.910000e-03   p_joint 2.808400e-02

Joint ci ratio: 3.227373e-02	ci left: 2.765982e-02	ci right 2.856908e-02	k: 14337	n:510000
Cons ci ratio: 1.252274e-01	ci left: 1.797536e-03	ci right 2.039551e-03	k: 977	n:510000
KS ci ratio: 8.484997e-03	ci left: 2.937780e-01	ci right 2.962832e-01	k: 150465	n:510000
ZNF846   510000 perm   198 sec   (2580 perm/sec)   p_kst 2.950294e-01   p_cons 1.915686e-03   p_joint 2.811176e-02

Joint ci ratio: 3.194407e-02	ci left: 2.769448e-02	ci right 2.859540e-02	k: 14634	n:520000
Cons ci ratio: 1.236562e-01	ci left: 1.809549e-03	ci right 2.049901e-03	k: 1002	n:520000
KS ci ratio: 8.401357e-03	ci left: 2.938721e-01	ci right 2.963533e-01	k: 153458	n:520000
ZNF846   520000 perm   204 sec   (2554 perm/sec)   p_kst 2.951115e-01   p_cons 1.926923e-03   p_joint 2.814231e-02

Joint ci ratio: 3.165268e-02	ci left: 2.767919e-02	ci right 2.857126e-02	k: 14905	n:530000
Cons ci ratio: 1.224414e-01	ci left: 1.811981e-03	ci right 2.050120e-03	k: 1022	n:530000
KS ci ratio: 8.322217e-03	ci left: 2.938591e-01	ci right 2.963167e-01	k: 156396	n:530000
ZNF846   530000 perm   210 sec   (2529 perm/sec)   p_kst 2.950868e-01   p_cons 1.928302e-03   p_joint 2.812264e-02

Joint ci ratio: 3.132878e-02	ci left: 2.773434e-02	ci right 2.861888e-02	k: 15214	n:540000
Cons ci ratio: 1.211454e-01	ci left: 1.817926e-03	ci right 2.054136e-03	k: 1044	n:540000
KS ci ratio: 8.243071e-03	ci left: 2.939577e-01	ci right 2.963927e-01	k: 159394	n:540000
ZNF846   540000 perm   215 sec   (2506 perm/sec)   p_kst 2.951741e-01   p_cons 1.933333e-03   p_joint 2.817407e-02

Joint ci ratio: 3.104964e-02	ci left: 2.772618e-02	ci right 2.860243e-02	k: 15489	n:550000
Cons ci ratio: 1.200024e-01	ci left: 1.820139e-03	ci right 2.054248e-03	k: 1064	n:550000
KS ci ratio: 8.169316e-03	ci left: 2.938912e-01	ci right 2.963037e-01	k: 162303	n:550000
ZNF846   550000 perm   222 sec   (2482 perm/sec)   p_kst 2.950964e-01   p_cons 1.934545e-03   p_joint 2.816182e-02

Joint ci ratio: 3.075976e-02	ci left: 2.775025e-02	ci right 2.861893e-02	k: 15782	n:560000
Cons ci ratio: 1.187816e-01	ci left: 1.825750e-03	ci right 2.058023e-03	k: 1086	n:560000
KS ci ratio: 8.097889e-03	ci left: 2.938075e-01	ci right 2.961982e-01	k: 165201	n:560000
ZNF846   560000 perm   228 sec   (2458 perm/sec)   p_kst 2.950018e-01   p_cons 1.939286e-03   p_joint 2.818214e-02

Joint ci ratio: 3.050814e-02	ci left: 2.771952e-02	ci right 2.858002e-02	k: 16044	n:570000
Cons ci ratio: 1.180782e-01	ci left: 1.815850e-03	ci right 2.045400e-03	k: 1099	n:570000
KS ci ratio: 8.026305e-03	ci left: 2.938303e-01	ci right 2.961999e-01	k: 168158	n:570000
ZNF846   570000 perm   234 sec   (2435 perm/sec)   p_kst 2.950140e-01   p_cons 1.928070e-03   p_joint 2.814737e-02

Joint ci ratio: 3.023588e-02	ci left: 2.773781e-02	ci right 2.859105e-02	k: 16334	n:580000
Cons ci ratio: 1.168624e-01	ci left: 1.823032e-03	ci right 2.050954e-03	k: 1122	n:580000
KS ci ratio: 7.956916e-03	ci left: 2.938351e-01	ci right 2.961842e-01	k: 171105	n:580000
ZNF846   580000 perm   240 sec   (2413 perm/sec)   p_kst 2.950086e-01   p_cons 1.934483e-03   p_joint 2.816207e-02

Joint ci ratio: 2.998193e-02	ci left: 2.773531e-02	ci right 2.858119e-02	k: 16612	n:590000
Cons ci ratio: 1.156329e-01	ci left: 1.831629e-03	ci right 2.058052e-03	k: 1146	n:590000
KS ci ratio: 7.887882e-03	ci left: 2.939144e-01	ci right 2.962436e-01	k: 174096	n:590000
ZNF846   590000 perm   247 sec   (2391 perm/sec)   p_kst 2.950780e-01   p_cons 1.942373e-03   p_joint 2.815593e-02

Joint ci ratio: 2.972160e-02	ci left: 2.775610e-02	ci right 2.859514e-02	k: 16904	n:600000
Cons ci ratio: 1.146870e-01	ci left: 1.831857e-03	ci right 2.056329e-03	k: 1165	n:600000
KS ci ratio: 7.820989e-03	ci left: 2.939711e-01	ci right 2.962809e-01	k: 177075	n:600000
ZNF846   600000 perm   253 sec   (2369 perm/sec)   p_kst 2.951250e-01   p_cons 1.941667e-03   p_joint 2.817333e-02

Joint ci ratio: 2.949088e-02	ci left: 2.773391e-02	ci right 2.856566e-02	k: 17170	n:610000
Cons ci ratio: 1.140051e-01	ci left: 1.824120e-03	ci right 2.046226e-03	k: 1179	n:610000
KS ci ratio: 7.755312e-03	ci left: 2.940506e-01	ci right 2.963415e-01	k: 180069	n:610000
ZNF846   610000 perm   260 sec   (2347 perm/sec)   p_kst 2.951951e-01   p_cons 1.932787e-03   p_joint 2.814754e-02

Joint ci ratio: 2.926373e-02	ci left: 2.771567e-02	ci right 2.854036e-02	k: 17438	n:620000
Cons ci ratio: 1.132877e-01	ci left: 1.818204e-03	ci right 2.038104e-03	k: 1194	n:620000
KS ci ratio: 7.691500e-03	ci left: 2.941147e-01	ci right 2.963872e-01	k: 183055	n:620000
ZNF846   620000 perm   267 sec   (2324 perm/sec)   p_kst 2.952500e-01   p_cons 1.925806e-03   p_joint 2.812581e-02

Joint ci ratio: 2.904765e-02	ci left: 2.768700e-02	ci right 2.850465e-02	k: 17699	n:630000
Cons ci ratio: 1.124441e-01	ci left: 1.817109e-03	ci right 2.035131e-03	k: 1212	n:630000
KS ci ratio: 7.633605e-03	ci left: 2.939390e-01	ci right 2.961930e-01	k: 185891	n:630000
ZNF846   630000 perm   273 sec   (2304 perm/sec)   p_kst 2.950651e-01   p_cons 1.923810e-03   p_joint 2.809365e-02

Joint ci ratio: 2.880660e-02	ci left: 2.771510e-02	ci right 2.852668e-02	k: 17996	n:640000
Cons ci ratio: 1.117557e-01	ci left: 1.811496e-03	ci right 2.027427e-03	k: 1227	n:640000
KS ci ratio: 7.573353e-03	ci left: 2.939687e-01	ci right 2.962050e-01	k: 188855	n:640000
ZNF846   640000 perm   280 sec   (2283 perm/sec)   p_kst 2.950859e-01   p_cons 1.917188e-03   p_joint 2.811875e-02

Joint ci ratio: 2.858512e-02	ci left: 2.771639e-02	ci right 2.852167e-02	k: 18276	n:650000
Cons ci ratio: 1.112142e-01	ci left: 1.801574e-03	ci right 2.015213e-03	k: 1239	n:650000
KS ci ratio: 7.514951e-03	ci left: 2.939729e-01	ci right 2.961920e-01	k: 191803	n:650000
ZNF846   650000 perm   287 sec   (2262 perm/sec)   p_kst 2.950815e-01   p_cons 1.906154e-03   p_joint 2.811692e-02

Joint ci ratio: 2.837417e-02	ci left: 2.770713e-02	ci right 2.850611e-02	k: 18549	n:660000
Cons ci ratio: 1.105921e-01	ci left: 1.794900e-03	ci right 2.006480e-03	k: 1253	n:660000
KS ci ratio: 7.458830e-03	ci left: 2.939241e-01	ci right 2.961261e-01	k: 194716	n:660000
ZNF846   660000 perm   294 sec   (2243 perm/sec)   p_kst 2.950242e-01   p_cons 1.898485e-03   p_joint 2.810455e-02

Joint ci ratio: 2.816399e-02	ci left: 2.770559e-02	ci right 2.849850e-02	k: 18827	n:670000
Cons ci ratio: 1.092490e-01	ci left: 1.813108e-03	ci right 2.024071e-03	k: 1284	n:670000
KS ci ratio: 7.403230e-03	ci left: 2.939171e-01	ci right 2.961026e-01	k: 197656	n:670000
ZNF846   670000 perm   301 sec   (2224 perm/sec)   p_kst 2.950090e-01   p_cons 1.916418e-03   p_joint 2.810000e-02

Joint ci ratio: 2.796518e-02	ci left: 2.769096e-02	ci right 2.847777e-02	k: 19096	n:680000
Cons ci ratio: 1.084918e-01	ci left: 1.812195e-03	ci right 2.021497e-03	k: 1302	n:680000
KS ci ratio: 7.350337e-03	ci left: 2.938266e-01	ci right 2.959957e-01	k: 200539	n:680000
ZNF846   680000 perm   308 sec   (2205 perm/sec)   p_kst 2.949103e-01   p_cons 1.914706e-03   p_joint 2.808235e-02

Joint ci ratio: 2.776831e-02	ci left: 2.768110e-02	ci right 2.846200e-02	k: 19368	n:690000
Cons ci ratio: 1.078320e-01	ci left: 1.808492e-03	ci right 2.016015e-03	k: 1318	n:690000
KS ci ratio: 7.296170e-03	ci left: 2.938749e-01	ci right 2.960283e-01	k: 203516	n:690000
ZNF846   690000 perm   316 sec   (2186 perm/sec)   p_kst 2.949507e-01   p_cons 1.910145e-03   p_joint 2.806957e-02

Joint ci ratio: 3.008630e-02	ci left: 2.332081e-02	ci right 2.403457e-02	k: 16573	n:700000
Cons ci ratio: 1.069436e-01	ci left: 1.813241e-03	ci right 2.019487e-03	k: 1340	n:700000
KS ci ratio: 7.244403e-03	ci left: 2.938519e-01	ci right 2.959898e-01	k: 206444	n:700000
ZNF846   700000 perm   323 sec   (2168 perm/sec)   p_kst 2.949200e-01   p_cons 1.914286e-03   p_joint 2.367571e-02

Joint ci ratio: 2.987165e-02	ci left: 2.332645e-02	ci right 2.403519e-02	k: 16812	n:710000
Cons ci ratio: 1.059212e-01	ci left: 1.823348e-03	ci right 2.028637e-03	k: 1366	n:710000
KS ci ratio: 7.190361e-03	ci left: 2.940238e-01	ci right 2.961469e-01	k: 209510	n:710000
ZNF846   710000 perm   330 sec   (2149 perm/sec)   p_kst 2.950845e-01   p_cons 1.923944e-03   p_joint 2.367887e-02

Joint ci ratio: 2.965084e-02	ci left: 2.334849e-02	ci right 2.405257e-02	k: 17063	n:720000
Cons ci ratio: 1.048146e-01	ci left: 1.837240e-03	ci right 2.041800e-03	k: 1395	n:720000
KS ci ratio: 7.139058e-03	ci left: 2.941008e-01	ci right 2.962092e-01	k: 212511	n:720000
ZNF846   720000 perm   338 sec   (2132 perm/sec)   p_kst 2.951542e-01   p_cons 1.937500e-03   p_joint 2.369861e-02

Joint ci ratio: 2.943399e-02	ci left: 2.337130e-02	ci right 2.407084e-02	k: 17315	n:730000
Cons ci ratio: 1.043675e-01	ci left: 1.828081e-03	ci right 2.030699e-03	k: 1407	n:730000
KS ci ratio: 7.090168e-03	ci left: 2.940977e-01	ci right 2.961916e-01	k: 215455	n:730000
ZNF846   730000 perm   345 sec   (2114 perm/sec)   p_kst 2.951438e-01   p_cons 1.927397e-03   p_joint 2.371918e-02

Joint ci ratio: 2.925083e-02	ci left: 2.334791e-02	ci right 2.404232e-02	k: 17533	n:740000
Cons ci ratio: 1.039628e-01	ci left: 1.817854e-03	ci right 2.018510e-03	k: 1418	n:740000
KS ci ratio: 7.040326e-03	ci left: 2.942095e-01	ci right 2.962894e-01	k: 218484	n:740000
ZNF846   740000 perm   353 sec   (2097 perm/sec)   p_kst 2.952486e-01   p_cons 1.916216e-03   p_joint 2.369324e-02

Joint ci ratio: 2.906517e-02	ci left: 2.333441e-02	ci right 2.402394e-02	k: 17758	n:750000
Cons ci ratio: 1.033097e-01	ci left: 1.816994e-03	ci right 2.016218e-03	k: 1436	n:750000
KS ci ratio: 6.994185e-03	ci left: 2.941598e-01	ci right 2.962258e-01	k: 221394	n:750000
ZNF846   750000 perm   361 sec   (2079 perm/sec)   p_kst 2.951920e-01   p_cons 1.914667e-03   p_joint 2.367733e-02

Joint ci ratio: 2.885591e-02	ci left: 2.336440e-02	ci right 2.404976e-02	k: 18016	n:760000
Cons ci ratio: 1.024924e-01	ci left: 1.822571e-03	ci right 2.020730e-03	k: 1459	n:760000
KS ci ratio: 6.947094e-03	ci left: 2.942220e-01	ci right 2.962743e-01	k: 224388	n:760000
ZNF846   760000 perm   369 sec   (2062 perm/sec)   p_kst 2.952474e-01   p_cons 1.919737e-03   p_joint 2.370526e-02

Joint ci ratio: 2.867360e-02	ci left: 2.335752e-02	ci right 2.403828e-02	k: 18246	n:770000
Cons ci ratio: 1.017631e-01	ci left: 1.825477e-03	ci right 2.022456e-03	k: 1480	n:770000
KS ci ratio: 6.902557e-03	ci left: 2.941852e-01	ci right 2.962241e-01	k: 227307	n:770000
ZNF846   770000 perm   376 sec   (2045 perm/sec)   p_kst 2.952039e-01   p_cons 1.922078e-03   p_joint 2.369610e-02

Joint ci ratio: 2.608376e-02	ci left: 2.777386e-02	ci right 2.850914e-02	k: 21949	n:780000
Cons ci ratio: 1.008474e-01	ci left: 1.835812e-03	ci right 2.032019e-03	k: 1507	n:780000
KS ci ratio: 6.857577e-03	ci left: 2.942276e-01	ci right 2.962534e-01	k: 230287	n:780000
ZNF846   780000 perm   384 sec   (2029 perm/sec)   p_kst 2.952397e-01   p_cons 1.932051e-03   p_joint 2.813974e-02

Joint ci ratio: 2.829977e-02	ci left: 2.337574e-02	ci right 2.404801e-02	k: 18731	n:790000
Cons ci ratio: 1.000868e-01	ci left: 1.840957e-03	ci right 2.036142e-03	k: 1530	n:790000
KS ci ratio: 6.814749e-03	ci left: 2.941905e-01	ci right 2.962034e-01	k: 233205	n:790000
ZNF846   790000 perm   392 sec   (2013 perm/sec)   p_kst 2.951962e-01   p_cons 1.936709e-03   p_joint 2.371013e-02

Joint ci ratio: 2.577381e-02	ci left: 2.774019e-02	ci right 2.846573e-02	k: 22481	n:800000
Cons ci ratio: 9.950370e-02	ci left: 1.839883e-03	ci right 2.033752e-03	k: 1548	n:800000
KS ci ratio: 6.771657e-03	ci left: 2.942193e-01	ci right 2.962197e-01	k: 236175	n:800000
ZNF846   800000 perm   400 sec   (1998 perm/sec)   p_kst 2.952187e-01   p_cons 1.935000e-03   p_joint 2.810125e-02

Outputting figure to mutsig2_images.part000000000200/ZNF846.2_1622_800000_0.29522_0.001935_0.028101.png
                gene_name: ZNF846
               theta_stop: 0.100 
                    nperm: 800000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.0019 
      ci_cons_bounds_left: 0.0018 
     ci_cons_bounds_right: 0.0020 
                  p_joint: 0.028 
     ci_joint_bounds_left: 0.028 
    ci_joint_bounds_right: 0.028 

Current progress: 30 percent done.
ZNFX1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.135979e-01	ci left: 1.003243e-01	ci right 1.125061e-01	k: 1063	n:10000
Cons ci ratio: 1.481806e-01	ci left: 6.053496e-02	ci right 7.032006e-02	k: 653	n:10000
KS ci ratio: 4.283441e-02	ci left: 4.459028e-01	ci right 4.655230e-01	k: 4557	n:10000
ZNFX1   10000 perm   2 sec   (4481 perm/sec)   p_kst 4.557000e-01   p_cons 6.530000e-02   p_joint 1.063000e-01

Joint ci ratio: 6.865601e-02	ci left: 1.353172e-01	ci right 1.449877e-01	k: 2802	n:20000
Cons ci ratio: 1.058684e-01	ci left: 6.074404e-02	ci right 6.758334e-02	k: 1282	n:20000
KS ci ratio: 3.019963e-02	ci left: 4.502776e-01	ci right 4.641349e-01	k: 9144	n:20000
ZNFX1   20000 perm   5 sec   (4092 perm/sec)   p_kst 4.572000e-01   p_cons 6.410000e-02   p_joint 1.401000e-01

Joint ci ratio: 7.328467e-02	ci left: 8.386701e-02	ci right 9.027989e-02	k: 2611	n:30000
Cons ci ratio: 8.693766e-02	ci left: 6.070091e-02	ci right 6.625067e-02	k: 1903	n:30000
KS ci ratio: 2.456935e-02	ci left: 4.533487e-01	ci right 4.646593e-01	k: 13770	n:30000
ZNFX1   30000 perm   8 sec   (3961 perm/sec)   p_kst 4.590000e-01   p_cons 6.343333e-02   p_joint 8.703333e-02

Outputting figure to mutsig2_images.part000000000200/ZNFX1.2_5809_30000_0.459_0.063433_0.087033.png
                gene_name: ZNFX1
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.063 
      ci_cons_bounds_left: 0.061 
     ci_cons_bounds_right: 0.066 
                  p_joint: 0.087 
     ci_joint_bounds_left: 0.084 
    ci_joint_bounds_right: 0.090 

Current progress: 40 percent done.
ZNHIT6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.325811e-02	ci left: 5.716584e-01	ci right 5.910942e-01	k: 5814	n:10000
Cons ci ratio: 3.561814e-02	ci left: 5.378822e-01	ci right 5.574900e-01	k: 5477	n:10000
KS ci ratio: 4.978634e-02	ci left: 3.730595e-01	ci right 3.922089e-01	k: 3826	n:10000
ZNHIT6   10000 perm   2 sec   (6388 perm/sec)   p_kst 3.826000e-01   p_cons 5.477000e-01   p_joint 5.814000e-01

Outputting figure to mutsig2_images.part000000000200/ZNHIT6.2_1453_10000_0.3826_0.5477_0.5814.png
                gene_name: ZNHIT6
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 50 percent done.
ZP4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.760682e-02	ci left: 2.430195e-01	ci right 2.601254e-01	k: 2515	n:10000
Cons ci ratio: 1.382589e-01	ci left: 6.923436e-02	ci right 7.961519e-02	k: 743	n:10000
KS ci ratio: 1.705912e-02	ci left: 8.334802e-01	ci right 8.479208e-01	k: 8408	n:10000
ZP4   10000 perm   2 sec   (6033 perm/sec)   p_kst 8.408000e-01   p_cons 7.430000e-02   p_joint 2.515000e-01

Joint ci ratio: 5.534138e-02	ci left: 1.949700e-01	ci right 2.061172e-01	k: 4010	n:20000
Cons ci ratio: 9.748302e-02	ci left: 7.114225e-02	ci right 7.848193e-02	k: 1495	n:20000
KS ci ratio: 1.231778e-02	ci left: 8.298834e-01	ci right 8.402190e-01	k: 16702	n:20000
ZP4   20000 perm   4 sec   (5331 perm/sec)   p_kst 8.351000e-01   p_cons 7.475000e-02   p_joint 2.005000e-01

Outputting figure to mutsig2_images.part000000000200/ZP4.2_1671_20000_0.8351_0.07475_0.2005.png
                gene_name: ZP4
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.84 
                   p_cons: 0.075 
      ci_cons_bounds_left: 0.071 
     ci_cons_bounds_right: 0.078 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.21 

Current progress: 60 percent done.
ZSCAN18
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.163696e-02	ci left: 4.599781e-01	ci right 4.796395e-01	k: 4698	n:10000
Cons ci ratio: 1.471055e-02	ci left: 8.699939e-01	ci right 8.829859e-01	k: 8766	n:10000
KS ci ratio: 1.073223e-01	ci left: 1.113483e-01	ci right 1.240753e-01	k: 1176	n:10000
ZSCAN18   10000 perm   2 sec   (6210 perm/sec)   p_kst 1.176000e-01   p_cons 8.766000e-01   p_joint 4.698000e-01

Joint ci ratio: 1.495668e-02	ci left: 7.686435e-01	ci right 7.802766e-01	k: 15490	n:20000
Cons ci ratio: 1.013239e-02	ci left: 8.776008e-01	ci right 8.865878e-01	k: 17643	n:20000
KS ci ratio: 7.550851e-02	ci left: 1.142482e-01	ci right 1.232630e-01	k: 2374	n:20000
ZSCAN18   20000 perm   4 sec   (5514 perm/sec)   p_kst 1.187000e-01   p_cons 8.821500e-01   p_joint 7.745000e-01

Outputting figure to mutsig2_images.part000000000200/ZSCAN18.2_1729_20000_0.1187_0.88215_0.7745.png
                gene_name: ZSCAN18
               theta_stop: 0.076 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.78 

Current progress: 70 percent done.
ZSCAN21
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.505158e-02	ci left: 7.009962e-01	ci right 7.188814e-01	k: 7100	n:10000
Cons ci ratio: 2.038162e-02	ci left: 7.790450e-01	ci right 7.951874e-01	k: 7872	n:10000
KS ci ratio: 5.938332e-02	ci left: 2.943978e-01	ci right 3.125168e-01	k: 3034	n:10000
ZSCAN21   10000 perm   2 sec   (6652 perm/sec)   p_kst 3.034000e-01   p_cons 7.872000e-01   p_joint 7.100000e-01

Outputting figure to mutsig2_images.part000000000200/ZSCAN21.2_1434_10000_0.3034_0.7872_0.71.png
                gene_name: ZSCAN21
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 80 percent done.
ZSCAN5B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.110596e-02	ci left: 4.663694e-01	ci right 4.860444e-01	k: 4762	n:10000
Cons ci ratio: 4.226054e-02	ci left: 4.525901e-01	ci right 4.722318e-01	k: 4624	n:10000
KS ci ratio: 4.698613e-02	ci left: 4.006365e-01	ci right 4.200158e-01	k: 4103	n:10000
ZSCAN5B   10000 perm   2 sec   (6108 perm/sec)   p_kst 4.103000e-01   p_cons 4.624000e-01   p_joint 4.762000e-01

Outputting figure to mutsig2_images.part000000000200/ZSCAN5B.2_1504_10000_0.4103_0.4624_0.4762.png
                gene_name: ZSCAN5B
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 90 percent done.
ZSWIM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.920140e-02	ci left: 3.786320e-01	ci right 3.978331e-01	k: 3882	n:10000
Cons ci ratio: 1.090790e-02	ci left: 9.229644e-01	ci right 9.331845e-01	k: 9282	n:10000
KS ci ratio: 9.947870e-02	ci left: 1.276742e-01	ci right 1.411395e-01	k: 1343	n:10000
ZSWIM2   10000 perm   2 sec   (6128 perm/sec)   p_kst 1.343000e-01   p_cons 9.282000e-01   p_joint 3.882000e-01

Outputting figure to mutsig2_images.part000000000200/ZSWIM2.2_1938_10000_0.1343_0.9282_0.3882.png
                gene_name: ZSWIM2
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 100 percent done.
Finished call_mutsig_cluster
Remaining analyses will be handled during gather.
analyze_mutation_data finished.
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/215935/iteration1/scatter.0000000200
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.170.3957/ -whichjob 200 -i CESC -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/CESC/1910007/0.ProcessCoverageForMutSig.Finished/CESC.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/CESC/1909979/0.MutSigPreprocess.Finished/CESC.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/db/ucsc/hg19/R.mat -bd /xchip/cga1/annotation/db/ucsc/hg19 -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt -jobcount 200


PS:

Read file <scatter.err> for stderr output of this job.

*** Scatter stdandard err:

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:07:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23651
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:07:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23653
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23657
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:07:58 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23662
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:02 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23664
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:03 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23667
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23670
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:18 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23673
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:23 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23676
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:23 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23679
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:21 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23681
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:22 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23684
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:25 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23686
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:25 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23688
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23691
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23693
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23695
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23699
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23702
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23705
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23720
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23722
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23727
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23730
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:08:57 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23733
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23736
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23738
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23742
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23745
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:14 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23748
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23751
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23759
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:25 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23764
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:34 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23771
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23778
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23802
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:09:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23806
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:10:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23809
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:10:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23812
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:10:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23815
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:10:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23817
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:10:45 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23822
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:10:52 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23826
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:10:52 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23829
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23833
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23838
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23841
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23844
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23846
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:19 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23848
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:22 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23851
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:19 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23856
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:23 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23859
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23861
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:45 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23864
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:29 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23868
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23874
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23878
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23881
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23886
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23888
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23891
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23893
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23896
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:11:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23898
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:03 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23902
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23904
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23906
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23909
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23914
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23919
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:20 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23924
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:23 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23928
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23932
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23935
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23938
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23941
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:39 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23945
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:43 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23947
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:45 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23951
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:45 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23954
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:45 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23959
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23962
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:54 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23966
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:54 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23969
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23971
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:12:58 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23978
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23981
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23984
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:07 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23986
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23989
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23993
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:34 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23996
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 23998
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24000
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24003
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24006
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24009
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:42 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24012
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:13:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24015
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24017
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24020
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24023
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24025
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24028
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24030
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24032
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24034
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:22 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24038
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:26 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24040
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24045
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24049
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24052
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24055
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24060
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24062
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24064
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24067
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24070
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:14:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24073
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:07 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24076
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:07 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24081
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:09 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24084
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24088
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24095
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:14 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24099
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:21 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24119
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:25 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24122
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24125
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24128
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:26 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24130
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24133
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24137
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24140
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24142
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24149
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24154
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24158
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24161
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24165
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24169
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24171
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:15:58 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24175
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24178
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24181
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24185
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24187
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:15 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24190
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:18 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24195
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24197
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:23 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24202
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24204
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24210
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24215
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:39 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24218
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24224
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24226
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24230
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:16:58 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24233
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24238
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:03 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24240
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:06 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24243
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24294
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24299
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24303
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24305
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:22 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24310
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:28 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24313
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24316
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:26 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24339
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24348
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:52:43 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24352
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24358
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24362
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24367
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24370
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24373
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24377
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24380
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24382
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24388
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:57 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24392
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:57 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24396
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:57 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24401
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:17:56 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24408
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24411
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24416
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24423
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24429
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:09 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24434
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:18 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24439
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24442
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24448
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:22 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24461
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24467
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:24 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24472
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24474
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24477
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24479
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 16:18:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24482
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
*** Scatter retry log:
==> scatter.0000000001.tries <==
1
==> scatter.0000000002.tries <==
1
==> scatter.0000000003.tries <==
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
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1
==> scatter.0000000089.tries <==
1
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1
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1
==> scatter.0000000092.tries <==
1
==> scatter.0000000093.tries <==
1
==> scatter.0000000094.tries <==
1
==> scatter.0000000095.tries <==
1
==> scatter.0000000096.tries <==
1
==> scatter.0000000097.tries <==
1
==> scatter.0000000098.tries <==
1
==> scatter.0000000099.tries <==
1
==> scatter.0000000100.tries <==
1
==> scatter.0000000101.tries <==
1
==> scatter.0000000102.tries <==
1
==> scatter.0000000103.tries <==
1
==> scatter.0000000104.tries <==
1
==> scatter.0000000105.tries <==
1
==> scatter.0000000106.tries <==
1
==> scatter.0000000107.tries <==
1
==> scatter.0000000108.tries <==
1
==> scatter.0000000109.tries <==
1
==> scatter.0000000110.tries <==
1
==> scatter.0000000111.tries <==
1
==> scatter.0000000112.tries <==
1
==> scatter.0000000113.tries <==
1
==> scatter.0000000114.tries <==
1
==> scatter.0000000115.tries <==
1
==> scatter.0000000116.tries <==
1
==> scatter.0000000117.tries <==
1
==> scatter.0000000118.tries <==
1
==> scatter.0000000119.tries <==
1
==> scatter.0000000120.tries <==
1
==> scatter.0000000121.tries <==
1
==> scatter.0000000122.tries <==
1
==> scatter.0000000123.tries <==
1
==> scatter.0000000124.tries <==
1
==> scatter.0000000125.tries <==
1
==> scatter.0000000126.tries <==
1
==> scatter.0000000127.tries <==
1
==> scatter.0000000128.tries <==
1
==> scatter.0000000129.tries <==
1
==> scatter.0000000130.tries <==
1
==> scatter.0000000131.tries <==
1
==> scatter.0000000132.tries <==
1
==> scatter.0000000133.tries <==
1
==> scatter.0000000134.tries <==
1
==> scatter.0000000135.tries <==
1
==> scatter.0000000136.tries <==
1
==> scatter.0000000137.tries <==
1
==> scatter.0000000138.tries <==
1
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1
==> scatter.0000000140.tries <==
1
==> scatter.0000000141.tries <==
1
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1
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1
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1
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1
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1
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1
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1
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1
==> scatter.0000000150.tries <==
1
==> scatter.0000000151.tries <==
1
==> scatter.0000000152.tries <==
1
==> scatter.0000000153.tries <==
1
==> scatter.0000000154.tries <==
1
==> scatter.0000000155.tries <==
1
==> scatter.0000000156.tries <==
1
==> scatter.0000000157.tries <==
1
==> scatter.0000000158.tries <==
1
==> scatter.0000000159.tries <==
1
==> scatter.0000000160.tries <==
1
==> scatter.0000000161.tries <==
1
==> scatter.0000000162.tries <==
1
==> scatter.0000000163.tries <==
1
==> scatter.0000000164.tries <==
1
==> scatter.0000000165.tries <==
1
==> scatter.0000000166.tries <==
1
==> scatter.0000000167.tries <==
1
==> scatter.0000000168.tries <==
1
==> scatter.0000000169.tries <==
1
==> scatter.0000000170.tries <==
1
==> scatter.0000000171.tries <==
1
==> scatter.0000000172.tries <==
2
==> scatter.0000000173.tries <==
1
==> scatter.0000000174.tries <==
1
==> scatter.0000000175.tries <==
1
==> scatter.0000000176.tries <==
1
==> scatter.0000000177.tries <==
1
==> scatter.0000000178.tries <==
1
==> scatter.0000000179.tries <==
1
==> scatter.0000000180.tries <==
1
==> scatter.0000000181.tries <==
1
==> scatter.0000000182.tries <==
1
==> scatter.0000000183.tries <==
1
==> scatter.0000000184.tries <==
1
==> scatter.0000000185.tries <==
1
==> scatter.0000000186.tries <==
1
==> scatter.0000000187.tries <==
1
==> scatter.0000000188.tries <==
1
==> scatter.0000000189.tries <==
1
==> scatter.0000000190.tries <==
1
==> scatter.0000000191.tries <==
1
==> scatter.0000000192.tries <==
1
==> scatter.0000000193.tries <==
1
==> scatter.0000000194.tries <==
1
==> scatter.0000000195.tries <==
1
==> scatter.0000000196.tries <==
1
==> scatter.0000000197.tries <==
1
==> scatter.0000000198.tries <==
1
==> scatter.0000000199.tries <==
1
==> scatter.0000000200.tries <==
1


PS:

Read file <scatter-gather.err.txt> for stderr output of this job.

*** Scatter Gather stdandard err:

Xvnc Free Edition 4.1.2
Copyright (C) 2002-2005 RealVNC Ltd.
See http://www.realvnc.com for information on VNC.
Underlying X server release 70101000, The X.Org Foundation


Wed Oct 24 19:42:02 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 24484
 vncext:      created VNC server for screen 0
FreeFontPath: FPE "unix/:7100" refcount is 2, should be 1; fixing.
ls: iteration1/sg-next-iteration.txt: No such file or directory


PS:

Read file <iterator.err.txt> for stderr output of this job.

